[{"intvolume":"       383","citation":{"short":"W. Ying, Y. Wang, H. Wei, Y. Luo, Q. Ma, H. Zhu, H. Janssens, N. Vukašinović, M. Kvasnica, J.M. Winne, Y. Gao, S. Tan, J. Friml, X. Liu, E. Russinova, L. Sun, Science 383 (2024) eadj4591.","ista":"Ying W, Wang Y, Wei H, Luo Y, Ma Q, Zhu H, Janssens H, Vukašinović N, Kvasnica M, Winne JM, Gao Y, Tan S, Friml J, Liu X, Russinova E, Sun L. 2024. Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export. Science. 383(6689), eadj4591.","apa":"Ying, W., Wang, Y., Wei, H., Luo, Y., Ma, Q., Zhu, H., … Sun, L. (2024). Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adj4591\">https://doi.org/10.1126/science.adj4591</a>","ama":"Ying W, Wang Y, Wei H, et al. Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export. <i>Science</i>. 2024;383(6689):eadj4591. doi:<a href=\"https://doi.org/10.1126/science.adj4591\">10.1126/science.adj4591</a>","ieee":"W. Ying <i>et al.</i>, “Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export,” <i>Science</i>, vol. 383, no. 6689. American Association for the Advancement of Science, p. eadj4591, 2024.","chicago":"Ying, Wei, Yaowei Wang, Hong Wei, Yongming Luo, Qian Ma, Heyuan Zhu, Hilde Janssens, et al. “Structure and Function of the Arabidopsis ABC Transporter ABCB19 in Brassinosteroid Export.” <i>Science</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/science.adj4591\">https://doi.org/10.1126/science.adj4591</a>.","mla":"Ying, Wei, et al. “Structure and Function of the Arabidopsis ABC Transporter ABCB19 in Brassinosteroid Export.” <i>Science</i>, vol. 383, no. 6689, American Association for the Advancement of Science, 2024, p. eadj4591, doi:<a href=\"https://doi.org/10.1126/science.adj4591\">10.1126/science.adj4591</a>."},"publication_identifier":{"eissn":["1095-9203"]},"publisher":"American Association for the Advancement of Science","publication_status":"published","abstract":[{"text":"Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but bind receptors at the cell surface, necessitating a yet to be identified export mechanism. Here, we show that a member of the ATP-binding cassette (ABC) transporter superfamily, ABCB19, functions as a brassinosteroid exporter. We present its structure in both the substrate-unbound and the brassinosteroid-bound states. Bioactive brassinosteroids are potent activators of ABCB19 ATP hydrolysis activity, and transport assays showed that ABCB19 transports brassinosteroids. In Arabidopsis thaliana, ABCB19 and its close homolog, ABCB1, positively regulate brassinosteroid responses. Our results uncover an elusive export mechanism for bioactive brassinosteroids that is tightly coordinated with brassinosteroid signaling.","lang":"eng"}],"oa_version":"Submitted Version","acknowledgement":"We thank the Cryo-EM Center of the University of Science and Technology of China for the EM facility support, Y. Yin (Iowa State University, Ames, IA, USA) for providing the anti-BES1 antibody, Y. Gao and all other staff members for their technical support on cryo-EM data collection, S. Vanneste (VIB, Ghent University, Ghent, Belgium) for useful discussions, and M. De Cock for help in preparing the manuscript.\r\nThis work was supported by the National Natural Science Foundation of China (grants 31870732 and 32322041 to L.S., grant 31900885 to X.L., and grant 32321001 to L.S.); the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDB37020103 to L.S.); the Natural Science Foundation of Anhui Province (grant 2008085MC90 to X.L. and grant 2008085J15 to L.S.); Fundamental Research Funds for the Central Universities (grant WK9100000031 to L.S.); USTC Research Funds of the Double First-Class Initiative (grant YD9100002004 to L.S. and grant YD9100002020 to X.L.); Research Foundation-Flanders (grant G002121N to E.R. and postdoctoral fellowships 12R7822N and 12R7819N to N.V.); and Chinese Scholarship Council predoctoral fellowships (Y.W. and H.Z.). L.S. is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.","doi":"10.1126/science.adj4591","volume":383,"quality_controlled":"1","year":"2024","status":"public","date_published":"2024-03-22T00:00:00Z","_id":"15251","isi":1,"pmid":1,"language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"scopus_import":"1","oa":1,"article_processing_charge":"No","OA_place":"repository","date_created":"2024-03-31T22:01:12Z","publication":"Science","title":"Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export","main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/1854/LU-01HTMBK3P3PPNB73YFCMFXP3ZZ"}],"issue":"6689","month":"03","date_updated":"2025-09-04T13:19:48Z","fulldoi":"https://doi.org/10.1126/science.adj4591","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","author":[{"full_name":"Ying, Wei","last_name":"Ying","first_name":"Wei"},{"first_name":"Yaowei","last_name":"Wang","full_name":"Wang, Yaowei"},{"last_name":"Wei","first_name":"Hong","full_name":"Wei, Hong"},{"last_name":"Luo","first_name":"Yongming","full_name":"Luo, Yongming"},{"first_name":"Qian","last_name":"Ma","full_name":"Ma, Qian"},{"full_name":"Zhu, Heyuan","last_name":"Zhu","first_name":"Heyuan"},{"last_name":"Janssens","first_name":"Hilde","full_name":"Janssens, Hilde"},{"full_name":"Vukašinović, Nemanja","last_name":"Vukašinović","first_name":"Nemanja"},{"last_name":"Kvasnica","first_name":"Miroslav","full_name":"Kvasnica, Miroslav"},{"full_name":"Winne, Johan M.","last_name":"Winne","first_name":"Johan M."},{"last_name":"Gao","first_name":"Yongxiang","full_name":"Gao, Yongxiang"},{"last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"full_name":"Liu, Xin","last_name":"Liu","first_name":"Xin"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"},{"first_name":"Linfeng","last_name":"Sun","full_name":"Sun, Linfeng"}],"day":"22","page":"eadj4591","article_type":"original","OA_type":"green","external_id":{"pmid":["38513023"],"isi":["001252955200028"]}},{"article_type":"original","external_id":{"arxiv":["2304.11348"]},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"137-142","day":"01","author":[{"orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","first_name":"Lorenzo"}],"arxiv":1,"month":"01","issue":"1","date_updated":"2025-04-14T12:59:08Z","date_created":"2024-03-31T22:01:12Z","publication":"Mathematical Communications","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.11348","open_access":"1"}],"title":"A characterization of maps of bounded compression","language":[{"iso":"eng"}],"article_processing_charge":"No","project":[{"name":"Configuration Spaces over Non-Smooth Spaces","grant_number":"E208","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"}],"oa":1,"scopus_import":"1","department":[{"_id":"JaMa"}],"volume":29,"quality_controlled":"1","acknowledgement":"The author gratefully acknowledges funding of his current position by the Austrian Science\r\nFund (FWF), grant ESPRIT208. He is grateful to Enrico Pasqualetto for pointing out some\r\nreferences on maps of bounded compression.","_id":"15252","date_published":"2024-01-01T00:00:00Z","status":"public","year":"2024","publication_status":"published","publisher":"Udruga Matematicara Osijek","publication_identifier":{"issn":["1331-0623"],"eissn":["1848-8013"]},"citation":{"ista":"Dello Schiavo L. 2024. A characterization of maps of bounded compression. Mathematical Communications. 29(1), 137–142.","short":"L. Dello Schiavo, Mathematical Communications 29 (2024) 137–142.","chicago":"Dello Schiavo, Lorenzo. “A Characterization of Maps of Bounded Compression.” <i>Mathematical Communications</i>. Udruga Matematicara Osijek, 2024.","ieee":"L. Dello Schiavo, “A characterization of maps of bounded compression,” <i>Mathematical Communications</i>, vol. 29, no. 1. Udruga Matematicara Osijek, pp. 137–142, 2024.","mla":"Dello Schiavo, Lorenzo. “A Characterization of Maps of Bounded Compression.” <i>Mathematical Communications</i>, vol. 29, no. 1, Udruga Matematicara Osijek, 2024, pp. 137–42.","ama":"Dello Schiavo L. A characterization of maps of bounded compression. <i>Mathematical Communications</i>. 2024;29(1):137-142.","apa":"Dello Schiavo, L. (2024). A characterization of maps of bounded compression. <i>Mathematical Communications</i>. Udruga Matematicara Osijek."},"intvolume":"        29","oa_version":"Preprint","abstract":[{"lang":"eng","text":"A measurable map between measure spaces is shown to have bounded compression if and only if its image via the measure-algebra functor is Lipschitz-continuous w.r.t. the measure-algebra distances. This provides a natural interpretation of maps of bounded compression/deformation by means of the measure-algebra functor and corrobo-rates the assertion that maps of bounded deformation are a natural class of morphisms for the category of complete and separable metric measure spaces."}],"corr_author":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","arxiv":1,"page":"995-1018","author":[{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"last_name":"Upadhyay","first_name":"Jalaj","full_name":"Upadhyay, Jalaj"},{"last_name":"Upadhyay","first_name":"Sarvagya","full_name":"Upadhyay, Sarvagya"}],"day":"04","external_id":{"arxiv":["2307.08970"]},"publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms","date_created":"2024-03-31T22:01:13Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.08970"}],"title":"A unifying framework for differentially private sums under continual observation","month":"01","fulldoi":"https://doi.org/10.1137/1.9781611977912.38","date_updated":"2025-04-14T13:50:49Z","language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"MoHe"}],"scopus_import":"1","project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"grant_number":"Z00422","name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"article_processing_charge":"No","citation":{"ista":"Henzinger M, Upadhyay J, Upadhyay S. 2024. A unifying framework for differentially private sums under continual observation. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2024, 995–1018.","short":"M. Henzinger, J. Upadhyay, S. Upadhyay, in:, Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2024, pp. 995–1018.","mla":"Henzinger, Monika, et al. “A Unifying Framework for Differentially Private Sums under Continual Observation.” <i>Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2024, Society for Industrial and Applied Mathematics, 2024, pp. 995–1018, doi:<a href=\"https://doi.org/10.1137/1.9781611977912.38\">10.1137/1.9781611977912.38</a>.","ieee":"M. Henzinger, J. Upadhyay, and S. Upadhyay, “A unifying framework for differentially private sums under continual observation,” in <i>Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Alexandria, VA, United States, 2024, vol. 2024, pp. 995–1018.","chicago":"Henzinger, Monika, Jalaj Upadhyay, and Sarvagya Upadhyay. “A Unifying Framework for Differentially Private Sums under Continual Observation.” In <i>Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2024:995–1018. Society for Industrial and Applied Mathematics, 2024. <a href=\"https://doi.org/10.1137/1.9781611977912.38\">https://doi.org/10.1137/1.9781611977912.38</a>.","ama":"Henzinger M, Upadhyay J, Upadhyay S. A unifying framework for differentially private sums under continual observation. In: <i>Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2024. Society for Industrial and Applied Mathematics; 2024:995-1018. doi:<a href=\"https://doi.org/10.1137/1.9781611977912.38\">10.1137/1.9781611977912.38</a>","apa":"Henzinger, M., Upadhyay, J., &#38; Upadhyay, S. (2024). A unifying framework for differentially private sums under continual observation. In <i>Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2024, pp. 995–1018). Alexandria, VA, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977912.38\">https://doi.org/10.1137/1.9781611977912.38</a>"},"conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2024-01-07","end_date":"2024-01-10","location":"Alexandria, VA, United States"},"intvolume":"      2024","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","ec_funded":1,"publication_identifier":{"eisbn":["9781611977912"]},"abstract":[{"lang":"eng","text":"We study the problem of maintaining a differentially private decaying sum under continual observation. We give a unifying framework and an efficient algorithm for this problem for any sufficiently smooth function. Our algorithm is the first differentially private algorithm that does not have a multiplicative error for polynomially decaying weights. Our algorithm improves on all prior works on differentially private decaying sums under continual observation and recovers exactly the additive error for the special case of continual counting from Henzinger et al. (SODA 2023) as a corollary.\r\nOur algorithm is a variant of the matrix mechanism whose error depends on the γ2 and γF norm of the underlying matrix. We give a constructive proof for an almost exact upper bound on the γ2 and γF norm and an almost tight lower bound on the γ2 norm for a large class of lower-triangular matrices. This is the first non-trivial lower bound for lower-triangular matrices whose non-zero entries are not all the same. It includes matrices for all continual decaying sums problems, resulting in an upper bound on the additive error of any differentially private decaying sums algorithm under continual observation.\r\nWe also explore some implications of our result in discrepancy theory and operator algebra. Given the importance of the γ2 norm in computer science and the extensive work in mathematics, we believe our result will have further applications."}],"corr_author":"1","oa_version":"Preprint","doi":"10.1137/1.9781611977912.38","acknowledgement":"This  project  has  received  funding  from  the  European  Research  Council  (ERC)under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No.101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and the AustrianScience Fund (FWF) project Z 422-N, project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, andproject “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netideeSCIENCE  Stiftung,  2020–2024.   JU’s  research  was  funded  by  the  Decanal  Research  Grant.   We  thank  the  anonymousreviewers for their useful feedback and pointing us to the results in Matousek et al","quality_controlled":"1","volume":2024,"status":"public","year":"2024","_id":"15253","date_published":"2024-01-04T00:00:00Z"},{"day":"05","author":[{"full_name":"Kulich, Ivan","id":"57a1567c-8314-11eb-9063-c9ddc3451a54","last_name":"Kulich","first_name":"Ivan"},{"id":"07cf4637-baaf-11ee-9227-e1de57d1d69b","full_name":"Schmid, Julia","first_name":"Julia","last_name":"Schmid"},{"first_name":"Anastasiia","last_name":"Teplova","full_name":"Teplova, Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","first_name":"Linlin","last_name":"Qi"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/beneath-the-surface/"}]},"type":"journal_article","external_id":{"pmid":["38441122"]},"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"article_type":"original","file":[{"date_updated":"2024-04-03T13:18:00Z","file_size":11451904,"file_name":"2024_eLife_Kulich.pdf","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"15288","content_type":"application/pdf","checksum":"a73a84d3bf97a6d09d24308ca6dd0a0c","date_created":"2024-04-03T13:18:00Z"}],"has_accepted_license":"1","title":"Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism","date_created":"2024-04-02T11:35:58Z","publication":"eLife","file_date_updated":"2024-04-03T13:18:00Z","date_updated":"2025-04-23T07:45:02Z","fulldoi":"https://doi.org/10.7554/elife.91523","license":"https://creativecommons.org/licenses/by/4.0/","month":"03","ddc":["580"],"department":[{"_id":"JiFr"}],"scopus_import":"1","oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"article_number":"91523","article_processing_charge":"Yes","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"pmid":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.","lang":"eng"}],"corr_author":"1","oa_version":"Published Version","tmp":{"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)","image":"/images/cc_by.png"},"intvolume":"        12","citation":{"ieee":"I. Kulich, J. Schmid, A. Teplova, L. Qi, and J. Friml, “Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2024.","chicago":"Kulich, Ivan, Julia Schmid, Anastasiia Teplova, Linlin Qi, and Jiří Friml. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>. eLife Sciences Publications, 2024. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>.","mla":"Kulich, Ivan, et al. “Rapid Translocation of NGR Proteins Driving Polarization of PIN-Activating D6 Protein Kinase during Root Gravitropism.” <i>ELife</i>, vol. 12, 91523, eLife Sciences Publications, 2024, doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>.","apa":"Kulich, I., Schmid, J., Teplova, A., Qi, L., &#38; Friml, J. (2024). Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.91523\">https://doi.org/10.7554/elife.91523</a>","ama":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. <i>eLife</i>. 2024;12. doi:<a href=\"https://doi.org/10.7554/elife.91523\">10.7554/elife.91523</a>","short":"I. Kulich, J. Schmid, A. Teplova, L. Qi, J. Friml, ELife 12 (2024).","ista":"Kulich I, Schmid J, Teplova A, Qi L, Friml J. 2024. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. eLife. 12, 91523."},"publication_identifier":{"issn":["2050-084X"]},"DOAJ_listed":"1","ec_funded":1,"publisher":"eLife Sciences Publications","publication_status":"published","year":"2024","status":"public","date_published":"2024-03-05T00:00:00Z","_id":"15257","acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No 742985 and Austrian Science Fund (FWF): I3630-775 B25 to J.F. This research was also supported by the Lab Support Facility (LSF) and the Imaging and Optics Facility (IOF) of IST Austria, namely Tereza Bělinová for her help with the imaging. JS was supported by FemTECH fellowship.","doi":"10.7554/elife.91523","quality_controlled":"1","volume":12},{"isi":1,"ddc":["000"],"pmid":1,"language":[{"iso":"eng"}],"scopus_import":"1","department":[{"_id":"TiVo"}],"oa":1,"article_number":"e1011797","article_processing_charge":"Yes","intvolume":"        20","citation":{"short":"S.M. Hall, D. Kochin, C. Carne, P. Herterich, K.L. Lewers, M. Abdelhack, A. Ramasubramanian, J.F. Michael Alphonse, V. Ung, S. El-Gebali, C. Currin, E. Plomp, R. Thompson, M. Sharan, PLOS Computational Biology 20 (2024).","ista":"Hall SM, Kochin D, Carne C, Herterich P, Lewers KL, Abdelhack M, Ramasubramanian A, Michael Alphonse JF, Ung V, El-Gebali S, Currin C, Plomp E, Thompson R, Sharan M. 2024. Ten simple rules for pushing boundaries of inclusion at academic events. PLOS Computational Biology. 20(3), e1011797.","apa":"Hall, S. M., Kochin, D., Carne, C., Herterich, P., Lewers, K. L., Abdelhack, M., … Sharan, M. (2024). Ten simple rules for pushing boundaries of inclusion at academic events. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1011797\">https://doi.org/10.1371/journal.pcbi.1011797</a>","ama":"Hall SM, Kochin D, Carne C, et al. Ten simple rules for pushing boundaries of inclusion at academic events. <i>PLOS Computational Biology</i>. 2024;20(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011797\">10.1371/journal.pcbi.1011797</a>","ieee":"S. M. Hall <i>et al.</i>, “Ten simple rules for pushing boundaries of inclusion at academic events,” <i>PLOS Computational Biology</i>, vol. 20, no. 3. Public Library of Science, 2024.","mla":"Hall, Siobhan Mackenzie, et al. “Ten Simple Rules for Pushing Boundaries of Inclusion at Academic Events.” <i>PLOS Computational Biology</i>, vol. 20, no. 3, e1011797, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011797\">10.1371/journal.pcbi.1011797</a>.","chicago":"Hall, Siobhan Mackenzie, Daniel Kochin, Carmel Carne, Patricia Herterich, Kristen Lenay Lewers, Mohamed Abdelhack, Arun Ramasubramanian, et al. “Ten Simple Rules for Pushing Boundaries of Inclusion at Academic Events.” <i>PLOS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1011797\">https://doi.org/10.1371/journal.pcbi.1011797</a>."},"publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","publisher":"Public Library of Science","DOAJ_listed":"1","abstract":[{"lang":"eng","text":"Inclusion at academic events is facing increased scrutiny as the communities these events serve raise their expectations for who can practically attend. Active efforts in recent years to bring more diversity to academic events have brought progress and created momentum. However, we must reflect on these efforts and determine which underrepresented groups are being disadvantaged. Inclusion at academic events is important to ensure diversity of discourse and opinion, to help build networks, and to avoid academic siloing. All of these contribute to the development of a robust and resilient academic field. We have developed these Ten Simple Rules both to amplify the voices that have been speaking out and to celebrate the progress of many Equity, Diversity, and Inclusivity practices that continue to drive the organisation of academic events. The Rules aim to raise awareness as well as provide actionable suggestions and tools to support these initiatives further. This aims to support academic organisations such as the Deep Learning Indaba, Neuromatch Academy, the IBRO-Simons Computational Neuroscience Imbizo, Biodiversity Information Standards (TDWG), Arabs in Neuroscience, FAIRPoints, and OLS (formerly Open Life Science). This article is a call to action for organisers to reevaluate the impact and reach of their inclusive practices."}],"oa_version":"Published Version","tmp":{"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)","image":"/images/cc_by.png"},"acknowledgement":"We would like to recognise the feedback and ideas shared with us by all attendees during the\r\nfocus groups that contributed to the development of this paper. Acknowledgements are given\r\nto Elisee Jafsia, Umar Farouk Ahmad, Zohra Slim, Mizanur Rahman, Rev. Katie Tupling,\r\nChristopher Emmanuel, Abdalrhman Mostafa, Pradeep Eranti, Toby Hodges, Avishkar\r\nBhoopchand, and Carolyn Dickson. We would like to thank our community members and\r\nacknowledge their bravery for sharing their stories that shaped the narrative of these Ten Simple\r\nRules. The stories shared with us formed the case studies, and while they are anonymous\r\nfor privacy and protection reasons, it is these stories that were on our mind during the entire\r\nprocess and kept us going. We acknowledge the efforts of the organisers that contribute to the\r\nhighly successful events that are the inspiration for the ideas presented here: the Deep\r\nLearning Indaba, Neuromatch Academy, the IBRO Simons Computational Neuroscience\r\nImbizo, and OLS. OLS also supported this project through their mentorship programme,\r\nOpen Seeds.","doi":"10.1371/journal.pcbi.1011797","quality_controlled":"1","volume":20,"year":"2024","status":"public","date_published":"2024-03-01T00:00:00Z","_id":"15258","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","author":[{"first_name":"Siobhan Mackenzie","last_name":"Hall","full_name":"Hall, Siobhan Mackenzie"},{"full_name":"Kochin, Daniel","last_name":"Kochin","first_name":"Daniel"},{"first_name":"Carmel","last_name":"Carne","full_name":"Carne, Carmel"},{"full_name":"Herterich, Patricia","last_name":"Herterich","first_name":"Patricia"},{"last_name":"Lewers","first_name":"Kristen Lenay","full_name":"Lewers, Kristen Lenay"},{"full_name":"Abdelhack, Mohamed","last_name":"Abdelhack","first_name":"Mohamed"},{"last_name":"Ramasubramanian","first_name":"Arun","full_name":"Ramasubramanian, Arun"},{"last_name":"Michael Alphonse","first_name":"Juno Felecia","full_name":"Michael Alphonse, Juno Felecia"},{"full_name":"Ung, Visotheary","first_name":"Visotheary","last_name":"Ung"},{"full_name":"El-Gebali, Sara","last_name":"El-Gebali","first_name":"Sara"},{"orcid":"0000-0002-4809-5059","full_name":"Currin, Christopher","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","first_name":"Christopher","last_name":"Currin"},{"full_name":"Plomp, Esther","first_name":"Esther","last_name":"Plomp"},{"last_name":"Thompson","first_name":"Rachel","full_name":"Thompson, Rachel"},{"last_name":"Sharan","first_name":"Malvika","full_name":"Sharan, Malvika"}],"day":"01","file":[{"file_name":"2024_PloS_Hall.pdf","date_updated":"2024-04-03T13:29:36Z","file_size":858521,"relation":"main_file","access_level":"open_access","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"1f0f837c5b4341f54f6347370ed8c1b7","file_id":"15289","date_created":"2024-04-03T13:29:36Z"}],"article_type":"original","OA_type":"gold","external_id":{"isi":["001181690200005"],"pmid":["38427633"]},"OA_place":"publisher","publication":"PLOS Computational Biology","date_created":"2024-04-02T11:37:32Z","has_accepted_license":"1","title":"Ten simple rules for pushing boundaries of inclusion at academic events","issue":"3","month":"03","file_date_updated":"2024-04-03T13:29:36Z","fulldoi":"https://doi.org/10.1371/journal.pcbi.1011797","date_updated":"2025-09-04T13:24:19Z"},{"author":[{"full_name":"Beyer, Chad","last_name":"Beyer","first_name":"Chad"},{"orcid":"0000-0002-4809-5059","full_name":"Currin, Christopher","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","last_name":"Currin","first_name":"Christopher"},{"last_name":"Williams","first_name":"Taryn","full_name":"Williams, Taryn"},{"full_name":"Stein, Dan J.","last_name":"Stein","first_name":"Dan J."}],"day":"01","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001221136000001"],"pmid":["38564872"]},"OA_type":"gold","article_type":"original","file":[{"date_created":"2025-01-13T10:47:20Z","file_id":"18839","content_type":"application/pdf","checksum":"aadb57448b5f170761ed72cbcc31ba16","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2025-01-13T10:47:20Z","file_size":2874425,"file_name":"2024_ComprehensivePsychiatry_Beyer.pdf"}],"has_accepted_license":"1","title":"Meta-analysis of the comparative efficacy of benzodiazepines and antidepressants for psychic versus somatic symptoms of generalized anxiety disorder","date_created":"2024-04-07T22:00:55Z","publication":"Comprehensive Psychiatry","date_updated":"2025-09-04T13:30:08Z","fulldoi":"https://doi.org/10.1016/j.comppsych.2024.152479","file_date_updated":"2025-01-13T10:47:20Z","month":"07","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["570"],"isi":1,"article_processing_charge":"Yes","scopus_import":"1","department":[{"_id":"TiVo"}],"article_number":"152479","oa":1,"language":[{"iso":"eng"}],"pmid":1,"oa_version":"Published Version","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"abstract":[{"lang":"eng","text":"Background: Benzodiazepines and antidepressants are effective agents for the treatment of generalized anxiety disorder (GAD), with the HAM-A frequently used as a primary outcome measure. The GAD literature is inconsistent regarding which medications are more effective for somatic versus psychic symptoms of GAD, and treatment guidelines do not advocate for prescribing based on subtype. This meta-analysis aimed to determine whether benzodiazepines and antidepressants have a differential impact on the somatic versus psychic subscales of the HAM-A in GAD.\r\n\r\nMethods: An electronic search was undertaken for randomized controlled trials of either benzodiazepines or antidepressants for GAD that reported treatment response using the HAM-A subscales. Data were extracted by independent reviewers. A random effects assessment of weighted mean difference with 95% confidence intervals and subgroup difference was applied. All analysis was done on SPSS 26. An assessment of bias, and of quality of evidence was performed.\r\n\r\nResults: 24 randomized controlled trials met the inclusion criteria: 18 antidepressant trials, 5 benzodiazepine trials and 1 of both. 14 studies were assessed as having between some and high risk of bias, while 10 were assessed as having low risk of bias. Benzodiazepines (WMD of 1.81 [CI 1.03, 2.58]) were significantly more effective than antidepressants (WMD of 0.83 [CI 0.64, 1.02]) for reducing somatic symptoms of GAD (Chi2 = 5.81, p = 0.02), and were also more effective (WMD of 2.46 [CI 1.83, 3.09]) in reducing psychic symptoms than antidepressants (WMD of 1.83 [CI 1.55, 2.10]), although this comparison did not reach statistical significance (Chi2 = 3.31, p = 0.07).\r\n\r\nConclusion: The finding that benzodiazepines were significantly more effective than antidepressants for somatic symptoms needs to be weighed up against potential benefits of antidepressants over benzodiazepines. It may be useful for future treatment guidelines for GAD to explicitly consider symptom subtype."}],"publication_identifier":{"eissn":["1532-8384"],"issn":["0010-440X"]},"DOAJ_listed":"1","publication_status":"published","publisher":"Elsevier","intvolume":"       132","citation":{"short":"C. Beyer, C. Currin, T. Williams, D.J. Stein, Comprehensive Psychiatry 132 (2024).","ista":"Beyer C, Currin C, Williams T, Stein DJ. 2024. Meta-analysis of the comparative efficacy of benzodiazepines and antidepressants for psychic versus somatic symptoms of generalized anxiety disorder. Comprehensive Psychiatry. 132, 152479.","chicago":"Beyer, Chad, Christopher Currin, Taryn Williams, and Dan J. Stein. “Meta-Analysis of the Comparative Efficacy of Benzodiazepines and Antidepressants for Psychic versus Somatic Symptoms of Generalized Anxiety Disorder.” <i>Comprehensive Psychiatry</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.comppsych.2024.152479\">https://doi.org/10.1016/j.comppsych.2024.152479</a>.","mla":"Beyer, Chad, et al. “Meta-Analysis of the Comparative Efficacy of Benzodiazepines and Antidepressants for Psychic versus Somatic Symptoms of Generalized Anxiety Disorder.” <i>Comprehensive Psychiatry</i>, vol. 132, 152479, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.comppsych.2024.152479\">10.1016/j.comppsych.2024.152479</a>.","ieee":"C. Beyer, C. Currin, T. Williams, and D. J. Stein, “Meta-analysis of the comparative efficacy of benzodiazepines and antidepressants for psychic versus somatic symptoms of generalized anxiety disorder,” <i>Comprehensive Psychiatry</i>, vol. 132. Elsevier, 2024.","apa":"Beyer, C., Currin, C., Williams, T., &#38; Stein, D. J. (2024). Meta-analysis of the comparative efficacy of benzodiazepines and antidepressants for psychic versus somatic symptoms of generalized anxiety disorder. <i>Comprehensive Psychiatry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comppsych.2024.152479\">https://doi.org/10.1016/j.comppsych.2024.152479</a>","ama":"Beyer C, Currin C, Williams T, Stein DJ. Meta-analysis of the comparative efficacy of benzodiazepines and antidepressants for psychic versus somatic symptoms of generalized anxiety disorder. <i>Comprehensive Psychiatry</i>. 2024;132. doi:<a href=\"https://doi.org/10.1016/j.comppsych.2024.152479\">10.1016/j.comppsych.2024.152479</a>"},"date_published":"2024-07-01T00:00:00Z","_id":"15295","year":"2024","status":"public","volume":132,"quality_controlled":"1","doi":"10.1016/j.comppsych.2024.152479"},{"author":[{"first_name":"Mariana","last_name":"Lopushanski","full_name":"Lopushanski, Mariana"},{"id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory","last_name":"Ivanov","first_name":"Grigory"}],"day":"14","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A constructive algorithm for building rectifiable curves in weakly convex sets","publication":"AIP Conference Proceedings","date_created":"2024-04-07T22:00:55Z","fulldoi":"https://doi.org/10.1063/5.0195908","date_updated":"2024-04-08T07:40:53Z","issue":"1","month":"03","article_processing_charge":"No","department":[{"_id":"UlWa"}],"scopus_import":"1","article_number":"080002","language":[{"iso":"eng"}],"oa_version":"None","abstract":[{"lang":"eng","text":"In this paper we build a constructive algorithm that returns a rectifiable curve that connects two points in a weakly convex set in a Hilbert space. We have proven that this algorithm converges and obtained an estimate on the curve’s length and compare the length of the curve obtained to known results."}],"publication_identifier":{"eissn":["1551-7616"],"issn":["0094-243X"]},"publication_status":"published","publisher":"AIP Publishing","intvolume":"      3030","conference":{"start_date":"2022-10-26","name":"ICCMSE: International Conference of Computational Methods in Sciences and Engiineering","location":"Virtual","end_date":"2022-10-29"},"citation":{"short":"M. Lopushanski, G. Ivanov, in:, AIP Conference Proceedings, AIP Publishing, 2024.","ista":"Lopushanski M, Ivanov G. 2024. A constructive algorithm for building rectifiable curves in weakly convex sets. AIP Conference Proceedings. ICCMSE: International Conference of Computational Methods in Sciences and Engiineering vol. 3030, 080002.","ama":"Lopushanski M, Ivanov G. A constructive algorithm for building rectifiable curves in weakly convex sets. In: <i>AIP Conference Proceedings</i>. Vol 3030. AIP Publishing; 2024. doi:<a href=\"https://doi.org/10.1063/5.0195908\">10.1063/5.0195908</a>","apa":"Lopushanski, M., &#38; Ivanov, G. (2024). A constructive algorithm for building rectifiable curves in weakly convex sets. In <i>AIP Conference Proceedings</i> (Vol. 3030). Virtual: AIP Publishing. <a href=\"https://doi.org/10.1063/5.0195908\">https://doi.org/10.1063/5.0195908</a>","ieee":"M. Lopushanski and G. Ivanov, “A constructive algorithm for building rectifiable curves in weakly convex sets,” in <i>AIP Conference Proceedings</i>, Virtual, 2024, vol. 3030, no. 1.","mla":"Lopushanski, Mariana, and Grigory Ivanov. “A Constructive Algorithm for Building Rectifiable Curves in Weakly Convex Sets.” <i>AIP Conference Proceedings</i>, vol. 3030, no. 1, 080002, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0195908\">10.1063/5.0195908</a>.","chicago":"Lopushanski, Mariana, and Grigory Ivanov. “A Constructive Algorithm for Building Rectifiable Curves in Weakly Convex Sets.” In <i>AIP Conference Proceedings</i>, Vol. 3030. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0195908\">https://doi.org/10.1063/5.0195908</a>."},"date_published":"2024-03-14T00:00:00Z","_id":"15296","year":"2024","status":"public","volume":3030,"quality_controlled":"1","doi":"10.1063/5.0195908"},{"publication":"Developmental Cell","date_created":"2024-04-08T12:07:57Z","title":"Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization","has_accepted_license":"1","month":"05","issue":"10","file_date_updated":"2024-08-20T11:22:16Z","date_updated":"2025-09-04T13:32:08Z","fulldoi":"https://doi.org/10.1016/j.devcel.2024.03.009","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/how-plants-heal-wounds/","description":"News on ISTA website"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","page":"1333-1344.e4","author":[{"full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Lukas","last_name":"Hörmayer"},{"last_name":"Montesinos López","first_name":"Juan C","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"N","last_name":"Trozzi","full_name":"Trozzi, N"},{"full_name":"Spona, Leonhard","id":"b52391fb-f636-11ee-939c-8a8c47552e8a","last_name":"Spona","first_name":"Leonhard"},{"last_name":"Yoshida","first_name":"Saiko","full_name":"Yoshida, Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marhavá, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","last_name":"Marhavá"},{"orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","last_name":"Caballero Mancebo","first_name":"Silvia"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"first_name":"Y","last_name":"Dagdas","full_name":"Dagdas, Y"},{"last_name":"Majda","first_name":"M","full_name":"Majda, M"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"day":"20","article_type":"original","file":[{"creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","file_name":"2024_DevelopmentalCell_Hoermayer.pdf","file_size":5195262,"date_updated":"2024-08-20T11:22:16Z","date_created":"2024-08-20T11:22:16Z","content_type":"application/pdf","checksum":"22b374fb50a40d380b7686c84258d271","file_id":"17452"}],"external_id":{"isi":["001301584600001"],"pmid":["38579717"]},"citation":{"ieee":"L. Hörmayer <i>et al.</i>, “Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization,” <i>Developmental Cell</i>, vol. 59, no. 10. Elsevier, p. 1333–1344.e4, 2024.","mla":"Hörmayer, Lukas, et al. “Mechanical Forces in Plant Tissue Matrix Orient Cell Divisions via Microtubule Stabilization.” <i>Developmental Cell</i>, vol. 59, no. 10, Elsevier, 2024, p. 1333–1344.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">10.1016/j.devcel.2024.03.009</a>.","chicago":"Hörmayer, Lukas, Juan C Montesinos López, N Trozzi, Leonhard Spona, Saiko Yoshida, Petra Marhavá, Silvia Caballero Mancebo, et al. “Mechanical Forces in Plant Tissue Matrix Orient Cell Divisions via Microtubule Stabilization.” <i>Developmental Cell</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">https://doi.org/10.1016/j.devcel.2024.03.009</a>.","apa":"Hörmayer, L., Montesinos López, J. C., Trozzi, N., Spona, L., Yoshida, S., Marhavá, P., … Friml, J. (2024). Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">https://doi.org/10.1016/j.devcel.2024.03.009</a>","ama":"Hörmayer L, Montesinos López JC, Trozzi N, et al. Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. <i>Developmental Cell</i>. 2024;59(10):1333-1344.e4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.03.009\">10.1016/j.devcel.2024.03.009</a>","short":"L. Hörmayer, J.C. Montesinos López, N. Trozzi, L. Spona, S. Yoshida, P. Marhavá, S. Caballero Mancebo, E. Benková, C.-P.J. Heisenberg, Y. Dagdas, M. Majda, J. Friml, Developmental Cell 59 (2024) 1333–1344.e4.","ista":"Hörmayer L, Montesinos López JC, Trozzi N, Spona L, Yoshida S, Marhavá P, Caballero Mancebo S, Benková E, Heisenberg C-PJ, Dagdas Y, Majda M, Friml J. 2024. Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization. Developmental Cell. 59(10), 1333–1344.e4."},"intvolume":"        59","publisher":"Elsevier","ec_funded":1,"publication_status":"published","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"corr_author":"1","abstract":[{"lang":"eng","text":"Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture."}],"tmp":{"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)","image":"/images/cc_by.png"},"oa_version":"Published Version","doi":"10.1016/j.devcel.2024.03.009","acknowledgement":"We are thankful to Simon Gilroy, Alexander Jones, and Lieven De Veylder for sharing published material. We thank the Imaging & Optics and Life Science Facilities at IST Austria, the Biooptics facility at GMI, and the Cellular Imaging Facility at DBMV UNIL for providing invaluable assistance. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 742985, from the FWF under the stand-alone grant P29988, and from EMBO (ALTF 253-2023).","volume":59,"quality_controlled":"1","status":"public","year":"2024","_id":"15301","date_published":"2024-05-20T00:00:00Z","isi":1,"ddc":["570"],"pmid":1,"language":[{"iso":"eng"}],"oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"scopus_import":"1","department":[{"_id":"JiFr"},{"_id":"EvBe"},{"_id":"CaHe"}],"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"},{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988"}],"article_processing_charge":"Yes (via OA deal)"},{"publication_identifier":{"issn":["1007-5704"]},"ec_funded":1,"publication_status":"published","publisher":"Elsevier","intvolume":"       134","citation":{"chicago":"Agasthya, Lokahith N, and Caroline J Muller. “Dynamics and Scaling of Internally Cooled Convection.” <i>Communications in Nonlinear Science and Numerical Simulation</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cnsns.2024.108011\">https://doi.org/10.1016/j.cnsns.2024.108011</a>.","mla":"Agasthya, Lokahith N., and Caroline J. Muller. “Dynamics and Scaling of Internally Cooled Convection.” <i>Communications in Nonlinear Science and Numerical Simulation</i>, vol. 134, 108011, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.cnsns.2024.108011\">10.1016/j.cnsns.2024.108011</a>.","ieee":"L. N. Agasthya and C. J. Muller, “Dynamics and scaling of internally cooled convection,” <i>Communications in Nonlinear Science and Numerical Simulation</i>, vol. 134. Elsevier, 2024.","apa":"Agasthya, L. N., &#38; Muller, C. J. (2024). Dynamics and scaling of internally cooled convection. <i>Communications in Nonlinear Science and Numerical Simulation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cnsns.2024.108011\">https://doi.org/10.1016/j.cnsns.2024.108011</a>","ama":"Agasthya LN, Muller CJ. Dynamics and scaling of internally cooled convection. <i>Communications in Nonlinear Science and Numerical Simulation</i>. 2024;134. doi:<a href=\"https://doi.org/10.1016/j.cnsns.2024.108011\">10.1016/j.cnsns.2024.108011</a>","ista":"Agasthya LN, Muller CJ. 2024. Dynamics and scaling of internally cooled convection. Communications in Nonlinear Science and Numerical Simulation. 134, 108011.","short":"L.N. Agasthya, C.J. Muller, Communications in Nonlinear Science and Numerical Simulation 134 (2024)."},"oa_version":"Published Version","tmp":{"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)","image":"/images/cc_by.png"},"abstract":[{"text":"Our goal is to investigate fundamental properties of the system of internally cooled convection. The system consists of an upward thermal flux at the lower boundary, a mean temperature lapse-rate and a constant cooling term in the bulk with the bulk cooling in thermal equilibrium with the input heat flux. This simple model represents idealised dry convection in the atmospheric boundary layer, where the cooling mimics the radiative cooling to space notably through longwave radiation. We perform linear stability analysis of the model for different values of the mean stratification to derive the critical forcing above which the fluid is convectively unstable to small perturbations. The dynamic behavior of the fluid system is described and the scaling of various important measured quantities such as the total vertical convective heat flux and the upward mass flux is measured. We introduce a lapse-rate dependent dimensionless Rayleigh-number Ray that determines the behavior of the system, finding that the convective heat-flux and mass-flux scale approximately as Ray0.5 and Ray0.7 respectively. The area-fraction of the domain that is occupied by upward and downward moving fluid and the skewness of the vertical velocity are studied to understand the asymmetry inherent in the system. We conclude with a short discussion on the relevance to atmospheric convection and the scope for further investigations of atmospheric convection using similar simplified approaches.","lang":"eng"}],"corr_author":"1","volume":134,"quality_controlled":"1","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska–Curie grant agreement No. 101034413. CM gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","doi":"10.1016/j.cnsns.2024.108011","date_published":"2024-07-01T00:00:00Z","_id":"15313","year":"2024","status":"public","isi":1,"ddc":["550"],"language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041"}],"department":[{"_id":"CaMu"}],"scopus_import":"1","article_number":"108011","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2024-04-14T22:01:01Z","publication":"Communications in Nonlinear Science and Numerical Simulation","OA_place":"publisher","has_accepted_license":"1","title":"Dynamics and scaling of internally cooled convection","month":"07","fulldoi":"https://doi.org/10.1016/j.cnsns.2024.108011","date_updated":"2025-09-04T13:37:48Z","file_date_updated":"2025-01-09T09:05:31Z","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Agasthya","first_name":"Lokahith N","full_name":"Agasthya, Lokahith N","id":"cd100965-0804-11ed-9c55-f4878ff4e877"},{"first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"}],"day":"01","arxiv":1,"article_type":"original","file":[{"date_created":"2025-01-09T09:05:31Z","file_id":"18795","content_type":"application/pdf","checksum":"9b7c2b8281d0b7bc7f08e0468168324c","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access","date_updated":"2025-01-09T09:05:31Z","file_size":1257925,"file_name":"2024_CommNonlinear_Agasthya.pdf"}],"external_id":{"isi":["001238294600001"],"arxiv":["2311.04114"]},"OA_type":"hybrid"},{"isi":1,"article_processing_charge":"No","article_number":"111464","scopus_import":"1","department":[{"_id":"MaIb"}],"language":[{"iso":"eng"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Development of electroactive materials exhibiting high performance with superior stability is crucial in the field of supercapacitors and battery research. We report on synthesis of highly stable composite of semi-polycrystalline polyaniline and graphene (SPani-graphene) and its application in supercapacitor electrodes. The electrochemical behavior and device performance of the electrodes were investigated through cyclic voltammetry (CV), galvanostatic charge-discharge GCD) and electrochemical impedance spectroscopy (EIS) in a 3-electrode and a 2-electrode (device) cell configurations, repectively. The cell specific capacitance (Cell Csp) achieved from the 2-electrode symmetric cell configuration was 525.5 F g−1 at 0.1 A g−1 using polymer gel electrolyte (PGE). The PGE in this work is xanthan gum jellied in 1 M aq. Na2SO4. The maximum energy density and power density achieved from the device was 46.7 Wh kg−1 and 16.16 kW kg−1, respectively, at 0.4 A g−1. Furthermore, the device exhibits an excellent retention of cell specific capacitance and coulombic efficiency of 97 % and 94 %, respectively, over 10,000 continuous GCD cycles, indicating an excellent rate capability as well as a promising power management. To investigate the material's electrochemical durability, a detailed EIS study has been carried out using both, 3-electrode, and 2-electrode cell configurations, before and after long cycling test (over 10,000 continuous GCD cycles). Our thorough experimentation delivers satisfactory results and has been explained in detail in the manuscript. Hereby, we propose that the EIS technique can be adopted for investigating materials' electrochemical stability, in addition to long CV and GCD cycles in the field of supercapacitors and battery research."}],"publisher":"Elsevier","publication_status":"published","publication_identifier":{"eissn":["2352-152X"]},"citation":{"ista":"Mahato N, Singh S, Sreekanth TVM, Yoo K, Kim J. 2024. Polycrystalline phases engineered in-situ in polyaniline-graphene composite evoluting an exceptional stability and high charge storage capacity: An EIS investigative approach to evaluate material’s stability. Journal of Energy Storage. 88, 111464.","short":"N. Mahato, S. Singh, T.V.M. Sreekanth, K. Yoo, J. Kim, Journal of Energy Storage 88 (2024).","ama":"Mahato N, Singh S, Sreekanth TVM, Yoo K, Kim J. Polycrystalline phases engineered in-situ in polyaniline-graphene composite evoluting an exceptional stability and high charge storage capacity: An EIS investigative approach to evaluate material’s stability. <i>Journal of Energy Storage</i>. 2024;88. doi:<a href=\"https://doi.org/10.1016/j.est.2024.111464\">10.1016/j.est.2024.111464</a>","apa":"Mahato, N., Singh, S., Sreekanth, T. V. M., Yoo, K., &#38; Kim, J. (2024). Polycrystalline phases engineered in-situ in polyaniline-graphene composite evoluting an exceptional stability and high charge storage capacity: An EIS investigative approach to evaluate material’s stability. <i>Journal of Energy Storage</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.est.2024.111464\">https://doi.org/10.1016/j.est.2024.111464</a>","ieee":"N. Mahato, S. Singh, T. V. M. Sreekanth, K. Yoo, and J. Kim, “Polycrystalline phases engineered in-situ in polyaniline-graphene composite evoluting an exceptional stability and high charge storage capacity: An EIS investigative approach to evaluate material’s stability,” <i>Journal of Energy Storage</i>, vol. 88. Elsevier, 2024.","chicago":"Mahato, Neelima, Saurabh Singh, T. V.M. Sreekanth, Kisoo Yoo, and Jonghoon Kim. “Polycrystalline Phases Engineered In-Situ in Polyaniline-Graphene Composite Evoluting an Exceptional Stability and High Charge Storage Capacity: An EIS Investigative Approach to Evaluate Material’s Stability.” <i>Journal of Energy Storage</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.est.2024.111464\">https://doi.org/10.1016/j.est.2024.111464</a>.","mla":"Mahato, Neelima, et al. “Polycrystalline Phases Engineered In-Situ in Polyaniline-Graphene Composite Evoluting an Exceptional Stability and High Charge Storage Capacity: An EIS Investigative Approach to Evaluate Material’s Stability.” <i>Journal of Energy Storage</i>, vol. 88, 111464, Elsevier, 2024, doi:<a href=\"https://doi.org/10.1016/j.est.2024.111464\">10.1016/j.est.2024.111464</a>."},"intvolume":"        88","_id":"15314","date_published":"2024-05-30T00:00:00Z","status":"public","year":"2024","volume":88,"quality_controlled":"1","doi":"10.1016/j.est.2024.111464","acknowledgement":"This work was supported by Korea Institute of Energy Technology Evaluation and Planning (KETEP); and Ministry of Trade, Industry & Energy (MOTIE), Republic of Korea (Grant No. \r\n20210501010020).","author":[{"full_name":"Mahato, Neelima","last_name":"Mahato","first_name":"Neelima"},{"id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269","full_name":"Singh, Saurabh","first_name":"Saurabh","last_name":"Singh"},{"last_name":"Sreekanth","first_name":"T. V.M.","full_name":"Sreekanth, T. V.M."},{"first_name":"Kisoo","last_name":"Yoo","full_name":"Yoo, Kisoo"},{"full_name":"Kim, Jonghoon","last_name":"Kim","first_name":"Jonghoon"}],"day":"30","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001287584100001"]},"article_type":"original","title":"Polycrystalline phases engineered in-situ in polyaniline-graphene composite evoluting an exceptional stability and high charge storage capacity: An EIS investigative approach to evaluate material's stability","publication":"Journal of Energy Storage","date_created":"2024-04-14T22:01:01Z","date_updated":"2025-09-04T13:38:27Z","fulldoi":"https://doi.org/10.1016/j.est.2024.111464","month":"05"},{"ddc":["530"],"isi":1,"project":[{"grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"article_processing_charge":"Yes (in subscription journal)","oa":1,"article_number":"056601","department":[{"_id":"EdHa"}],"scopus_import":"1","language":[{"iso":"eng"}],"pmid":1,"tmp":{"image":"/images/cc_by.png","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"},"oa_version":"Published Version","corr_author":"1","abstract":[{"text":"Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualising the emergent behaviour of cells. We first review how this inference problem has been addressed in both freely migrating and confined cells. Next, we discuss why these dynamics typically take the form of underdamped stochastic equations of motion, and how such equations can be inferred from data. We then review applications of data-driven inference and machine learning approaches to heterogeneity in cell behaviour, subcellular degrees of freedom, and to the collective dynamics of multicellular systems. Across these applications, we emphasise how data-driven methods can be integrated with physical active matter models of migrating cells, and help reveal how underlying molecular mechanisms control cell behaviour. Together, these data-driven approaches are a promising avenue for building physical models of cell migration directly from experimental data, and for providing conceptual links between different length-scales of description.","lang":"eng"}],"publication_status":"published","publisher":"IOP Publishing","publication_identifier":{"issn":["0034-4885"],"eissn":["1361-6633"]},"citation":{"ama":"Brückner D, Broedersz CP. Learning dynamical models of single and collective cell migration: a review. <i>Reports on Progress in Physics</i>. 2024;87(5). doi:<a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">10.1088/1361-6633/ad36d2</a>","apa":"Brückner, D., &#38; Broedersz, C. P. (2024). Learning dynamical models of single and collective cell migration: a review. <i>Reports on Progress in Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">https://doi.org/10.1088/1361-6633/ad36d2</a>","chicago":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” <i>Reports on Progress in Physics</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">https://doi.org/10.1088/1361-6633/ad36d2</a>.","mla":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” <i>Reports on Progress in Physics</i>, vol. 87, no. 5, 056601, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">10.1088/1361-6633/ad36d2</a>.","ieee":"D. Brückner and C. P. Broedersz, “Learning dynamical models of single and collective cell migration: a review,” <i>Reports on Progress in Physics</i>, vol. 87, no. 5. IOP Publishing, 2024.","short":"D. Brückner, C.P. Broedersz, Reports on Progress in Physics 87 (2024).","ista":"Brückner D, Broedersz CP. 2024. Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. 87(5), 056601."},"intvolume":"        87","_id":"15315","date_published":"2024-04-04T00:00:00Z","status":"public","year":"2024","volume":87,"quality_controlled":"1","doi":"10.1088/1361-6633/ad36d2","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (German Research Foundation)—Project-ID 201269156—SFB 1032 (Project B12). D B B was supported by an NOMIS Fellowship and an EMBO Fellowship (ALTF 343-2022). We thank Joachim Rädler, Alexandra Fink, Erwin Frey, Pierre Ronceray, Ricard Alert, Edouard Hannezo, Henrik Flyvbjerg, Ulrich Schwarz, Joshua Shaevitz, Greg Stephens, Andrea Cavagna, Grzegorz Gradziuk, Fridtjof Brauns, Nikolas Claussen, Tom Brandstätter, Johannes Flommersfeld, Christoph Schreiber, Nicolas Arlt, Matthew Schmitt, Joris Messelink, Federico Gnesotto, Federica Mura, Bram Hoogland, Manon Wigbers, Isabella Graf, Jessica Lober, and many others for inspiring discussions. We also thank Claudia Flandoli for the artwork in figures 1, 5, 8 and 9.","day":"04","author":[{"last_name":"Brückner","first_name":"David","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"full_name":"Broedersz, Chase P.","first_name":"Chase P.","last_name":"Broedersz"}],"arxiv":1,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"pmid":["38518358"],"isi":["001196692400001"],"arxiv":["2309.00545"]},"file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"file_name":"2024_ReportPhysics_Brueckner.pdf","date_updated":"2024-08-20T11:00:03Z","file_size":4376898,"date_created":"2024-08-20T11:00:03Z","file_id":"17451","checksum":"c5910078230ade20f4dd83592e862a72","content_type":"application/pdf"}],"article_type":"review","title":"Learning dynamical models of single and collective cell migration: a review","has_accepted_license":"1","date_created":"2024-04-14T22:01:01Z","publication":"Reports on Progress in Physics","date_updated":"2025-09-04T13:39:07Z","fulldoi":"https://doi.org/10.1088/1361-6633/ad36d2","file_date_updated":"2024-08-20T11:00:03Z","month":"04","license":"https://creativecommons.org/licenses/by/3.0/","issue":"5"},{"isi":1,"language":[{"iso":"eng"}],"pmid":1,"article_processing_charge":"No","oa":1,"department":[{"_id":"MaHe"}],"scopus_import":"1","publication_status":"published","publisher":"AAAS","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"citation":{"ama":"Zocher S, Mccloskey A, Karasinsky A, et al. Lifelong persistence of nuclear RNAs in the mouse brain. <i>Science</i>. 2024;384(6691):53-59. doi:<a href=\"https://doi.org/10.1126/science.adf3481\">10.1126/science.adf3481</a>","apa":"Zocher, S., Mccloskey, A., Karasinsky, A., Schulte, R., Friedrich, U., Lesche, M., … Toda, T. (2024). Lifelong persistence of nuclear RNAs in the mouse brain. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.adf3481\">https://doi.org/10.1126/science.adf3481</a>","mla":"Zocher, Sara, et al. “Lifelong Persistence of Nuclear RNAs in the Mouse Brain.” <i>Science</i>, vol. 384, no. 6691, AAAS, 2024, pp. 53–59, doi:<a href=\"https://doi.org/10.1126/science.adf3481\">10.1126/science.adf3481</a>.","ieee":"S. Zocher <i>et al.</i>, “Lifelong persistence of nuclear RNAs in the mouse brain,” <i>Science</i>, vol. 384, no. 6691. AAAS, pp. 53–59, 2024.","chicago":"Zocher, Sara, Asako Mccloskey, Anne Karasinsky, Roberta Schulte, Ulrike Friedrich, Mathias Lesche, Nicole Rund, Fred H. Gage, Martin Hetzer, and Tomohisa Toda. “Lifelong Persistence of Nuclear RNAs in the Mouse Brain.” <i>Science</i>. AAAS, 2024. <a href=\"https://doi.org/10.1126/science.adf3481\">https://doi.org/10.1126/science.adf3481</a>.","short":"S. Zocher, A. Mccloskey, A. Karasinsky, R. Schulte, U. Friedrich, M. Lesche, N. Rund, F.H. Gage, M. Hetzer, T. Toda, Science 384 (2024) 53–59.","ista":"Zocher S, Mccloskey A, Karasinsky A, Schulte R, Friedrich U, Lesche M, Rund N, Gage FH, Hetzer M, Toda T. 2024. Lifelong persistence of nuclear RNAs in the mouse brain. Science. 384(6691), 53–59."},"intvolume":"       384","oa_version":"Submitted Version","abstract":[{"text":"Genomic DNA that resides in the nuclei of mammalian neurons can be as old as the organism itself. The life span of nuclear RNAs, which are critical for proper chromatin architecture and transcription regulation, has not been determined in adult tissues. In this work, we identified and characterized nuclear RNAs that do not turn over for at least 2 years in a subset of postnatally born cells in the mouse brain. These long-lived RNAs were stably retained in nuclei in a neural cell type–specific manner and were required for the maintenance of heterochromatin. Thus, the life span of neural cells may depend on both the molecular longevity of DNA for the storage of genetic information and also the extreme stability of RNA for the functional organization of chromatin.","lang":"eng"}],"corr_author":"1","volume":384,"quality_controlled":"1","doi":"10.1126/science.adf3481","acknowledgement":"European Research Council: ERC-2018-STG, 804468 EAGER; European Research Council: ERC-2023-COG, 101125034 NEUTIME; Deutsche Forschungsgemeinschaft: TO1347/4-1; Boehringer Ingelheim Stiftung; Deutsches Zentrum für Neurodegenerative Erkrankungen","_id":"15316","date_published":"2024-04-04T00:00:00Z","status":"public","year":"2024","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/nerve-cells-old-at-heart/","relation":"press_release"}]},"page":"53-59","day":"04","author":[{"full_name":"Zocher, Sara","first_name":"Sara","last_name":"Zocher"},{"full_name":"Mccloskey, Asako","first_name":"Asako","last_name":"Mccloskey"},{"full_name":"Karasinsky, Anne","last_name":"Karasinsky","first_name":"Anne"},{"first_name":"Roberta","last_name":"Schulte","full_name":"Schulte, Roberta"},{"last_name":"Friedrich","first_name":"Ulrike","full_name":"Friedrich, Ulrike"},{"first_name":"Mathias","last_name":"Lesche","full_name":"Lesche, Mathias"},{"full_name":"Rund, Nicole","last_name":"Rund","first_name":"Nicole"},{"first_name":"Fred H.","last_name":"Gage","full_name":"Gage, Fred H."},{"orcid":"0000-0002-2111-992X","full_name":"Hetzer, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"Hetzer"},{"first_name":"Tomohisa","last_name":"Toda","full_name":"Toda, Tomohisa"}],"article_type":"original","external_id":{"isi":["001253335100031"],"pmid":["38574132"]},"OA_type":"green","publication":"Science","date_created":"2024-04-14T22:01:01Z","OA_place":"repository","title":"Lifelong persistence of nuclear RNAs in the mouse brain","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7615865","open_access":"1"}],"month":"04","issue":"6691","date_updated":"2025-09-04T13:39:58Z","fulldoi":"https://doi.org/10.1126/science.adf3481"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","arxiv":1,"page":"1789-1845","author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo","last_name":"Dello Schiavo","first_name":"Lorenzo"},{"last_name":"Portinale","first_name":"Lorenzo","full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Federico","last_name":"Sau","full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425"}],"day":"01","article_type":"original","external_id":{"arxiv":["2112.14196"],"isi":["001198623200016"]},"publication":"Annals of Applied Probability","date_created":"2024-04-14T22:01:02Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2112.14196","open_access":"1"}],"title":"Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains","month":"04","issue":"2","date_updated":"2025-09-04T13:36:00Z","fulldoi":"https://doi.org/10.1214/23-AAP2007","isi":1,"language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","department":[{"_id":"JaMa"}],"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"M03211","name":"Reaching consensus in heterogeneous random opinion dynamics","_id":"3490b268-11ca-11ed-8bc3-e0ad03f48839"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Configuration Spaces over Non-Smooth Spaces","grant_number":"E208","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"},{"call_identifier":"FWF","name":"Dissipation and dispersion in nonlinear partial differential equations","grant_number":"W1245","_id":"260788DE-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","citation":{"mla":"Dello Schiavo, Lorenzo, et al. “Scaling Limits of Random Walks, Harmonic Profiles, and Stationary Nonequilibrium States in Lipschitz Domains.” <i>Annals of Applied Probability</i>, vol. 34, no. 2, Institute of Mathematical Statistics, 2024, pp. 1789–845, doi:<a href=\"https://doi.org/10.1214/23-AAP2007\">10.1214/23-AAP2007</a>.","ieee":"L. Dello Schiavo, L. Portinale, and F. Sau, “Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains,” <i>Annals of Applied Probability</i>, vol. 34, no. 2. Institute of Mathematical Statistics, pp. 1789–1845, 2024.","chicago":"Dello Schiavo, Lorenzo, Lorenzo Portinale, and Federico Sau. “Scaling Limits of Random Walks, Harmonic Profiles, and Stationary Nonequilibrium States in Lipschitz Domains.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2024. <a href=\"https://doi.org/10.1214/23-AAP2007\">https://doi.org/10.1214/23-AAP2007</a>.","ama":"Dello Schiavo L, Portinale L, Sau F. Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains. <i>Annals of Applied Probability</i>. 2024;34(2):1789-1845. doi:<a href=\"https://doi.org/10.1214/23-AAP2007\">10.1214/23-AAP2007</a>","apa":"Dello Schiavo, L., Portinale, L., &#38; Sau, F. (2024). Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-AAP2007\">https://doi.org/10.1214/23-AAP2007</a>","ista":"Dello Schiavo L, Portinale L, Sau F. 2024. Scaling limits of random walks, harmonic profiles, and stationary nonequilibrium states in Lipschitz domains. Annals of Applied Probability. 34(2), 1789–1845.","short":"L. Dello Schiavo, L. Portinale, F. Sau, Annals of Applied Probability 34 (2024) 1789–1845."},"intvolume":"        34","publication_status":"published","publisher":"Institute of Mathematical Statistics","ec_funded":1,"publication_identifier":{"issn":["1050-5164"]},"corr_author":"1","abstract":[{"lang":"eng","text":"We consider the open symmetric exclusion (SEP) and inclusion (SIP) processes on a bounded Lipschitz domain Ω, with both fast and slow boundary. For the random walks on Ω dual to SEP/SIP we establish: a functional-CLT-type convergence to the Brownian motion on Ω with either Neumann (slow boundary), Dirichlet (fast boundary), or Robin (at criticality) boundary conditions; the discrete-to-continuum convergence of the corresponding harmonic profiles. As a consequence, we rigorously derive the hydrodynamic and hydrostatic limits for SEP/SIP on Ω, and analyze their stationary nonequilibrium fluctuations. All scaling limit results for SEP/SIP concern finite-dimensional distribution convergence only, as our duality techniques do not require to establish tightness for the fields associated to the particle systems."}],"oa_version":"Preprint","doi":"10.1214/23-AAP2007","acknowledgement":"The first author gratefully acknowledges funding by the Austrian Science Fund (FWF) grant F65, by the European Research Council (ERC, grant agreement No 716117, awarded to Prof. Dr. Jan Maas). He also gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) grant ESPRIT 208.\r\nThe second author gratefully acknowledges funding by the Hausdorff Center for Mathematics at the University of Bonn. Part of this work was completed while this author was a member of the Institute of Science and Technology Austria. He gratefully acknowledges funding of his position at that time by the Austrian Science Fund (FWF) grants F65 and W1245.\r\nThe third author gratefully acknowledges funding by the Lise Meitner fellowship, Austrian Science Fund (FWF): M3211. Part of this work was completed while funded by the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.","quality_controlled":"1","volume":34,"status":"public","year":"2024","_id":"15317","date_published":"2024-04-01T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","page":"1007-1035","day":"01","author":[{"full_name":"Huebbers, Jan W.","first_name":"Jan W.","last_name":"Huebbers"},{"full_name":"Caldarescu, George A.","first_name":"George A.","last_name":"Caldarescu"},{"full_name":"Kubátová, Zdeňka","last_name":"Kubátová","first_name":"Zdeňka"},{"first_name":"Peter","last_name":"Sabol","full_name":"Sabol, Peter"},{"full_name":"Levecque, Sophie C.J.","first_name":"Sophie C.J.","last_name":"Levecque"},{"first_name":"Hannah","last_name":"Kuhn","full_name":"Kuhn, Hannah"},{"id":"57a1567c-8314-11eb-9063-c9ddc3451a54","full_name":"Kulich, Ivan","first_name":"Ivan","last_name":"Kulich"},{"first_name":"Anja","last_name":"Reinstädler","full_name":"Reinstädler, Anja"},{"full_name":"Büttgen, Kim","first_name":"Kim","last_name":"Büttgen"},{"last_name":"Manga-Robles","first_name":"Alba","full_name":"Manga-Robles, Alba"},{"full_name":"Mélida, Hugo","last_name":"Mélida","first_name":"Hugo"},{"first_name":"Markus","last_name":"Pauly","full_name":"Pauly, Markus"},{"first_name":"Ralph","last_name":"Panstruga","full_name":"Panstruga, Ralph"},{"full_name":"Žárský, Viktor","last_name":"Žárský","first_name":"Viktor"}],"file":[{"file_name":"2024_PlantCell_Huebbers.pdf","date_updated":"2024-04-17T06:57:54Z","file_size":2866098,"creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","checksum":"f9994d2e4748feec24c992b39871aba1","content_type":"application/pdf","file_id":"15326","date_created":"2024-04-17T06:57:54Z"}],"article_type":"original","external_id":{"pmid":["38124479"]},"date_created":"2024-04-14T22:01:02Z","publication":"Plant Cell","title":"Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew","has_accepted_license":"1","month":"04","issue":"4","file_date_updated":"2024-04-17T06:57:54Z","fulldoi":"https://doi.org/10.1093/plcell/koad319","date_updated":"2024-04-17T07:01:21Z","ddc":["580"],"pmid":1,"language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","department":[{"_id":"JiFr"}],"article_processing_charge":"Yes (in subscription journal)","citation":{"ista":"Huebbers JW, Caldarescu GA, Kubátová Z, Sabol P, Levecque SCJ, Kuhn H, Kulich I, Reinstädler A, Büttgen K, Manga-Robles A, Mélida H, Pauly M, Panstruga R, Žárský V. 2024. Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew. Plant Cell. 36(4), 1007–1035.","short":"J.W. Huebbers, G.A. Caldarescu, Z. Kubátová, P. Sabol, S.C.J. Levecque, H. Kuhn, I. Kulich, A. Reinstädler, K. Büttgen, A. Manga-Robles, H. Mélida, M. Pauly, R. Panstruga, V. Žárský, Plant Cell 36 (2024) 1007–1035.","mla":"Huebbers, Jan W., et al. “Interplay of EXO70 and MLO Proteins Modulates Trichome Cell Wall Composition and Susceptibility to Powdery Mildew.” <i>Plant Cell</i>, vol. 36, no. 4, Oxford University Press, 2024, pp. 1007–35, doi:<a href=\"https://doi.org/10.1093/plcell/koad319\">10.1093/plcell/koad319</a>.","chicago":"Huebbers, Jan W., George A. Caldarescu, Zdeňka Kubátová, Peter Sabol, Sophie C.J. Levecque, Hannah Kuhn, Ivan Kulich, et al. “Interplay of EXO70 and MLO Proteins Modulates Trichome Cell Wall Composition and Susceptibility to Powdery Mildew.” <i>Plant Cell</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/plcell/koad319\">https://doi.org/10.1093/plcell/koad319</a>.","ieee":"J. W. Huebbers <i>et al.</i>, “Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew,” <i>Plant Cell</i>, vol. 36, no. 4. Oxford University Press, pp. 1007–1035, 2024.","ama":"Huebbers JW, Caldarescu GA, Kubátová Z, et al. Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew. <i>Plant Cell</i>. 2024;36(4):1007-1035. doi:<a href=\"https://doi.org/10.1093/plcell/koad319\">10.1093/plcell/koad319</a>","apa":"Huebbers, J. W., Caldarescu, G. A., Kubátová, Z., Sabol, P., Levecque, S. C. J., Kuhn, H., … Žárský, V. (2024). Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew. <i>Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koad319\">https://doi.org/10.1093/plcell/koad319</a>"},"intvolume":"        36","publication_status":"published","publisher":"Oxford University Press","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298X"]},"abstract":[{"text":"Exocyst component of 70-kDa (EXO70) proteins are constituents of the exocyst complex implicated in vesicle tethering during exocytosis. MILDEW RESISTANCE LOCUS O (MLO) proteins are plant-specific calcium channels and some MLO isoforms enable fungal powdery mildew pathogenesis. We here detected an unexpected phenotypic overlap of Arabidopsis thaliana exo70H4 and mlo2 mlo6 mlo12 triple mutant plants regarding the biogenesis of leaf trichome secondary cell walls. Biochemical and Fourier transform infrared spectroscopic analyses corroborated deficiencies in the composition of trichome cell walls in these mutants. Transgenic lines expressing fluorophore-tagged EXO70H4 and MLO exhibited extensive colocalization of these proteins. Furthermore, mCherry-EXO70H4 mislocalized in trichomes of the mlo triple mutant and, vice versa, MLO6-GFP mislocalized in trichomes of the exo70H4 mutant. Expression of GFP-marked PMR4 callose synthase, a known cargo of EXO70H4-dependent exocytosis, revealed reduced cell wall delivery of GFP-PMR4 in trichomes of mlo triple mutant plants. In vivo protein–protein interaction assays in plant and yeast cells uncovered isoform-preferential interactions between EXO70.2 subfamily members and MLO proteins. Finally, exo70H4 and mlo6 mutants, when combined, showed synergistically enhanced resistance to powdery mildew attack. Taken together, our data point to an isoform-specific interplay of EXO70 and MLO proteins in the modulation of trichome cell wall biogenesis and powdery mildew susceptibility.","lang":"eng"}],"tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"oa_version":"Published Version","doi":"10.1093/plcell/koad319","volume":36,"quality_controlled":"1","status":"public","year":"2024","_id":"15319","date_published":"2024-04-01T00:00:00Z"},{"ddc":["530"],"language":[{"iso":"eng"}],"scopus_import":"1","department":[{"_id":"GeKa"}],"oa":1,"article_number":"L022002","article_processing_charge":"Yes","intvolume":"         6","citation":{"chicago":"Seoane Souto, Rubén, Martin Leijnse, Constantin Schrade, Marco Valentini, Georgios Katsaros, and Jeroen Danon. “Tuning the Josephson Diode Response with an Ac Current.” <i>Physical Review Research</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022002\">https://doi.org/10.1103/PhysRevResearch.6.L022002</a>.","mla":"Seoane Souto, Rubén, et al. “Tuning the Josephson Diode Response with an Ac Current.” <i>Physical Review Research</i>, vol. 6, no. 2, L022002, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022002\">10.1103/PhysRevResearch.6.L022002</a>.","ieee":"R. Seoane Souto, M. Leijnse, C. Schrade, M. Valentini, G. Katsaros, and J. Danon, “Tuning the Josephson diode response with an ac current,” <i>Physical Review Research</i>, vol. 6, no. 2. American Physical Society, 2024.","apa":"Seoane Souto, R., Leijnse, M., Schrade, C., Valentini, M., Katsaros, G., &#38; Danon, J. (2024). Tuning the Josephson diode response with an ac current. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022002\">https://doi.org/10.1103/PhysRevResearch.6.L022002</a>","ama":"Seoane Souto R, Leijnse M, Schrade C, Valentini M, Katsaros G, Danon J. Tuning the Josephson diode response with an ac current. <i>Physical Review Research</i>. 2024;6(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.6.L022002\">10.1103/PhysRevResearch.6.L022002</a>","ista":"Seoane Souto R, Leijnse M, Schrade C, Valentini M, Katsaros G, Danon J. 2024. Tuning the Josephson diode response with an ac current. Physical Review Research. 6(2), L022002.","short":"R. Seoane Souto, M. Leijnse, C. Schrade, M. Valentini, G. Katsaros, J. Danon, Physical Review Research 6 (2024)."},"publication_identifier":{"eissn":["2643-1564"]},"publication_status":"published","publisher":"American Physical Society","DOAJ_listed":"1","abstract":[{"text":"Josephson diodes are superconducting elements that show an asymmetry in the critical current depending on the direction of the current. Here, we theoretically explore how an alternating current bias can tune the response of such a diode. We show that for slow driving there is always a regime where the system can only carry zero-voltage dc current in one direction, thus effectively behaving as an ideal Josephson diode. Under fast driving, the diode efficiency is also tunable, although the ideal regime cannot be reached in this case. We also investigate the residual dissipation due to the time-dependent current bias and show that it remains small. All our conclusions are solely based on the critical current asymmetry of the junction, and are thus compatible with any Josephson diode.","lang":"eng"}],"oa_version":"Published Version","tmp":{"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)","image":"/images/cc_by.png"},"acknowledgement":"We acknowledge support from research grants Spanish CM Talento Program (Project No. 2022-T1/IND-24070), Spanish Ministry of Science, innovation, and Universities through Grant No. PID2022-140552NA-I00, Swedish Research Council under Grant Agreement No. 2020-03412, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 856526, Nanolund, FWF Project with [82],\r\nand Microsoft Corporation. ","doi":"10.1103/PhysRevResearch.6.L022002","volume":6,"quality_controlled":"1","year":"2024","status":"public","date_published":"2024-04-01T00:00:00Z","_id":"15320","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","author":[{"full_name":"Seoane Souto, Rubén","last_name":"Seoane Souto","first_name":"Rubén"},{"full_name":"Leijnse, Martin","last_name":"Leijnse","first_name":"Martin"},{"last_name":"Schrade","first_name":"Constantin","full_name":"Schrade, Constantin"},{"last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco"},{"last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Danon","first_name":"Jeroen","full_name":"Danon, Jeroen"}],"day":"01","file":[{"date_updated":"2024-04-17T07:14:53Z","file_size":1073544,"file_name":"2024_PhysReviewResearch_Souto.pdf","access_level":"open_access","relation":"main_file","creator":"dernst","success":1,"checksum":"7b9cb3b17d89f392bd582e30d7a72a29","content_type":"application/pdf","file_id":"15327","date_created":"2024-04-17T07:14:53Z"}],"article_type":"letter_note","date_created":"2024-04-14T22:01:02Z","publication":"Physical Review Research","has_accepted_license":"1","title":"Tuning the Josephson diode response with an ac current","issue":"2","month":"04","file_date_updated":"2024-04-17T07:14:53Z","fulldoi":"https://doi.org/10.1103/PhysRevResearch.6.L022002","date_updated":"2025-05-14T09:31:50Z"},{"author":[{"full_name":"Trinh, Giang","last_name":"Trinh","first_name":"Giang"},{"full_name":"Benhamou, Belaid","last_name":"Benhamou","first_name":"Belaid"},{"first_name":"Samuel","last_name":"Pastva","full_name":"Pastva, Samuel","orcid":"0000-0003-1993-0331","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b"},{"last_name":"Soliman","first_name":"Sylvain","full_name":"Soliman, Sylvain"}],"day":"25","page":"10714-10722","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","fulldoi":"https://doi.org/10.1609/aaai.v38i9.28943","date_updated":"2026-06-18T17:48:08Z","issue":"9","month":"03","title":"Scalable enumeration of trap spaces in boolean networks via answer set programming","main_file_link":[{"open_access":"1","url":"https://amu.hal.science/hal-04523118/"}],"publication":"Proceedings of the 38th AAAI Conference on Artificial Intelligence","date_created":"2024-04-14T22:01:02Z","scopus_import":"1","department":[{"_id":"ToHe"}],"oa":1,"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"ddc":["000"],"year":"2024","status":"public","date_published":"2024-03-25T00:00:00Z","_id":"15321","acknowledgement":"This work was supported by Institut Carnot STAR, Marseille, France and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","doi":"10.1609/aaai.v38i9.28943","quality_controlled":"1","volume":38,"abstract":[{"text":"Boolean Networks (BNs) are widely used as a modeling formalism in several domains, notably systems biology and computer science. A fundamental problem in BN analysis is the enumeration of trap spaces, which are hypercubes in the state space that cannot be escaped once entered. Several methods have been proposed for enumerating trap spaces, however they often suffer from scalability and efficiency issues, particularly for large and complex models. To our knowledge, the most efficient and recent methods for the trap space enumeration all rely on Answer Set Programming (ASP), which has been widely applied to the analysis of BNs. Motivated by these considerations, our work proposes a new method for enumerating trap spaces in BNs using ASP. We evaluate the method on a mix of 250+ real-world and 400+ randomly generated BNs, showing that it enables analysis of models beyond the capabilities of existing tools (namely pyboolnet, mpbn, trappist, and trapmvn).","lang":"eng"}],"oa_version":"Published Version","intvolume":"        38","citation":{"ama":"Trinh G, Benhamou B, Pastva S, Soliman S. Scalable enumeration of trap spaces in boolean networks via answer set programming. In: <i>Proceedings of the 38th AAAI Conference on Artificial Intelligence</i>. Vol 38. Association for the Advancement of Artificial Intelligence; 2024:10714-10722. doi:<a href=\"https://doi.org/10.1609/aaai.v38i9.28943\">10.1609/aaai.v38i9.28943</a>","apa":"Trinh, G., Benhamou, B., Pastva, S., &#38; Soliman, S. (2024). Scalable enumeration of trap spaces in boolean networks via answer set programming. In <i>Proceedings of the 38th AAAI Conference on Artificial Intelligence</i> (Vol. 38, pp. 10714–10722). Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v38i9.28943\">https://doi.org/10.1609/aaai.v38i9.28943</a>","ieee":"G. Trinh, B. Benhamou, S. Pastva, and S. Soliman, “Scalable enumeration of trap spaces in boolean networks via answer set programming,” in <i>Proceedings of the 38th AAAI Conference on Artificial Intelligence</i>, 2024, vol. 38, no. 9, pp. 10714–10722.","chicago":"Trinh, Giang, Belaid Benhamou, Samuel Pastva, and Sylvain Soliman. “Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming.” In <i>Proceedings of the 38th AAAI Conference on Artificial Intelligence</i>, 38:10714–22. Association for the Advancement of Artificial Intelligence, 2024. <a href=\"https://doi.org/10.1609/aaai.v38i9.28943\">https://doi.org/10.1609/aaai.v38i9.28943</a>.","mla":"Trinh, Giang, et al. “Scalable Enumeration of Trap Spaces in Boolean Networks via Answer Set Programming.” <i>Proceedings of the 38th AAAI Conference on Artificial Intelligence</i>, vol. 38, no. 9, Association for the Advancement of Artificial Intelligence, 2024, pp. 10714–22, doi:<a href=\"https://doi.org/10.1609/aaai.v38i9.28943\">10.1609/aaai.v38i9.28943</a>.","ista":"Trinh G, Benhamou B, Pastva S, Soliman S. 2024. Scalable enumeration of trap spaces in boolean networks via answer set programming. Proceedings of the 38th AAAI Conference on Artificial Intelligence. vol. 38, 10714–10722.","short":"G. Trinh, B. Benhamou, S. Pastva, S. Soliman, in:, Proceedings of the 38th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2024, pp. 10714–10722."},"publication_identifier":{"issn":["2159-5399"],"isbn":["1577358872"],"eissn":["2374-3468"]},"publication_status":"published","publisher":"Association for the Advancement of Artificial Intelligence","ec_funded":1},{"OA_type":"hybrid","external_id":{"isi":["001266917100005"],"pmid":["38506228"]},"article_type":"original","file":[{"file_id":"18792","checksum":"6dc023f0cc7052ad3cf0a42589d2e30f","content_type":"application/pdf","date_created":"2025-01-09T08:41:16Z","date_updated":"2025-01-09T08:41:16Z","file_name":"2024_JourCellScience_Gnyliukh.pdf","file_size":25845948,"access_level":"open_access","relation":"main_file","creator":"dernst","success":1}],"day":"01","author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia","first_name":"Nataliia","last_name":"Gnyliukh"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J"},{"last_name":"Nagel","first_name":"MK","full_name":"Nagel, MK"},{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"last_name":"Babic","first_name":"David","id":"db566d23-f6e0-11ea-865d-e6f270e968e7","full_name":"Babic, David"},{"first_name":"Annamaria","last_name":"Hlavata","full_name":"Hlavata, Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alotaibi","first_name":"SS","full_name":"Alotaibi, SS"},{"full_name":"Isono, E","first_name":"E","last_name":"Isono"},{"last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"status":"public","id":"14591","relation":"earlier_version"}]},"type":"journal_article","file_date_updated":"2025-01-09T08:41:16Z","date_updated":"2025-09-04T13:49:45Z","fulldoi":"https://doi.org/10.1242/jcs.261720","issue":"8","month":"04","has_accepted_license":"1","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana","OA_place":"publisher","date_created":"2024-04-19T09:54:59Z","publication":"Journal of Cell Science","scopus_import":"1","department":[{"_id":"MaLo"},{"_id":"JiFr"},{"_id":"CaBe"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa":1,"article_number":"jcs.261720","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Peptide receptors for auxin canalization in Arabidopsis","grant_number":"I06123","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"}],"article_processing_charge":"Yes (via OA deal)","pmid":1,"language":[{"iso":"eng"}],"ddc":["570"],"isi":1,"year":"2024","status":"public","date_published":"2024-04-01T00:00:00Z","_id":"15330","acknowledgement":"Nataliia Gnyliukh was partially funded by the European Union’s Horizon 2020 research and\r\ninnovation program (2018-2020) under the Marie Sklodowska-Curie Grant (agreement no.\r\n665385). Taif University Researchers Supporting Project: TURSP-HC2022/02. and Austrian\r\nScience Fund (FWF): I 6123-B.We thank Prof. Eileen Lafer and Liping Wang for their suggestions regarding the optimisation of protein expression and purification. We thank Prof. Sebastian Y. Bednarek for the useful comments and constructive criticism of the project. We thank Maciek Adamowski for providing genetic material. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Electron microscopy (EMF), Lab Support Facility (LSF) (particularly Dorota Jaworska) and the Bioimaging Facility (BIF).","doi":"10.1242/jcs.261720","quality_controlled":"1","volume":137,"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scission machinery in plants, but the precise roles of these proteins in this process are not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the sh3p123 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME."}],"corr_author":"1","oa_version":"Published Version","tmp":{"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)","image":"/images/cc_by.png"},"intvolume":"       137","citation":{"short":"N. Gnyliukh, A.J. Johnson, M. Nagel, A. Monzer, D. Babic, A. Hlavata, S. Alotaibi, E. Isono, M. Loose, J. Friml, Journal of Cell Science 137 (2024).","ista":"Gnyliukh N, Johnson AJ, Nagel M, Monzer A, Babic D, Hlavata A, Alotaibi S, Isono E, Loose M, Friml J. 2024. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. Journal of Cell Science. 137(8), jcs. 261720.","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, MK Nagel, Aline Monzer, David Babic, Annamaria Hlavata, SS Alotaibi, E Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>. The Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/jcs.261720\">https://doi.org/10.1242/jcs.261720</a>.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>, vol. 137, no. 8, jcs. 261720, The Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/jcs.261720\">10.1242/jcs.261720</a>.","ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana,” <i>Journal of Cell Science</i>, vol. 137, no. 8. The Company of Biologists, 2024.","ama":"Gnyliukh N, Johnson AJ, Nagel M, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. <i>Journal of Cell Science</i>. 2024;137(8). doi:<a href=\"https://doi.org/10.1242/jcs.261720\">10.1242/jcs.261720</a>","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M., Monzer, A., Babic, D., Hlavata, A., … Friml, J. (2024). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261720\">https://doi.org/10.1242/jcs.261720</a>"},"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"ec_funded":1,"publication_status":"published","publisher":"The Company of Biologists"},{"external_id":{"isi":["001284187100020"]},"file":[{"file_size":577128,"file_name":"2024_LNCS_Chalupa.pdf","date_updated":"2024-04-26T11:27:26Z","success":1,"creator":"cchlebak","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"208c855c60824bec936b8d01d0396474","file_id":"15347","date_created":"2024-04-26T11:27:26Z"}],"author":[{"last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek"},{"last_name":"Richter","first_name":"Cedric","full_name":"Richter, Cedric"}],"day":"05","page":"353–358","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"conference","file_date_updated":"2024-04-26T11:27:26Z","fulldoi":"https://doi.org/10.1007/978-3-031-57256-2_20","date_updated":"2025-09-04T13:48:25Z","month":"04","has_accepted_license":"1","title":"Bubaak-SpLit: Split what you cannot verify (Competition contribution)","publication":"30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems","date_created":"2024-04-20T18:14:06Z","department":[{"_id":"ToHe"}],"scopus_import":"1","oa":1,"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"ddc":["000"],"isi":1,"year":"2024","status":"public","date_published":"2024-04-05T00:00:00Z","_id":"15333","alternative_title":["LNCS"],"acknowledgement":"This work was partially supported by the ERC-2020-AdG 10102009 grant.","doi":"10.1007/978-3-031-57256-2_20","quality_controlled":"1","volume":14572,"abstract":[{"text":"BUBAAK-SpLit is a tool for dynamically splitting verification tasks into parts that can then be analyzed in parallel. It is built on top of BUBAAK, a tool designed for running combinations of verifiers in parallel. In contrast to BUBAAK, that directly invokes verifiers on the inputs, BUBAAK-SpLit first starts by splitting the input program into multiple modified versions called program splits. During the splitting process, BUBAAK-SpLit utilizes a weak verifier (in our case symbolic execution with a short timelimit) to analyze each generated program split. If the weak verifier fails on a program split, we split this program split again and start the verification process again on the generated program splits. We run the splitting process until a predefined number of hard-to-verify program splits is generated or a splitting limit is reached. During the main verification phase, we run a combination of BUBAAK-LEE and SLOWBEAST in parallel on the remaining unsolved parts of the verification task.","lang":"eng"}],"corr_author":"1","oa_version":"Published Version","tmp":{"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)","image":"/images/cc_by.png"},"intvolume":"     14572","citation":{"ama":"Chalupa M, Richter C. Bubaak-SpLit: Split what you cannot verify (Competition contribution). In: <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 14572. Springer Nature; 2024:353–358. doi:<a href=\"https://doi.org/10.1007/978-3-031-57256-2_20\">10.1007/978-3-031-57256-2_20</a>","apa":"Chalupa, M., &#38; Richter, C. (2024). Bubaak-SpLit: Split what you cannot verify (Competition contribution). In <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 14572, pp. 353–358). Luxembourg City, Luxembourg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-57256-2_20\">https://doi.org/10.1007/978-3-031-57256-2_20</a>","mla":"Chalupa, Marek, and Cedric Richter. “Bubaak-SpLit: Split What You Cannot Verify (Competition Contribution).” <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 14572, Springer Nature, 2024, pp. 353–358, doi:<a href=\"https://doi.org/10.1007/978-3-031-57256-2_20\">10.1007/978-3-031-57256-2_20</a>.","ieee":"M. Chalupa and C. Richter, “Bubaak-SpLit: Split what you cannot verify (Competition contribution),” in <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, Luxembourg City, Luxembourg, 2024, vol. 14572, pp. 353–358.","chicago":"Chalupa, Marek, and Cedric Richter. “Bubaak-SpLit: Split What You Cannot Verify (Competition Contribution).” In <i>30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 14572:353–358. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-57256-2_20\">https://doi.org/10.1007/978-3-031-57256-2_20</a>.","short":"M. Chalupa, C. Richter, in:, 30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2024, pp. 353–358.","ista":"Chalupa M, Richter C. 2024. Bubaak-SpLit: Split what you cannot verify (Competition contribution). 30th International Conference on Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 14572, 353–358."},"conference":{"location":"Luxembourg City, Luxembourg","end_date":"2024-04-11","start_date":"2024-04-06","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"publication_identifier":{"eisbn":["9783031572562"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031572555"]},"publication_status":"published","ec_funded":1,"publisher":"Springer Nature"},{"file_date_updated":"2024-04-23T07:30:48Z","fulldoi":"https://doi.org/10.1007/s00526-024-02715-7","date_updated":"2025-09-04T13:45:40Z","month":"05","issue":"4","title":"Sharp interface limit for a Navier–Stokes/Allen–Cahn system in the case of a vanishing mobility","has_accepted_license":"1","publication":"Calculus of Variations and Partial Differential Equations","date_created":"2024-04-21T22:00:52Z","external_id":{"arxiv":["2304.12096"],"isi":["001199418100002"]},"file":[{"date_created":"2024-04-23T07:30:48Z","content_type":"application/pdf","checksum":"b1095fad4cae596f52cc616a973bdde2","file_id":"15343","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2024-04-23T07:30:48Z","file_size":975186,"file_name":"2024_CalculusEquations_Abels.pdf"}],"article_type":"original","arxiv":1,"day":"01","author":[{"first_name":"Helmut","last_name":"Abels","full_name":"Abels, Helmut"},{"first_name":"Mingwen","last_name":"Fei","full_name":"Fei, Mingwen"},{"full_name":"Moser, Maximilian","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","first_name":"Maximilian","last_name":"Moser"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","status":"public","year":"2024","_id":"15334","date_published":"2024-05-01T00:00:00Z","doi":"10.1007/s00526-024-02715-7","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.\r\nM. Fei was partially supported by NSF of China under Grant No. 12271004 and Anhui Provincial Funding Project under Grant Nos. gxbjZD2022009 and 2308085J10. Moreover, M. Moser has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 948819).","quality_controlled":"1","volume":63,"abstract":[{"text":"We consider the sharp interface limit of a Navier-Stokes/Allen Cahn equation in a bounded smooth domain in two space dimensions, in the case of vanishing mobility mε=ε√, where the small parameter ε>0 related to the thickness of the diffuse interface is sent to zero. For well-prepared initial data and sufficiently small times, we rigorously prove convergence to the classical two-phase Navier-Stokes system with surface tension. The idea of the proof is to use asymptotic expansions to construct an approximate solution and to estimate the difference of the exact and approximate solutions with a spectral estimate for the (at the approximate solution) linearized Allen-Cahn operator. In the calculations we use a fractional order ansatz and new ansatz terms in higher orders leading to a suitable ε-scaled and coupled model problem. Moreover, we apply the novel idea of introducing ε-dependent coordinates.","lang":"eng"}],"tmp":{"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)","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"ista":"Abels H, Fei M, Moser M. 2024. Sharp interface limit for a Navier–Stokes/Allen–Cahn system in the case of a vanishing mobility. Calculus of Variations and Partial Differential Equations. 63(4), 94.","short":"H. Abels, M. Fei, M. Moser, Calculus of Variations and Partial Differential Equations 63 (2024).","mla":"Abels, Helmut, et al. “Sharp Interface Limit for a Navier–Stokes/Allen–Cahn System in the Case of a Vanishing Mobility.” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 63, no. 4, 94, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00526-024-02715-7\">10.1007/s00526-024-02715-7</a>.","ieee":"H. Abels, M. Fei, and M. Moser, “Sharp interface limit for a Navier–Stokes/Allen–Cahn system in the case of a vanishing mobility,” <i>Calculus of Variations and Partial Differential Equations</i>, vol. 63, no. 4. Springer Nature, 2024.","chicago":"Abels, Helmut, Mingwen Fei, and Maximilian Moser. “Sharp Interface Limit for a Navier–Stokes/Allen–Cahn System in the Case of a Vanishing Mobility.” <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00526-024-02715-7\">https://doi.org/10.1007/s00526-024-02715-7</a>.","ama":"Abels H, Fei M, Moser M. Sharp interface limit for a Navier–Stokes/Allen–Cahn system in the case of a vanishing mobility. <i>Calculus of Variations and Partial Differential Equations</i>. 2024;63(4). doi:<a href=\"https://doi.org/10.1007/s00526-024-02715-7\">10.1007/s00526-024-02715-7</a>","apa":"Abels, H., Fei, M., &#38; Moser, M. (2024). Sharp interface limit for a Navier–Stokes/Allen–Cahn system in the case of a vanishing mobility. <i>Calculus of Variations and Partial Differential Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00526-024-02715-7\">https://doi.org/10.1007/s00526-024-02715-7</a>"},"intvolume":"        63","publisher":"Springer Nature","publication_status":"published","ec_funded":1,"publication_identifier":{"eissn":["1432-0835"],"issn":["0944-2669"]},"oa":1,"article_number":"94","department":[{"_id":"JuFi"}],"scopus_import":"1","project":[{"call_identifier":"H2020","name":"Bridging Scales in Random Materials","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"article_processing_charge":"Yes (via OA deal)","language":[{"iso":"eng"}],"ddc":["510"],"isi":1},{"isi":1,"ddc":["570"],"pmid":1,"language":[{"iso":"eng"}],"article_number":"e2318041121","oa":1,"scopus_import":"1","department":[{"_id":"LoSw"}],"article_processing_charge":"Yes (in subscription journal)","citation":{"ama":"Godavarthi SK, Hiramoto M, Ignatyev Y, et al. Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(15). doi:<a href=\"https://doi.org/10.1073/pnas.2318041121\">10.1073/pnas.2318041121</a>","apa":"Godavarthi, S. K., Hiramoto, M., Ignatyev, Y., Levin, J. B., Li, H. Q., Pratelli, M., … Spitzer, N. C. (2024). Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2318041121\">https://doi.org/10.1073/pnas.2318041121</a>","chicago":"Godavarthi, Swetha K., Masaki Hiramoto, Yuri Ignatyev, Jacqueline B. Levin, Hui Quan Li, Marta Pratelli, Jennifer Borchardt, et al. “Postsynaptic Receptors Regulate Presynaptic Transmitter Stability through Transsynaptic Bridges.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2318041121\">https://doi.org/10.1073/pnas.2318041121</a>.","mla":"Godavarthi, Swetha K., et al. “Postsynaptic Receptors Regulate Presynaptic Transmitter Stability through Transsynaptic Bridges.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 15, e2318041121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2318041121\">10.1073/pnas.2318041121</a>.","ieee":"S. K. Godavarthi <i>et al.</i>, “Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 15. National Academy of Sciences, 2024.","short":"S.K. Godavarthi, M. Hiramoto, Y. Ignatyev, J.B. Levin, H.Q. Li, M. Pratelli, J. Borchardt, C. Czajkowski, L.N. Borodinsky, L.B. Sweeney, H.T. Cline, N.C. Spitzer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Godavarthi SK, Hiramoto M, Ignatyev Y, Levin JB, Li HQ, Pratelli M, Borchardt J, Czajkowski C, Borodinsky LN, Sweeney LB, Cline HT, Spitzer NC. 2024. Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges. Proceedings of the National Academy of Sciences of the United States of America. 121(15), e2318041121."},"intvolume":"       121","publisher":"National Academy of Sciences","publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"abstract":[{"text":"Stable matching of neurotransmitters with their receptors is fundamental to synapse function and reliable communication in neural circuits. Presynaptic neurotransmitters regulate the stabilization of postsynaptic transmitter receptors. Whether postsynaptic receptors regulate stabilization of presynaptic transmitters has received less attention. Here, we show that blockade of endogenous postsynaptic acetylcholine receptors (AChR) at the neuromuscular junction destabilizes the cholinergic phenotype in motor neurons and stabilizes an earlier, developmentally transient glutamatergic phenotype. Further, expression of exogenous postsynaptic gamma-aminobutyric acid type A receptors (GABAA receptors) in muscle cells stabilizes an earlier, developmentally transient GABAergic motor neuron phenotype. Both AChR and GABAA receptors are linked to presynaptic neurons through transsynaptic bridges. Knockdown of specific components of these transsynaptic bridges prevents stabilization of the cholinergic or GABAergic phenotypes. Bidirectional communication can enforce a match between transmitter and receptor and ensure the fidelity of synaptic transmission. Our findings suggest a potential role of dysfunctional transmitter receptors in neurological disorders that involve the loss of the presynaptic transmitter.","lang":"eng"}],"tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"oa_version":"Published Version","doi":"10.1073/pnas.2318041121","acknowledgement":"We  thank  all  members  of  the  Spitzer  laboratory  for  discussions  and  critical  feedback;  K.  Marek  for  discussions  of  acknowledgment  signals; I. Gregor and R. Aricescu for discussions of receptor pharmacology and transsynaptic  bridges;  C.  Kintner  for  advice  on  Xenopus  blastomere  lineage;  A.  Ray and E. Park for guidance on miniature analysis; A. Glavis- Bloom, S.U. Choi, S. Atkins, M. Gupta, and S. Malladi for technical assistance; and D. K. Berg and L. R. Squire for comments on the manuscript. This work was supported by NSF 2051555 and the Overland Foundation. Microscopy for five- channel imaging utilized the UCSD School of Medicine Microscopy Core, supported by NIH grant NS047101.","volume":121,"quality_controlled":"1","status":"public","year":"2024","_id":"15335","date_published":"2024-04-09T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","day":"09","author":[{"full_name":"Godavarthi, Swetha K.","last_name":"Godavarthi","first_name":"Swetha K."},{"full_name":"Hiramoto, Masaki","last_name":"Hiramoto","first_name":"Masaki"},{"first_name":"Yuri","last_name":"Ignatyev","full_name":"Ignatyev, Yuri"},{"full_name":"Levin, Jacqueline B.","last_name":"Levin","first_name":"Jacqueline B."},{"full_name":"Li, Hui Quan","first_name":"Hui Quan","last_name":"Li"},{"full_name":"Pratelli, Marta","last_name":"Pratelli","first_name":"Marta"},{"first_name":"Jennifer","last_name":"Borchardt","full_name":"Borchardt, Jennifer"},{"full_name":"Czajkowski, Cynthia","first_name":"Cynthia","last_name":"Czajkowski"},{"first_name":"Laura N.","last_name":"Borodinsky","full_name":"Borodinsky, Laura N."},{"first_name":"Lora Beatrice Jaeger","last_name":"Sweeney","orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"},{"first_name":"Hollis T.","last_name":"Cline","full_name":"Cline, Hollis T."},{"last_name":"Spitzer","first_name":"Nicholas C.","full_name":"Spitzer, Nicholas C."}],"article_type":"original","file":[{"date_updated":"2024-04-23T06:53:14Z","file_size":16187094,"file_name":"2024_PNAS_Godavarthi.pdf","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"15340","content_type":"application/pdf","checksum":"f3b4ffad4ef3d1c443414edf0cd2392c","date_created":"2024-04-23T06:53:14Z"}],"external_id":{"isi":["001243892800004"],"pmid":["38568976"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","date_created":"2024-04-21T22:00:53Z","title":"Postsynaptic receptors regulate presynaptic transmitter stability through transsynaptic bridges","has_accepted_license":"1","month":"04","issue":"15","file_date_updated":"2024-04-23T06:53:14Z","date_updated":"2025-09-04T13:42:01Z","fulldoi":"https://doi.org/10.1073/pnas.2318041121"}]