[{"language":[{"iso":"eng"}],"department":[{"_id":"MaLo"}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","author":[{"full_name":"Dos Santos Caldas, Paulo R","first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","last_name":"Dos Santos Caldas"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler","full_name":"Radler, Philipp"},{"last_name":"Sommer","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin"}],"publisher":"Elsevier","publication_status":"published","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","grant_number":"679239"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"quality_controlled":"1","_id":"7572","editor":[{"first_name":"Phong ","last_name":"Tran","full_name":"Tran, Phong "}],"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"}],"scopus_import":"1","type":"book_chapter","citation":{"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>","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.","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.","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.","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>.","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>","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>."},"publication_identifier":{"issn":["0091679X"]},"year":"2020","page":"145-161","external_id":{"isi":["000611826500008"]},"oa":1,"date_updated":"2023-10-04T09:50:24Z","alternative_title":["Methods in Cell Biology"],"date_published":"2020-02-27T00:00:00Z","intvolume":"       158","month":"02","ec_funded":1,"oa_version":"Preprint","isi":1,"related_material":{"record":[{"id":"8358","status":"public","relation":"part_of_dissertation"}]},"publication":"Methods in Cell Biology","doi":"10.1016/bs.mcb.2020.01.006","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"status":"public","day":"27","date_created":"2020-03-08T23:00:47Z","volume":158},{"project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":" F06504","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Di erential Systems"},{"call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"}],"publication_status":"published","_id":"7573","quality_controlled":"1","citation":{"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.","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.","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234.","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>","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>.","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>","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>."},"publication_identifier":{"issn":["00217824"]},"abstract":[{"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.","lang":"eng"}],"arxiv":1,"scopus_import":"1","type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"JaMa"}],"title":"Homogenisation of one-dimensional discrete optimal transport","author":[{"last_name":"Gladbach","first_name":"Peter","full_name":"Gladbach, Peter"},{"last_name":"Kopfer","first_name":"Eva","full_name":"Kopfer, Eva"},{"last_name":"Maas","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Maas, Jan"},{"first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","full_name":"Portinale, Lorenzo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Elsevier","related_material":{"record":[{"id":"10030","relation":"dissertation_contains","status":"public"}]},"oa_version":"Preprint","ec_funded":1,"isi":1,"publication":"Journal de Mathematiques Pures et Appliquees","doi":"10.1016/j.matpur.2020.02.008","main_file_link":[{"url":"https://arxiv.org/abs/1905.05757","open_access":"1"}],"date_created":"2020-03-08T23:00:47Z","day":"01","status":"public","volume":139,"year":"2020","page":"204-234","external_id":{"isi":["000539439400008"],"arxiv":["1905.05757"]},"date_updated":"2023-09-07T13:31:05Z","oa":1,"issue":"7","date_published":"2020-07-01T00:00:00Z","intvolume":"       139","month":"07","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."},{"project":[{"grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"publication_status":"published","_id":"7580","quality_controlled":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"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</i>. Proceedings of the National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921027117\">https://doi.org/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</i>. 2020;117(12):6504-6549. doi:<a href=\"https://doi.org/10.1073/pnas.1921027117\">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</i>, vol. 117, no. 12. Proceedings of the National Academy of Sciences, pp. 6504–6549, 2020.","short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences 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. 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</i>, vol. 117, no. 12, Proceedings of the National Academy of Sciences, 2020, pp. 6504–49, 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</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921027117\">https://doi.org/10.1073/pnas.1921027117</a>"},"scopus_import":"1","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."}],"type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"MaLo"},{"_id":"CaBe"}],"title":"Stochastic activation and bistability in a Rab GTPase regulatory network","author":[{"full_name":"Bezeljak, Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","first_name":"Urban","last_name":"Bezeljak","orcid":"0000-0003-1365-5631"},{"first_name":"Hrushikesh","last_name":"Loya","full_name":"Loya, Hrushikesh"},{"last_name":"Kaczmarek","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","first_name":"Beata M","full_name":"Kaczmarek, Beata M"},{"full_name":"Saunders, Timothy E.","last_name":"Saunders","first_name":"Timothy E."},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Proceedings of the National Academy of Sciences","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","description":"News on IST Homepage"}],"record":[{"relation":"dissertation_contains","status":"public","id":"8341"}]},"oa_version":"Preprint","isi":1,"publication":"Proceedings of the National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/776567"}],"doi":"10.1073/pnas.1921027117","date_created":"2020-03-12T05:32:26Z","status":"public","day":"24","volume":117,"year":"2020","external_id":{"isi":["000521821800040"]},"page":"6504-6549","date_updated":"2023-09-07T13:17:06Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa":1,"issue":"12","date_published":"2020-03-24T00:00:00Z","intvolume":"       117","month":"03"},{"oa":1,"issue":"3","date_updated":"2025-05-07T11:12:28Z","article_number":"299","date_published":"2020-03-01T00:00:00Z","month":"03","intvolume":"         9","year":"2020","external_id":{"pmid":["32121542"],"isi":["000525315000035"]},"day":"01","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-03-15T23:00:52Z","ddc":["580"],"volume":9,"pmid":1,"oa_version":"Published Version","ec_funded":1,"isi":1,"publication":"Plants","doi":"10.3390/plants9030299","title":"Molecular evolution and diversification of proteins involved in miRNA maturation pathway","author":[{"full_name":"Moturu, Taraka Ramji","first_name":"Taraka Ramji","last_name":"Moturu"},{"full_name":"Sinha, Sansrity","last_name":"Sinha","first_name":"Sansrity"},{"first_name":"Hymavathi","last_name":"Salava","full_name":"Salava, Hymavathi"},{"full_name":"Thula, Sravankumar","last_name":"Thula","first_name":"Sravankumar"},{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"full_name":"Vařeková, Radka Svobodová","first_name":"Radka Svobodová","last_name":"Vařeková"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_name":"2020_Plants_Moturu.pdf","date_created":"2020-03-23T13:37:00Z","date_updated":"2020-07-14T12:48:00Z","file_size":2373484,"creator":"dernst","file_id":"7614","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6d5af3e17266a48996b4af4e67e88a85"}],"publisher":"MDPI","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"article_processing_charge":"No","quality_controlled":"1","_id":"7582","scopus_import":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","file_date_updated":"2020-07-14T12:48:00Z","citation":{"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>","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.","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.","short":"T.R. Moturu, S. Sinha, H. Salava, S. Thula, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Plants 9 (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>.","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>","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>."},"publication_identifier":{"eissn":["22237747"]},"publication_status":"published","project":[{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}]},{"year":"2020","external_id":{"isi":["000517335000001"],"pmid":["32118314"]},"date_updated":"2023-08-18T07:07:36Z","oa":1,"intvolume":"        39","month":"03","date_published":"2020-03-02T00:00:00Z","article_number":"e103358","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.","isi":1,"oa_version":"Published Version","doi":"10.15252/embj.2019103358","publication":"EMBO Journal","ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2020-03-15T23:00:55Z","status":"public","day":"02","pmid":1,"volume":39,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"GaNo"}],"file":[{"file_name":"2020_EMBO_Weinert.pdf","date_created":"2020-03-23T13:51:11Z","date_updated":"2020-07-14T12:48:00Z","content_type":"application/pdf","file_id":"7615","file_size":12243278,"creator":"dernst","checksum":"82750a7a93e3740decbce8474004111a","access_level":"open_access","relation":"main_file"}],"title":"Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Weinert, Stefanie","last_name":"Weinert","first_name":"Stefanie"},{"full_name":"Gimber, Niclas","last_name":"Gimber","first_name":"Niclas"},{"first_name":"Dorothea","last_name":"Deuschel","full_name":"Deuschel, Dorothea"},{"full_name":"Stuhlmann, Till","first_name":"Till","last_name":"Stuhlmann"},{"last_name":"Puchkov","first_name":"Dmytro","full_name":"Puchkov, Dmytro"},{"full_name":"Farsi, Zohreh","first_name":"Zohreh","last_name":"Farsi"},{"last_name":"Ludwig","first_name":"Carmen F.","full_name":"Ludwig, Carmen F."},{"full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"first_name":"Karen I.","last_name":"López-Cayuqueo","full_name":"López-Cayuqueo, Karen I."},{"full_name":"Planells-Cases, Rosa","first_name":"Rosa","last_name":"Planells-Cases"},{"full_name":"Jentsch, Thomas J.","last_name":"Jentsch","first_name":"Thomas J."}],"has_accepted_license":"1","publisher":"EMBO Press","publication_status":"published","_id":"7586","quality_controlled":"1","publication_identifier":{"issn":["02614189"],"eissn":["14602075"]},"citation":{"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.","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.","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).","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>","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>.","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>"},"file_date_updated":"2020-07-14T12:48:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"scopus_import":"1"},{"quality_controlled":"1","_id":"7593","scopus_import":"1","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."}],"file_date_updated":"2020-09-24T07:03:20Z","type":"journal_article","citation":{"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>","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>.","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.","short":"H.M. Moon, S. Hippenmeyer, L. Luo, A. Wynshaw-Boris, ELife 9 (2020).","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.","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>","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>."},"publication_identifier":{"issn":["2050-084X"]},"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Hyang Mi","last_name":"Moon","full_name":"Moon, Hyang Mi"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"},{"full_name":"Wynshaw-Boris, Anthony","last_name":"Wynshaw-Boris","first_name":"Anthony"}],"title":"LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility","file":[{"file_name":"2020_elife_Moon.pdf","success":1,"date_created":"2020-09-24T07:03:20Z","date_updated":"2020-09-24T07:03:20Z","file_size":15089438,"creator":"dernst","content_type":"application/pdf","file_id":"8567","checksum":"396ceb2dd10b102ef4e699666b9342c3","access_level":"open_access","relation":"main_file"}],"publisher":"eLife Sciences Publications","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"article_processing_charge":"No","status":"public","day":"11","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2020-03-20T13:16:41Z","volume":9,"pmid":1,"oa_version":"Published Version","isi":1,"publication":"eLife","main_file_link":[{"url":"https://doi.org/10.1101/751958","open_access":"1"}],"doi":"10.7554/elife.51512","oa":1,"date_updated":"2023-08-18T07:06:31Z","article_number":"51512","date_published":"2020-03-11T00:00:00Z","month":"03","intvolume":"         9","year":"2020","external_id":{"isi":["000522835800001"],"pmid":["32159512"]}},{"oa_version":"Published Version","ec_funded":1,"doi":"10.1103/PhysRevResearch.2.013353","publication":"Physical Review Research","day":"20","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-03-20T15:21:10Z","ddc":["530"],"volume":2,"year":"2020","issue":"1","oa":1,"date_updated":"2021-01-12T08:14:23Z","article_number":"013353","month":"03","intvolume":"         2","date_published":"2020-03-20T00:00:00Z","publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"quality_controlled":"1","_id":"7594","file_date_updated":"2020-07-14T12:48:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"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>","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>","short":"D. Gotfryd, E. Paerschke, J. Chaloupka, A.M. Oles, K. Wohlfeld, Physical Review Research 2 (2020).","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.","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.","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>."},"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"MiLe"}],"article_processing_charge":"No","file":[{"date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-23T10:18:38Z","file_name":"2020_PhysRevResearch_Gotfryd.pdf","relation":"main_file","access_level":"open_access","checksum":"1be551fd5f5583635076017d7391ffdc","file_id":"7610","content_type":"application/pdf","creator":"dernst","file_size":1436735}],"title":"How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Gotfryd","first_name":"Dorota","full_name":"Gotfryd, Dorota"},{"full_name":"Paerschke, Ekaterina","last_name":"Paerschke","orcid":"0000-0003-0853-8182","first_name":"Ekaterina","id":"8275014E-6063-11E9-9B7F-6338E6697425"},{"full_name":"Chaloupka, Jiri","first_name":"Jiri","last_name":"Chaloupka"},{"first_name":"Andrzej M.","last_name":"Oles","full_name":"Oles, Andrzej M."},{"full_name":"Wohlfeld, Krzysztof","first_name":"Krzysztof","last_name":"Wohlfeld"}],"publisher":"American Physical Society","has_accepted_license":"1"},{"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship","grant_number":"723-2015"}],"publication_status":"published","citation":{"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>.","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.","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.","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>.","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>"},"publication_identifier":{"eissn":["20550278"]},"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."}],"scopus_import":"1","type":"journal_article","_id":"7600","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"article_type":"original","publisher":"Springer Nature","title":"The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis","author":[{"full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi"},{"last_name":"Kong","first_name":"Wei","full_name":"Kong, Wei"},{"full_name":"Yang, Xiao-Li","first_name":"Xiao-Li","last_name":"Yang"},{"full_name":"Molnar, Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Gergely","last_name":"Molnar"},{"full_name":"Vondráková, Zuzana","first_name":"Zuzana","last_name":"Vondráková"},{"last_name":"Filepová","first_name":"Roberta","full_name":"Filepová, Roberta"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Xue, Hong-Wei","last_name":"Xue","first_name":"Hong-Wei"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Nature Plants","doi":"10.1038/s41477-020-0648-9","main_file_link":[{"url":"https://doi.org/10.1101/755504","open_access":"1"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41477-020-0719-y"}]},"ec_funded":1,"oa_version":"Preprint","isi":1,"volume":6,"pmid":1,"date_created":"2020-03-21T16:34:16Z","day":"01","status":"public","external_id":{"pmid":["32393881"],"isi":["000531787500006"]},"page":"556-569","year":"2020","date_published":"2020-05-01T00:00:00Z","month":"05","intvolume":"         6","date_updated":"2023-08-18T07:05:57Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa":1},{"department":[{"_id":"JiFr"}],"article_processing_charge":"No","page":"22","year":"2020","language":[{"iso":"eng"}],"publisher":"Cold Spring Harbor Laboratory","month":"02","date_published":"2020-02-19T00:00:00Z","title":"Plasmodesmata-like intercellular connections by plant remorin in animal cells","author":[{"last_name":"Wei","first_name":"Zhuang","full_name":"Wei, Zhuang"},{"last_name":"Tan","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","full_name":"Tan, Shutang"},{"last_name":"Liu","first_name":"Tao","full_name":"Liu, Tao"},{"last_name":"Wu","first_name":"Yuan","full_name":"Wu, Yuan"},{"last_name":"Lei","first_name":"Ji-Gang","full_name":"Lei, Ji-Gang"},{"full_name":"Chen, ZhengJun","first_name":"ZhengJun","last_name":"Chen"},{"full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Xue, Hong-Wei","last_name":"Xue","first_name":"Hong-Wei"},{"full_name":"Liao, Kan","first_name":"Kan","last_name":"Liao"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:14:26Z","main_file_link":[{"url":"https://doi.org/10.1101/791137","open_access":"1"}],"doi":"10.1101/791137","publication_status":"published","publication":"bioRxiv","oa_version":"Preprint","type":"preprint","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."}],"citation":{"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>","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>","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.","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>."},"day":"19","status":"public","date_created":"2020-03-21T16:34:42Z","_id":"7601"},{"year":"2020","external_id":{"isi":["000518903600001"]},"date_updated":"2023-08-18T07:05:18Z","oa":1,"date_published":"2020-02-19T00:00:00Z","intvolume":"        11","month":"02","article_number":"91","oa_version":"Published Version","isi":1,"publication":"Frontiers in Plant Science","doi":"10.3389/fpls.2020.00091","ddc":["580"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-03-22T23:00:46Z","status":"public","day":"19","volume":11,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"FyKo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Alternative splicing and DNA damage response in plants","author":[{"first_name":"Barbara Anna","last_name":"Nimeth","full_name":"Nimeth, Barbara Anna"},{"full_name":"Riegler, Stefan","orcid":"0000-0003-3413-1343","last_name":"Riegler","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","first_name":"Stefan"},{"full_name":"Kalyna, Maria","first_name":"Maria","last_name":"Kalyna"}],"file":[{"access_level":"open_access","relation":"main_file","checksum":"57c37209f7b6712ced86c0f11b2be74e","file_size":507414,"creator":"dernst","content_type":"application/pdf","file_id":"7607","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-03-23T09:03:40Z","file_name":"2020_FrontiersPlants_Nimeth.pdf"}],"has_accepted_license":"1","publisher":"Frontiers","publication_status":"published","_id":"7603","quality_controlled":"1","publication_identifier":{"eissn":["1664462X"]},"citation":{"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>.","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>","short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","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.","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91.","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>.","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>"},"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:48:01Z"},{"year":"2020","license":"https://creativecommons.org/licenses/by/3.0/","conference":{"location":"Neuchatal, Switzerland","start_date":"2019-12-17","end_date":"2019-12-19","name":"OPODIS: International Conference on Principles of Distributed Systems"},"external_id":{"arxiv":["1911.06347"]},"page":"15:1-15:16","oa":1,"date_updated":"2023-02-23T13:12:12Z","date_published":"2020-02-01T00:00:00Z","alternative_title":["LIPIcs"],"month":"02","intvolume":"       153","oa_version":"Published Version","publication":"23rd International Conference on Principles of Distributed Systems","doi":"10.4230/LIPIcs.OPODIS.2019.15","status":"public","day":"01","ddc":["000"],"tmp":{"short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png"},"date_created":"2020-03-22T23:00:46Z","volume":153,"language":[{"iso":"eng"}],"department":[{"_id":"DaAl"}],"article_processing_charge":"No","author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fedorov, Alexander","first_name":"Alexander","last_name":"Fedorov"},{"full_name":"Koval, Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"In search of the fastest concurrent union-find algorithm","file":[{"file_name":"2019_LIPIcs_Alistarh.pdf","date_created":"2020-03-23T09:22:48Z","date_updated":"2020-07-14T12:48:01Z","content_type":"application/pdf","file_id":"7609","file_size":13074131,"creator":"dernst","access_level":"open_access","checksum":"d66f07ecb609d9f02433e39f80a447e9","relation":"main_file"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","has_accepted_license":"1","publication_status":"published","quality_controlled":"1","_id":"7605","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"}],"scopus_import":"1","arxiv":1,"file_date_updated":"2020-07-14T12:48:01Z","type":"conference","publication_identifier":{"isbn":["9783959771337"],"issn":["18688969"]},"citation":{"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>.","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>.","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.","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.","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.","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>"}},{"author":[{"full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","last_name":"Rademacher","first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425"}],"title":"Central limit theorem for Bose gases interacting through singular potentials","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"8784","content_type":"application/pdf","file_size":478683,"creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"3bdd41f10ad947b67a45b98f507a7d4a","success":1,"file_name":"2020_LettersMathPhysics_Rademacher.pdf","date_created":"2020-11-20T12:04:26Z","date_updated":"2020-11-20T12:04:26Z"}],"publisher":"Springer Nature","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","_id":"7611","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","file_date_updated":"2020-11-20T12:04:26Z","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"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>","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>","ista":"Rademacher SAE. 2020. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 110, 2143–2174.","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.","short":"S.A.E. Rademacher, Letters in Mathematical Physics 110 (2020) 2143–2174.","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>."},"publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"oa":1,"date_updated":"2023-09-05T15:14:50Z","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_published":"2020-03-12T00:00:00Z","month":"03","intvolume":"       110","year":"2020","page":"2143-2174","external_id":{"isi":["000551556000006"]},"status":"public","day":"12","ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-03-23T11:11:47Z","volume":110,"oa_version":"Published Version","ec_funded":1,"isi":1,"publication":"Letters in Mathematical Physics","doi":"10.1007/s11005-020-01286-w"},{"volume":110,"date_created":"2020-03-25T15:57:48Z","status":"public","day":"01","publication":"Letters in Mathematical Physics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.10455"}],"doi":"10.1007/s11005-020-01282-0","ec_funded":1,"oa_version":"Preprint","isi":1,"date_published":"2020-08-01T00:00:00Z","intvolume":"       110","month":"08","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":"2023-08-18T10:17:26Z","oa":1,"issue":"8","external_id":{"isi":["000551556000002"],"arxiv":["1903.10455"]},"page":"2039-2052","year":"2020","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"citation":{"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>.","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>","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.","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.","ista":"Pitrik J, Virosztek D. 2020. Quantum Hellinger distances revisited. Letters in Mathematical Physics. 110(8), 2039–2052.","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>"},"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"}],"arxiv":1,"scopus_import":"1","type":"journal_article","_id":"7618","quality_controlled":"1","project":[{"_id":"26A455A6-B435-11E9-9278-68D0E5697425","name":"Geometric study of Wasserstein spaces and free probability","grant_number":"846294","call_identifier":"H2020"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publisher":"Springer Nature","author":[{"last_name":"Pitrik","first_name":"Jozsef","full_name":"Pitrik, Jozsef"},{"orcid":"0000-0003-1109-5511","last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Virosztek, Daniel"}],"title":"Quantum Hellinger distances revisited","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"article_type":"original"},{"quality_controlled":"1","_id":"7619","type":"journal_article","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"citation":{"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>","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.","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.","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.","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>.","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>","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>."},"publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"publication_status":"published","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-7048-4627","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","full_name":"Zhang, Xixi"},{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski"},{"last_name":"Marhavá","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavá, Petra"},{"orcid":"0000-0002-0471-8285","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang"},{"full_name":"Zhang, Yuzhou","first_name":"Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956","last_name":"Zhang"},{"full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","first_name":"Lesia","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"last_name":"Pukyšová","first_name":"Vendula","full_name":"Pukyšová, Vendula"},{"full_name":"Sánchez, Adrià Sans","first_name":"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."},{"last_name":"Nodzynski","first_name":"Tomasz","full_name":"Nodzynski, Tomasz"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"title":"Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters","publisher":"American Society of Plant Biologists","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"article_processing_charge":"No","day":"01","status":"public","date_created":"2020-03-28T07:39:22Z","pmid":1,"volume":32,"isi":1,"ec_funded":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1105/tpc.19.00869","open_access":"1"}],"doi":"10.1105/tpc.19.00869","publication":"The Plant Cell","issue":"5","acknowledged_ssus":[{"_id":"Bio"}],"oa":1,"date_updated":"2023-09-05T12:21:06Z","intvolume":"        32","month":"05","date_published":"2020-05-01T00:00:00Z","year":"2020","external_id":{"isi":["000545741500030"],"pmid":["32193204"]},"page":"1644-1664"},{"isi":1,"oa_version":"Published Version","doi":"10.1088/1361-6404/ab6414","publication":"European Journal of Physics","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-03-31T11:25:04Z","ddc":["530"],"day":"24","status":"public","volume":41,"year":"2020","external_id":{"arxiv":["1910.03290"],"isi":["000537425400001"]},"date_updated":"2023-08-18T10:18:29Z","issue":"3","oa":1,"intvolume":"        41","month":"02","date_published":"2020-02-24T00:00:00Z","article_number":"034001","publication_status":"published","_id":"7622","quality_controlled":"1","citation":{"ama":"Plesch M, Plesník S, Ruzickova N. The IYPT and the “Ring Oiler” problem. <i>European Journal of Physics</i>. 2020;41(3). doi:<a href=\"https://doi.org/10.1088/1361-6404/ab6414\">10.1088/1361-6404/ab6414</a>","ieee":"M. Plesch, S. Plesník, and N. Ruzickova, “The IYPT and the ‘Ring Oiler’ problem,” <i>European Journal of Physics</i>, vol. 41, no. 3. IOP Publishing, 2020.","short":"M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (2020).","ista":"Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001.","chicago":"Plesch, Martin, Samuel Plesník, and Natalia Ruzickova. “The IYPT and the ‘Ring Oiler’ Problem.” <i>European Journal of Physics</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1361-6404/ab6414\">https://doi.org/10.1088/1361-6404/ab6414</a>.","apa":"Plesch, M., Plesník, S., &#38; Ruzickova, N. (2020). The IYPT and the “Ring Oiler” problem. <i>European Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6404/ab6414\">https://doi.org/10.1088/1361-6404/ab6414</a>","mla":"Plesch, Martin, et al. “The IYPT and the ‘Ring Oiler’ Problem.” <i>European Journal of Physics</i>, vol. 41, no. 3, 034001, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.1088/1361-6404/ab6414\">10.1088/1361-6404/ab6414</a>."},"publication_identifier":{"eissn":["13616404"],"issn":["01430807"]},"type":"journal_article","file_date_updated":"2020-07-14T12:48:01Z","abstract":[{"text":"The International Young Physicists' Tournament (IYPT) continued in 2018 in Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The IYPT is a modern scientific competition for teams of high school students, also known as the Physics World Cup. It involves long-term theoretical and experimental work focused on solving 17 publicly announced open-ended problems in teams of five. On top of that, teams have to present their solutions in front of other teams and a scientific jury, and get opposed and reviewed by their peers. Here we present a brief information about the competition with a specific focus on one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical problem appeared to be of such a complexity that even the dozens of participating teams and jurying scientists were not able to solve all of its subtleties.","lang":"eng"}],"arxiv":1,"scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"FyKo"}],"file":[{"relation":"main_file","checksum":"47dda164e33b6c0c6c3ed14aad298376","access_level":"open_access","creator":"dernst","file_size":1533672,"file_id":"7641","content_type":"application/pdf","date_created":"2020-04-06T08:53:53Z","date_updated":"2020-07-14T12:48:01Z","file_name":"2020_EuropJourPhysics_Plesch.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"The IYPT and the 'Ring Oiler' problem","author":[{"first_name":"Martin","last_name":"Plesch","full_name":"Plesch, Martin"},{"first_name":"Samuel","last_name":"Plesník","full_name":"Plesník, Samuel"},{"last_name":"Ruzickova","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia"}],"has_accepted_license":"1","publisher":"IOP Publishing"},{"publication_status":"published","project":[{"grant_number":"LS13-029","_id":"25AD6156-B435-11E9-9278-68D0E5697425","name":"Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments"}],"type":"journal_article","arxiv":1,"abstract":[{"lang":"eng","text":"A two-dimensional mathematical model for cells migrating without adhesion capabilities is presented and analyzed. Cells are represented by their cortex, which is modeled as an elastic curve, subject to an internal pressure force. Net polymerization or depolymerization in the cortex is modeled via local addition or removal of material, driving a cortical flow. The model takes the form of a fully nonlinear degenerate parabolic system. An existence analysis is carried out by adapting ideas from the theory of gradient flows. Numerical simulations show that these simple rules can account for the behavior observed in experiments, suggesting a possible mechanical mechanism for adhesion-independent motility."}],"scopus_import":"1","publication_identifier":{"issn":["02182025"]},"citation":{"ama":"Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. Modeling adhesion-independent cell migration. <i>Mathematical Models and Methods in Applied Sciences</i>. 2020;30(3):513-537. doi:<a href=\"https://doi.org/10.1142/S021820252050013X\">10.1142/S021820252050013X</a>","ista":"Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. 2020. Modeling adhesion-independent cell migration. Mathematical Models and Methods in Applied Sciences. 30(3), 513–537.","short":"G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, M.K. Sixt, Mathematical Models and Methods in Applied Sciences 30 (2020) 513–537.","ieee":"G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, and M. K. Sixt, “Modeling adhesion-independent cell migration,” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 30, no. 3. World Scientific, pp. 513–537, 2020.","chicago":"Jankowiak, Gaspard, Diane Peurichard, Anne Reversat, Christian Schmeiser, and Michael K Sixt. “Modeling Adhesion-Independent Cell Migration.” <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific, 2020. <a href=\"https://doi.org/10.1142/S021820252050013X\">https://doi.org/10.1142/S021820252050013X</a>.","apa":"Jankowiak, G., Peurichard, D., Reversat, A., Schmeiser, C., &#38; Sixt, M. K. (2020). Modeling adhesion-independent cell migration. <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific. <a href=\"https://doi.org/10.1142/S021820252050013X\">https://doi.org/10.1142/S021820252050013X</a>","mla":"Jankowiak, Gaspard, et al. “Modeling Adhesion-Independent Cell Migration.” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 30, no. 3, World Scientific, 2020, pp. 513–37, doi:<a href=\"https://doi.org/10.1142/S021820252050013X\">10.1142/S021820252050013X</a>."},"quality_controlled":"1","_id":"7623","department":[{"_id":"MiSi"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"World Scientific","title":"Modeling adhesion-independent cell migration","author":[{"first_name":"Gaspard","last_name":"Jankowiak","full_name":"Jankowiak, Gaspard"},{"first_name":"Diane","last_name":"Peurichard","full_name":"Peurichard, Diane"},{"orcid":"0000-0003-0666-8928","last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Reversat, Anne"},{"last_name":"Schmeiser","first_name":"Christian","full_name":"Schmeiser, Christian"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1142/S021820252050013X","main_file_link":[{"url":"https://arxiv.org/abs/1903.09426","open_access":"1"}],"publication":"Mathematical Models and Methods in Applied Sciences","isi":1,"oa_version":"Preprint","volume":30,"status":"public","day":"18","date_created":"2020-03-31T11:25:05Z","external_id":{"isi":["000525349900003"],"arxiv":["1903.09426"]},"page":"513-537","year":"2020","acknowledgement":"This work has been supported by the Vienna Science and Technology Fund, Grant no. LS13-029. G.J. and C.S. also acknowledge support by the Austrian Science Fund, Grants no. W1245, F 65, and W1261, as well as by the Fondation Sciences Mathématiques de Paris, and by Paris-Sciences-et-Lettres.","intvolume":"        30","month":"03","date_published":"2020-03-18T00:00:00Z","issue":"3","oa":1,"date_updated":"2023-08-18T10:18:56Z"},{"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Forkert","first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","full_name":"Forkert, Dominik L"}],"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","file":[{"creator":"dernst","file_size":3297129,"content_type":"application/pdf","file_id":"7657","relation":"main_file","access_level":"open_access","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","file_name":"Thesis_Forkert_PDFA.pdf","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-14T10:47:59Z"},{"relation":"source_file","checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81","access_level":"closed","file_id":"7658","content_type":"application/x-zip-compressed","file_size":1063908,"creator":"dernst","date_created":"2020-04-14T10:47:59Z","date_updated":"2020-07-14T12:48:01Z","file_name":"Thesis_Forkert_source.zip"}],"article_processing_charge":"No","department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"citation":{"apa":"Forkert, D. L. (2020). <i>Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7629\">https://doi.org/10.15479/AT:ISTA:7629</a>","mla":"Forkert, Dominik L. <i>Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7629\">10.15479/AT:ISTA:7629</a>.","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7629\">10.15479/AT:ISTA:7629</a>","chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7629\">https://doi.org/10.15479/AT:ISTA:7629</a>."},"abstract":[{"lang":"eng","text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals."}],"type":"dissertation","file_date_updated":"2020-07-14T12:48:01Z","_id":"7629","project":[{"call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","date_published":"2020-03-31T00:00:00Z","alternative_title":["ISTA Thesis"],"month":"03","date_updated":"2023-09-07T13:03:12Z","oa":1,"page":"154","year":"2020","date_created":"2020-04-02T06:40:23Z","ddc":["510"],"day":"31","status":"public","supervisor":[{"full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas","orcid":"0000-0002-0845-1338"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7629","oa_version":"Published Version","ec_funded":1},{"has_accepted_license":"1","publisher":"Springer Nature","file":[{"file_size":2621249,"creator":"dernst","content_type":"application/pdf","file_id":"7644","access_level":"open_access","relation":"main_file","checksum":"e6cfaaaf7986532132934400038b824a","file_name":"2020_ScientificReports_Tombaz.pdf","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-06T10:44:23Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Tuce","last_name":"Tombaz","full_name":"Tombaz, Tuce"},{"full_name":"Dunn, Benjamin A.","first_name":"Benjamin A.","last_name":"Dunn"},{"last_name":"Hovde","first_name":"Karoline","full_name":"Hovde, Karoline"},{"full_name":"Cubero, Ryan J","first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","last_name":"Cubero"},{"full_name":"Mimica, Bartul","first_name":"Bartul","last_name":"Mimica"},{"full_name":"Mamidanna, Pranav","last_name":"Mamidanna","first_name":"Pranav"},{"last_name":"Roudi","first_name":"Yasser","full_name":"Roudi, Yasser"},{"first_name":"Jonathan R.","last_name":"Whitlock","full_name":"Whitlock, Jonathan R."}],"title":"Action representation in the mouse parieto-frontal network","article_processing_charge":"No","department":[{"_id":"SaSi"}],"language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"eissn":["20452322"]},"citation":{"chicago":"Tombaz, Tuce, Benjamin A. Dunn, Karoline Hovde, Ryan J Cubero, Bartul Mimica, Pranav Mamidanna, Yasser Roudi, and Jonathan R. Whitlock. “Action Representation in the Mouse Parieto-Frontal Network.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-62089-6\">https://doi.org/10.1038/s41598-020-62089-6</a>.","short":"T. Tombaz, B.A. Dunn, K. Hovde, R.J. Cubero, B. Mimica, P. Mamidanna, Y. Roudi, J.R. Whitlock, Scientific Reports 10 (2020).","ista":"Tombaz T, Dunn BA, Hovde K, Cubero RJ, Mimica B, Mamidanna P, Roudi Y, Whitlock JR. 2020. Action representation in the mouse parieto-frontal network. Scientific reports. 10(1), 5559.","ieee":"T. Tombaz <i>et al.</i>, “Action representation in the mouse parieto-frontal network,” <i>Scientific reports</i>, vol. 10, no. 1. Springer Nature, 2020.","ama":"Tombaz T, Dunn BA, Hovde K, et al. Action representation in the mouse parieto-frontal network. <i>Scientific reports</i>. 2020;10(1). doi:<a href=\"https://doi.org/10.1038/s41598-020-62089-6\">10.1038/s41598-020-62089-6</a>","mla":"Tombaz, Tuce, et al. “Action Representation in the Mouse Parieto-Frontal Network.” <i>Scientific Reports</i>, vol. 10, no. 1, 5559, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-62089-6\">10.1038/s41598-020-62089-6</a>.","apa":"Tombaz, T., Dunn, B. A., Hovde, K., Cubero, R. J., Mimica, B., Mamidanna, P., … Whitlock, J. R. (2020). Action representation in the mouse parieto-frontal network. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-62089-6\">https://doi.org/10.1038/s41598-020-62089-6</a>"},"file_date_updated":"2020-07-14T12:48:01Z","type":"journal_article","abstract":[{"lang":"eng","text":"The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical network supporting goal-directed behaviour, with functions including sensorimotor transformations and decision making. In primates, this network links performed and observed actions via mirror neurons, which fire both when individuals perform an action and when they observe the same action performed by a conspecific. Mirror neurons are believed to be important for social learning, but it is not known whether mirror-like neurons occur in similar networks in other social species, such as rodents, or if they can be measured in such models using paradigms where observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching and wheel-running tasks, and found that cell populations in both areas robustly encoded several naturalistic behaviours. However, neural responses to the same set of observed actions were absent, although we verified that observer mice were attentive to performers and that PPC neurons responded reliably to visual cues. Statistical modelling also indicated that executed actions outperformed observed actions in predicting neural responses. These results raise the possibility that sensorimotor action recognition in rodents could take place outside of the parieto-frontal circuit, and underscore that detecting socially-driven neural coding depends critically on the species and behavioural paradigm used."}],"scopus_import":"1","_id":"7632","quality_controlled":"1","publication_status":"published","month":"03","intvolume":"        10","date_published":"2020-03-27T00:00:00Z","article_number":"5559","date_updated":"2023-08-18T10:25:13Z","issue":"1","oa":1,"external_id":{"isi":["000560406800007"]},"year":"2020","volume":10,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2020-04-05T22:00:47Z","day":"27","status":"public","doi":"10.1038/s41598-020-62089-6","publication":"Scientific reports","isi":1,"oa_version":"Published Version"},{"year":"2020","external_id":{"isi":["000564476500020"]},"page":"276-291","conference":{"name":"PPOPP: Principles and Practice of Parallel Programming","start_date":"2020-02-22","end_date":"2020-02-26","location":"San Diego, CA, United States"},"date_updated":"2024-02-28T12:55:14Z","oa":1,"date_published":"2020-02-19T00:00:00Z","month":"02","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program, grant agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). ","oa_version":"Published Version","ec_funded":1,"isi":1,"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","doi":"10.1145/3332466.3374542","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3332466.3374542"}],"date_created":"2020-04-05T22:00:49Z","status":"public","day":"19","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"DaAl"}],"title":"Non-blocking interpolation search trees with doubly-logarithmic running time","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown"},{"full_name":"Prokopec, Aleksandar","first_name":"Aleksandar","last_name":"Prokopec"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"publisher":"Association for Computing Machinery","project":[{"grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","_id":"7636","quality_controlled":"1","publication_identifier":{"isbn":["9781450368186"]},"citation":{"apa":"Brown, T. A., Prokopec, A., &#38; Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3332466.3374542\">https://doi.org/10.1145/3332466.3374542</a>","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2020, pp. 276–91, doi:<a href=\"https://doi.org/10.1145/3332466.3374542\">10.1145/3332466.3374542</a>.","ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery; 2020:276-291. doi:<a href=\"https://doi.org/10.1145/3332466.3374542\">10.1145/3332466.3374542</a>","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, San Diego, CA, United States, 2020, pp. 276–291.","ista":"Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice of Parallel Programming, 276–291.","short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, 276–91. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.1145/3332466.3374542\">https://doi.org/10.1145/3332466.3374542</a>."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures."}],"type":"conference"},{"year":"2020","page":"864-891","external_id":{"arxiv":["1811.06448"],"isi":["000508175400001"]},"issue":"2","oa":1,"date_updated":"2023-08-18T10:26:07Z","intvolume":"        33","month":"01","date_published":"2020-01-10T00:00:00Z","isi":1,"oa_version":"Preprint","doi":"10.1088/1361-6544/ab5174","main_file_link":[{"url":"https://arxiv.org/abs/1811.06448","open_access":"1"}],"publication":"Nonlinearity","status":"public","day":"10","date_created":"2020-04-05T22:00:49Z","volume":33,"article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JuFi"}],"article_processing_charge":"No","author":[{"full_name":"Cornalba, Federico","first_name":"Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425","orcid":"0000-0002-6269-5149","last_name":"Cornalba"},{"last_name":"Shardlow","first_name":"Tony","full_name":"Shardlow, Tony"},{"last_name":"Zimmer","first_name":"Johannes","full_name":"Zimmer, Johannes"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"From weakly interacting particles to a regularised Dean-Kawasaki model","publisher":"IOP Publishing","publication_status":"published","quality_controlled":"1","_id":"7637","type":"journal_article","arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"The evolution of finitely many particles obeying Langevin dynamics is described by Dean–Kawasaki equations, a class of stochastic equations featuring a non-Lipschitz multiplicative noise in divergence form. We derive a regularised Dean–Kawasaki model based on second order Langevin dynamics by analysing a system of particles interacting via a pairwise potential. Key tools of our analysis are the propagation of chaos and Simon's compactness criterion. The model we obtain is a small-noise stochastic perturbation of the undamped McKean–Vlasov equation. We also provide a high-probability result for existence and uniqueness for our model."}],"publication_identifier":{"eissn":["13616544"],"issn":["09517715"]},"citation":{"chicago":"Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” <i>Nonlinearity</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1361-6544/ab5174\">https://doi.org/10.1088/1361-6544/ab5174</a>.","ama":"Cornalba F, Shardlow T, Zimmer J. From weakly interacting particles to a regularised Dean-Kawasaki model. <i>Nonlinearity</i>. 2020;33(2):864-891. doi:<a href=\"https://doi.org/10.1088/1361-6544/ab5174\">10.1088/1361-6544/ab5174</a>","short":"F. Cornalba, T. Shardlow, J. Zimmer, Nonlinearity 33 (2020) 864–891.","ista":"Cornalba F, Shardlow T, Zimmer J. 2020. From weakly interacting particles to a regularised Dean-Kawasaki model. Nonlinearity. 33(2), 864–891.","ieee":"F. Cornalba, T. Shardlow, and J. Zimmer, “From weakly interacting particles to a regularised Dean-Kawasaki model,” <i>Nonlinearity</i>, vol. 33, no. 2. IOP Publishing, pp. 864–891, 2020.","mla":"Cornalba, Federico, et al. “From Weakly Interacting Particles to a Regularised Dean-Kawasaki Model.” <i>Nonlinearity</i>, vol. 33, no. 2, IOP Publishing, 2020, pp. 864–91, doi:<a href=\"https://doi.org/10.1088/1361-6544/ab5174\">10.1088/1361-6544/ab5174</a>.","apa":"Cornalba, F., Shardlow, T., &#38; Zimmer, J. (2020). From weakly interacting particles to a regularised Dean-Kawasaki model. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6544/ab5174\">https://doi.org/10.1088/1361-6544/ab5174</a>"}}]