[{"day":"19","file":[{"access_level":"open_access","creator":"cchlebak","date_updated":"2021-10-21T13:51:49Z","relation":"main_file","content_type":"application/pdf","checksum":"d99fcd51aebde19c21314e3de0148007","file_id":"10169","date_created":"2021-10-21T13:51:49Z","file_name":"2021_NatComm_Appel.pdf","file_size":5111706,"success":1}],"date_updated":"2024-10-21T06:02:05Z","oa_version":"Published Version","issue":"1","oa":1,"language":[{"iso":"eng"}],"month":"10","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1038/s41467-021-26360-2","ddc":["610"],"publication_status":"published","abstract":[{"lang":"eng","text":"The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay."}],"status":"public","date_published":"2021-10-19T00:00:00Z","publisher":"Springer Nature","intvolume":"        12","isi":1,"type":"journal_article","keyword":["general physics and astronomy","general biochemistry","genetics and molecular biology","general chemistry"],"citation":{"apa":"Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>","short":"L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021).","chicago":"Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26360-2\">https://doi.org/10.1038/s41467-021-26360-2</a>.","ista":"Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078.","ieee":"L.-M. Appel <i>et al.</i>, “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","mla":"Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” <i>Nature Communications</i>, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>.","ama":"Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26360-2\">10.1038/s41467-021-26360-2</a>"},"scopus_import":"1","article_number":"6078","quality_controlled":"1","has_accepted_license":"1","_id":"10163","file_date_updated":"2021-10-21T13:51:49Z","author":[{"full_name":"Appel, Lisa-Marie","first_name":"Lisa-Marie","last_name":"Appel"},{"full_name":"Franke, Vedran","last_name":"Franke","first_name":"Vedran"},{"last_name":"Bruno","first_name":"Melania","full_name":"Bruno, Melania"},{"full_name":"Grishkovskaya, Irina","last_name":"Grishkovskaya","first_name":"Irina"},{"full_name":"Kasiliauskaite, Aiste","first_name":"Aiste","last_name":"Kasiliauskaite"},{"first_name":"Tanja","last_name":"Kaufmann","full_name":"Kaufmann, Tanja"},{"full_name":"Schoeberl, Ursula E.","last_name":"Schoeberl","first_name":"Ursula E."},{"last_name":"Puchinger","first_name":"Martin G.","full_name":"Puchinger, Martin G."},{"first_name":"Sebastian","last_name":"Kostrhon","full_name":"Kostrhon, Sebastian"},{"full_name":"Ebenwaldner, Carmen","first_name":"Carmen","last_name":"Ebenwaldner"},{"full_name":"Sebesta, Marek","first_name":"Marek","last_name":"Sebesta"},{"last_name":"Beltzung","first_name":"Etienne","full_name":"Beltzung, Etienne"},{"full_name":"Mechtler, Karl","first_name":"Karl","last_name":"Mechtler"},{"full_name":"Lin, Gen","first_name":"Gen","last_name":"Lin"},{"last_name":"Vlasova","first_name":"Anna","full_name":"Vlasova, Anna"},{"full_name":"Leeb, Martin","last_name":"Leeb","first_name":"Martin"},{"last_name":"Pavri","first_name":"Rushad","full_name":"Pavri, Rushad"},{"first_name":"Alexander","last_name":"Stark","full_name":"Stark, Alexander"},{"full_name":"Akalin, Altuna","first_name":"Altuna","last_name":"Akalin"},{"full_name":"Stefl, Richard","first_name":"Richard","last_name":"Stefl"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A"},{"full_name":"Djinovic-Carugo, Kristina","first_name":"Kristina","last_name":"Djinovic-Carugo"},{"full_name":"Slade, Dea","last_name":"Slade","first_name":"Dea"}],"publication_identifier":{"eissn":["2041-1723"]},"article_processing_charge":"No","acknowledgement":"D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.","date_created":"2021-10-20T14:40:32Z","department":[{"_id":"CaBe"}],"related_material":{"link":[{"description":"Preprint ","url":"https://www.biorxiv.org/content/10.1101/2020.02.11.943159","relation":"earlier_version"}]},"publication":"Nature Communications","year":"2021","volume":12,"title":"PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC","external_id":{"isi":["000709050300001"]},"article_type":"original"},{"department":[{"_id":"BeVi"}],"acknowledgement":"We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific Computing Group for their support. This work was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 715257).","date_created":"2021-10-21T07:46:06Z","article_processing_charge":"Yes (via OA deal)","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["0962-8452"],"eissn":["1471-2954"]},"title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","external_id":{"pmid":["34547909"],"isi":["000697643700001"]},"article_type":"original","volume":288,"year":"2021","project":[{"call_identifier":"H2020","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings of the Royal Society B: Biological Sciences","related_material":{"record":[{"relation":"research_data","id":"9949","status":"public"}],"link":[{"url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1","relation":"supplementary_material"}]},"type":"journal_article","isi":1,"intvolume":"       288","publisher":"The Royal Society","author":[{"last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","first_name":"Ann K","full_name":"Huylmans, Ann K"},{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"first_name":"Francisco","last_name":"Hontoria","full_name":"Hontoria, Francisco"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"file_date_updated":"2021-10-22T11:48:02Z","_id":"10166","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","article_number":"20211720","citation":{"chicago":"Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2021. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>.","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","apa":"Huylmans, A. K., Macon, A., Hontoria, F., &#38; Vicoso, B. (2021). Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>","ama":"Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2021;288(1959). doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>","ista":"Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 288(1959), 20211720.","ieee":"A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959. The Royal Society, 2021.","mla":"Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>."},"keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"pmid":1,"doi":"10.1098/rspb.2021.1720","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"09","date_published":"2021-09-22T00:00:00Z","status":"public","publication_status":"published","abstract":[{"text":"While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.","lang":"eng"}],"ddc":["595"],"file":[{"checksum":"76e7f253b7040bca2ad76f82bd7c45c0","date_created":"2021-10-22T11:48:02Z","file_id":"10172","success":1,"file_size":995806,"file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","creator":"cchlebak","access_level":"open_access","date_updated":"2021-10-22T11:48:02Z","content_type":"application/pdf","relation":"main_file"}],"day":"22","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"issue":"1959","oa_version":"Published Version","date_updated":"2025-04-14T07:41:20Z"},{"article_processing_charge":"No","acknowledgement":"We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse, Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory.”","date_created":"2021-10-24T22:01:32Z","publication_identifier":{"issn":["0022-2488"]},"department":[{"_id":"MiLe"}],"volume":62,"title":"Topological field theory on r-spin surfaces and the Arf-invariant","article_type":"original","external_id":{"arxiv":["1802.09978"],"isi":["000755638500010"]},"publication":"Journal of Mathematical Physics","year":"2021","intvolume":"        62","publisher":"AIP Publishing","isi":1,"type":"journal_article","quality_controlled":"1","scopus_import":"1","article_number":"102302","citation":{"mla":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” <i>Journal of Mathematical Physics</i>, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0037826\">10.1063/5.0037826</a>.","ieee":"I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and the Arf-invariant,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 10. AIP Publishing, 2021.","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302.","ama":"Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant. <i>Journal of Mathematical Physics</i>. 2021;62(10). doi:<a href=\"https://doi.org/10.1063/5.0037826\">10.1063/5.0037826</a>","apa":"Runkel, I., &#38; Szegedy, L. (2021). Topological field theory on r-spin surfaces and the Arf-invariant. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0037826\">https://doi.org/10.1063/5.0037826</a>","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).","chicago":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0037826\">https://doi.org/10.1063/5.0037826</a>."},"_id":"10176","author":[{"full_name":"Runkel, Ingo","first_name":"Ingo","last_name":"Runkel"},{"full_name":"Szegedy, Lorant","first_name":"Lorant","last_name":"Szegedy","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","orcid":"0000-0003-2834-5054"}],"month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1802.09978","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1063/5.0037826","publication_status":"published","abstract":[{"text":"We give a combinatorial model for r-spin surfaces with parameterized boundary based on Novak (“Lattice topological field theories in two dimensions,” Ph.D. thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of ℤ𝑟-valued indices assigned to the edges of a polygonal decomposition. This combinatorial model is designed for our state-sum construction of two-dimensional topological field theories on r-spin surfaces. We show that an example of such a topological field theory computes the Arf-invariant of an r-spin surface as introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant is constant on orbits of the mapping class group, providing an alternative proof of that fact.","lang":"eng"}],"date_published":"2021-10-01T00:00:00Z","status":"public","day":"01","corr_author":"1","oa_version":"Preprint","date_updated":"2025-07-10T11:49:44Z","issue":"10","arxiv":1,"oa":1,"language":[{"iso":"eng"}]},{"date_created":"2021-10-24T22:01:34Z","acknowledgement":"We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642).","article_processing_charge":"Yes (in subscription journal)","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"department":[{"_id":"Bio"}],"article_type":"original","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"volume":40,"year":"2021","publication":"EMBO Journal","intvolume":"        40","publisher":"Embo Press","type":"journal_article","isi":1,"has_accepted_license":"1","article_number":"e108714","scopus_import":"1","quality_controlled":"1","citation":{"ieee":"S. Bajaj <i>et al.</i>, “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” <i>EMBO Journal</i>, vol. 40, no. 23. Embo Press, 2021.","mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>, vol. 40, no. 23, e108714, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>.","ista":"Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714.","ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. 2021;40(23). doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>","apa":"Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>","short":"S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).","chicago":"Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>."},"author":[{"full_name":"Bajaj, Sunanjay","last_name":"Bajaj","first_name":"Sunanjay"},{"full_name":"Bagley, Joshua A.","first_name":"Joshua A.","last_name":"Bagley"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"last_name":"Vertesy","first_name":"Abel","full_name":"Vertesy, Abel"},{"last_name":"Nagumo Wong","first_name":"Sakurako","full_name":"Nagumo Wong, Sakurako"},{"full_name":"Krenn, Veronica","last_name":"Krenn","first_name":"Veronica"},{"full_name":"Lévi-Strauss, Julie","first_name":"Julie","last_name":"Lévi-Strauss"},{"first_name":"Juergen A.","last_name":"Knoblich","full_name":"Knoblich, Juergen A."}],"file_date_updated":"2021-12-13T14:54:14Z","_id":"10179","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","doi":"10.15252/embj.2021108714","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","abstract":[{"lang":"eng","text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling."}],"ddc":["610"],"date_published":"2021-10-18T00:00:00Z","status":"public","day":"18","file":[{"success":1,"file_size":7819881,"file_name":"2021_EMBO_Bajaj.pdf","checksum":"78d2d02e775322297e774f72810a41a4","date_created":"2021-12-13T14:54:14Z","file_id":"10541","content_type":"application/pdf","relation":"main_file","creator":"alisjak","access_level":"open_access","date_updated":"2021-12-13T14:54:14Z"}],"issue":"23","date_updated":"2023-08-14T08:05:23Z","oa_version":"Published Version","oa":1,"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"oa":1,"arxiv":1,"issue":"241","date_updated":"2025-06-26T11:53:12Z","oa_version":"Published Version","file":[{"content_type":"application/pdf","relation":"main_file","creator":"cziletti","access_level":"open_access","date_updated":"2021-10-27T15:34:18Z","success":1,"file_size":3527521,"file_name":"2021_JMachLearnRes_Hoefler.pdf","checksum":"3389d9d01fc58f8fb4c1a53e14a8abbf","date_created":"2021-10-27T15:34:18Z","file_id":"10192"}],"corr_author":"1","day":"01","status":"public","date_published":"2021-09-01T00:00:00Z","publication_status":"published","abstract":[{"text":"The growing energy and performance costs of deep learning have driven the community to reduce the size of neural networks by selectively pruning components. Similarly to their biological counterparts, sparse networks generalize just as well, sometimes even better than, the original dense networks. Sparsity promises to reduce the memory footprint of regular networks to fit mobile devices, as well as shorten training time for ever growing networks. In this paper, we survey prior work on sparsity in deep learning and provide an extensive tutorial of sparsification for both inference and training. We describe approaches to remove and add elements of neural networks, different training strategies to achieve model sparsity, and mechanisms to exploit sparsity in practice. Our work distills ideas from more than 300 research papers and provides guidance to practitioners who wish to utilize sparsity today, as well as to researchers whose goal is to push the frontier forward. We include the necessary background on mathematical methods in sparsification, describe phenomena such as early structure adaptation, the intricate relations between sparsity and the training process, and show techniques for achieving acceleration on real hardware. We also define a metric of pruned parameter efficiency that could serve as a baseline for comparison of different sparse networks. We close by speculating on how sparsity can improve future workloads and outline major open problems in the field.","lang":"eng"}],"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://www.jmlr.org/papers/v22/21-0366.html"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"09","author":[{"last_name":"Hoefler","first_name":"Torsten","full_name":"Hoefler, Torsten"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Ben-Nun","first_name":"Tal","full_name":"Ben-Nun, Tal"},{"first_name":"Nikoli","last_name":"Dryden","full_name":"Dryden, Nikoli"},{"last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra","full_name":"Peste, Elena-Alexandra"}],"_id":"10180","file_date_updated":"2021-10-27T15:34:18Z","citation":{"ieee":"T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, and A. Krumes, “Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks,” <i>Journal of Machine Learning Research</i>, vol. 22, no. 241. ML Research Press, pp. 1–124, 2021.","mla":"Hoefler, Torsten, et al. “Sparsity in Deep Learning: Pruning and Growth for Efficient Inference and Training in Neural Networks.” <i>Journal of Machine Learning Research</i>, vol. 22, no. 241, ML Research Press, 2021, pp. 1–124.","ista":"Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Krumes A. 2021. Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. Journal of Machine Learning Research. 22(241), 1–124.","ama":"Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Krumes A. Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. <i>Journal of Machine Learning Research</i>. 2021;22(241):1-124.","apa":"Hoefler, T., Alistarh, D.-A., Ben-Nun, T., Dryden, N., &#38; Krumes, A. (2021). Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. <i>Journal of Machine Learning Research</i>. ML Research Press.","short":"T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, A. Krumes, Journal of Machine Learning Research 22 (2021) 1–124.","chicago":"Hoefler, Torsten, Dan-Adrian Alistarh, Tal Ben-Nun, Nikoli Dryden, and Alexandra Krumes. “Sparsity in Deep Learning: Pruning and Growth for Efficient Inference and Training in Neural Networks.” <i>Journal of Machine Learning Research</i>. ML Research Press, 2021."},"has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","type":"journal_article","publisher":"ML Research Press","intvolume":"        22","year":"2021","publication":"Journal of Machine Learning Research","article_type":"original","title":"Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks","external_id":{"arxiv":["2102.00554"]},"volume":22,"page":"1-124","OA_place":"publisher","department":[{"_id":"DaAl"}],"publication_identifier":{"eissn":["1533-7928"],"issn":["1532-4435"]},"acknowledgement":"We thank Doug Burger, Steve Scott, Marco Heddes, and the respective teams at Microsoft for inspiring discussions on the topic. We thank Angelika Steger for uplifting debates about the connections to biological brains, Sidak Pal Singh for his support regarding experimental results, and Utku Evci as well as Xin Wang for comments on previous versions of this\r\nwork. Special thanks go to Bernhard Schölkopf, our JMLR editor Samy Bengio, and the three anonymous reviewers who provided excellent comprehensive, pointed, and deep review comments that improved the quality of our manuscript significantly.","date_created":"2021-10-24T22:01:34Z","article_processing_charge":"No"},{"ddc":["000"],"publication_status":"published","abstract":[{"lang":"eng","text":"We introduce a novel technique to automatically decompose an input object’s volume into a set of parts that can be represented by two opposite height fields. Such decomposition enables the manufacturing of individual parts using two-piece reusable rigid molds. Our decomposition strategy relies on a new energy formulation that utilizes a pre-computed signal on the mesh volume representing the accessibility for a predefined set of extraction directions. Thanks to this novel formulation, our method allows for efficient optimization of a fabrication-aware partitioning of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our approach by generating valid volume partitionings for a wide range of complex objects and physically reproducing several of them."}],"status":"public","date_published":"2021-12-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://vcg.isti.cnr.it/Publications/2021/AMBCP21"}],"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/3478513.3480555","date_updated":"2025-04-14T07:28:57Z","oa_version":"Submitted Version","issue":"6","language":[{"iso":"eng"}],"oa":1,"ec_funded":1,"day":"01","file":[{"checksum":"384ece7a9ad1026787ba9560b04336d5","date_created":"2021-10-27T07:08:07Z","file_id":"10185","file_size":107708317,"file_name":"rigidmolds-authorversion.pdf","creator":"bbickel","access_level":"open_access","date_updated":"2021-10-27T07:08:07Z","content_type":"application/pdf","relation":"main_file"}],"project":[{"grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"publication":"ACM Transactions on Graphics","year":"2021","volume":40,"article_type":"original","title":"Volume decomposition for two-piece rigid casting","external_id":{"isi":["000729846700077"]},"publication_identifier":{"eissn":["1557-7368 "],"issn":["0730-0301"]},"article_processing_charge":"No","acknowledgement":"The authors thank Marco Callieri for all his precious help with the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent fabrication-oriented computational design and modeling (grant no. 715767).","date_created":"2021-10-27T07:08:19Z","department":[{"_id":"BeBi"}],"citation":{"apa":"Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., &#38; Pietroni, N. (2021). Volume decomposition for two-piece rigid casting. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3478513.3480555\">https://doi.org/10.1145/3478513.3480555</a>","short":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 40 (2021).","chicago":"Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3478513.3480555\">https://doi.org/10.1145/3478513.3480555</a>.","ieee":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition for two-piece rigid casting,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 6. Association for Computing Machinery, 2021.","mla":"Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 6, 272, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3478513.3480555\">10.1145/3478513.3480555</a>.","ista":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272.","ama":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition for two-piece rigid casting. <i>ACM Transactions on Graphics</i>. 2021;40(6). doi:<a href=\"https://doi.org/10.1145/3478513.3480555\">10.1145/3478513.3480555</a>"},"quality_controlled":"1","scopus_import":"1","article_number":"272","has_accepted_license":"1","_id":"10184","file_date_updated":"2021-10-27T07:08:07Z","author":[{"last_name":"Alderighi","first_name":"Thomas","full_name":"Alderighi, Thomas"},{"last_name":"Malomo","first_name":"Luigi","full_name":"Malomo, Luigi"},{"full_name":"Bickel, Bernd","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"last_name":"Cignoni","first_name":"Paolo","full_name":"Cignoni, Paolo"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"}],"publisher":"Association for Computing Machinery","intvolume":"        40","isi":1,"type":"journal_article"},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","doi":"10.1038/s41467-021-26262-3","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Single photon emitters in atomically-thin semiconductors can be deterministically positioned using strain induced by underlying nano-structures. Here, we couple monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas providing both optical enhancement and monolayer deformation. For single photon emitters formed on such nano-antennas, we find very low (femto-Joule) saturation pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed on low-refractive-index SiO2 pillars. We show that the key to these observations is the increase on average by a factor of 5 of the quantum efficiency of the emitters coupled to the nano-antennas. This further allows us to gain new insights into their photoluminescence dynamics, revealing the roles of the dark exciton reservoir and Auger processes. We also find that the coherence time of such emitters is limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas as a platform for high-efficiency quantum light generation in monolayer semiconductors.","lang":"eng"}],"publication_status":"published","ddc":["530"],"date_published":"2021-10-18T00:00:00Z","status":"public","day":"18","file":[{"date_created":"2021-11-03T11:31:24Z","file_id":"10212","checksum":"8580d128389860f732028c521cd5949e","success":1,"file_name":"2021_NatComm_Sortino.pdf","file_size":1434201,"date_updated":"2021-11-03T11:31:24Z","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2023-08-14T08:12:12Z","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"date_created":"2021-10-31T23:01:30Z","acknowledgement":"L.S., P.G.Z., and A.I.T. thank the financial support of the European Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1. L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108. P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C., S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P., A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1. S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid (SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260.","article_processing_charge":"No","publication_identifier":{"eissn":["2041-1723"]},"department":[{"_id":"BjHo"}],"external_id":{"isi":["000708601800015"],"arxiv":["2103.16986"]},"title":"Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas","article_type":"original","volume":12,"year":"2021","publication":"Nature Communications","intvolume":"        12","publisher":"Springer Nature","type":"journal_article","isi":1,"has_accepted_license":"1","article_number":"6063","quality_controlled":"1","scopus_import":"1","citation":{"ieee":"L. Sortino <i>et al.</i>, “Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","mla":"Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” <i>Nature Communications</i>, vol. 12, 6063, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26262-3\">10.1038/s41467-021-26262-3</a>.","ista":"Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM, Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 12, 6063.","ama":"Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-26262-3\">10.1038/s41467-021-26262-3</a>","apa":"Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi, E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26262-3\">https://doi.org/10.1038/s41467-021-26262-3</a>","short":"L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi, A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12 (2021).","chicago":"Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash, Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza, and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26262-3\">https://doi.org/10.1038/s41467-021-26262-3</a>."},"author":[{"full_name":"Sortino, Luca","first_name":"Luca","last_name":"Sortino"},{"last_name":"Zotev","first_name":"Panaiot G.","full_name":"Zotev, Panaiot G."},{"full_name":"Phillips, Catherine L.","last_name":"Phillips","first_name":"Catherine L."},{"full_name":"Brash, Alistair J.","first_name":"Alistair J.","last_name":"Brash"},{"first_name":"Javier","last_name":"Cambiasso","full_name":"Cambiasso, Javier"},{"first_name":"Elena","last_name":"Marensi","id":"0BE7553A-1004-11EA-B805-18983DDC885E","orcid":"0000-0001-7173-4923","full_name":"Marensi, Elena"},{"first_name":"A. Mark","last_name":"Fox","full_name":"Fox, A. Mark"},{"full_name":"Maier, Stefan A.","last_name":"Maier","first_name":"Stefan A."},{"full_name":"Sapienza, Riccardo","last_name":"Sapienza","first_name":"Riccardo"},{"first_name":"Alexander I.","last_name":"Tartakovskii","full_name":"Tartakovskii, Alexander I."}],"_id":"10203","file_date_updated":"2021-11-03T11:31:24Z"},{"issue":"40","oa_version":"Submitted Version","date_updated":"2025-04-15T07:16:52Z","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"day":"20","file":[{"success":1,"file_size":4678788,"file_name":"2021_SoftMatter_acceptedversion_Osang.pdf","date_created":"2023-10-03T09:21:42Z","file_id":"14385","checksum":"b4da0c420530295e61b153960f6cb350","content_type":"application/pdf","relation":"main_file","date_updated":"2023-10-03T09:21:42Z","creator":"dernst","access_level":"open_access"}],"abstract":[{"text":"Two common representations of close packings of identical spheres consisting of hexagonal layers, called Barlow stackings, appear abundantly in minerals and metals. These motifs, however, occupy an identical portion of space and bear identical first-order topological signatures as measured by persistent homology. Here we present a novel method based on k-fold covers that unambiguously distinguishes between these patterns. Moreover, our approach provides topological evidence that the FCC motif is the more stable of the two in the context of evolving experimental sphere packings during the transition from disordered to an ordered state. We conclude that our approach can be generalised to distinguish between various Barlow stackings manifested in minerals and metals.","lang":"eng"}],"publication_status":"published","ddc":["540"],"date_published":"2021-10-20T00:00:00Z","status":"public","month":"10","doi":"10.1039/d1sm00774b","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","citation":{"chicago":"Osang, Georg F, Herbert Edelsbrunner, and Mohammad Saadatfar. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” <i>Soft Matter</i>. Royal Society of Chemistry , 2021. <a href=\"https://doi.org/10.1039/d1sm00774b\">https://doi.org/10.1039/d1sm00774b</a>.","short":"G.F. Osang, H. Edelsbrunner, M. Saadatfar, Soft Matter 17 (2021) 9107–9115.","apa":"Osang, G. F., Edelsbrunner, H., &#38; Saadatfar, M. (2021). Topological signatures and stability of hexagonal close packing and Barlow stackings. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/d1sm00774b\">https://doi.org/10.1039/d1sm00774b</a>","ama":"Osang GF, Edelsbrunner H, Saadatfar M. Topological signatures and stability of hexagonal close packing and Barlow stackings. <i>Soft Matter</i>. 2021;17(40):9107-9115. doi:<a href=\"https://doi.org/10.1039/d1sm00774b\">10.1039/d1sm00774b</a>","ieee":"G. F. Osang, H. Edelsbrunner, and M. Saadatfar, “Topological signatures and stability of hexagonal close packing and Barlow stackings,” <i>Soft Matter</i>, vol. 17, no. 40. Royal Society of Chemistry , pp. 9107–9115, 2021.","ista":"Osang GF, Edelsbrunner H, Saadatfar M. 2021. Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. 17(40), 9107–9115.","mla":"Osang, Georg F., et al. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” <i>Soft Matter</i>, vol. 17, no. 40, Royal Society of Chemistry , 2021, pp. 9107–15, doi:<a href=\"https://doi.org/10.1039/d1sm00774b\">10.1039/d1sm00774b</a>."},"author":[{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"first_name":"Mohammad","last_name":"Saadatfar","full_name":"Saadatfar, Mohammad"}],"_id":"10204","file_date_updated":"2023-10-03T09:21:42Z","intvolume":"        17","publisher":"Royal Society of Chemistry ","type":"journal_article","isi":1,"page":"9107-9115","external_id":{"pmid":["34569592"],"isi":["000700090000001"]},"article_type":"original","title":"Topological signatures and stability of hexagonal close packing and Barlow stackings","volume":17,"year":"2021","project":[{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183"},{"call_identifier":"FWF","grant_number":"Z00342","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"publication":"Soft Matter","date_created":"2021-10-31T23:01:30Z","acknowledgement":"MS acknowledges the support by Australian Research Council funding through the ARC Training Centre for M3D Innovation (IC180100008). MS thanks M. Hanifpour and N. Francois for their input and valuable discussions. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme, grant no. 788183 and from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","article_processing_charge":"No","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"department":[{"_id":"HeEd"}]},{"page":"42-61","related_material":{"record":[{"status":"public","id":"13234","relation":"extended_version"}]},"volume":"12974 ","title":"Into the unknown: active monitoring of neural networks","external_id":{"arxiv":["2009.06429"],"isi":["000719383800003"]},"publication":"21st International Conference on Runtime Verification","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"}],"year":"2021","place":"Cham","article_processing_charge":"No","date_created":"2021-10-31T23:01:31Z","acknowledgement":"We thank Christoph Lampert and Alex Greengold for fruitful discussions. This research was supported in part by the Simons Institute for the Theory of Computing, the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","publication_identifier":{"eisbn":["978-3-030-88494-9"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9-783-0308-8493-2"]},"conference":{"name":"RV: Runtime Verification","location":"Virtual","start_date":"2021-10-11","end_date":"2021-10-14"},"department":[{"_id":"ToHe"}],"scopus_import":"1","quality_controlled":"1","keyword":["monitoring","neural networks","novelty detection"],"citation":{"apa":"Lukina, A., Schilling, C., &#38; Henzinger, T. A. (2021). Into the unknown: active monitoring of neural networks. In <i>21st International Conference on Runtime Verification</i> (Vol. 12974, pp. 42–61). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">https://doi.org/10.1007/978-3-030-88494-9_3</a>","short":"A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.","chicago":"Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks.” In <i>21st International Conference on Runtime Verification</i>, 12974:42–61. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">https://doi.org/10.1007/978-3-030-88494-9_3</a>.","ista":"Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring of neural networks. 21st International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 42–61.","ieee":"A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring of neural networks,” in <i>21st International Conference on Runtime Verification</i>, Virtual, 2021, vol. 12974, pp. 42–61.","mla":"Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.” <i>21st International Conference on Runtime Verification</i>, vol. 12974, Springer Nature, 2021, pp. 42–61, doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">10.1007/978-3-030-88494-9_3</a>.","ama":"Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural networks. In: <i>21st International Conference on Runtime Verification</i>. Vol 12974. Cham: Springer Nature; 2021:42-61. doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">10.1007/978-3-030-88494-9_3</a>"},"_id":"10206","author":[{"full_name":"Lukina, Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","last_name":"Lukina","first_name":"Anna"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"publisher":"Springer Nature","isi":1,"type":"conference","publication_status":"published","abstract":[{"text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. The typical approach is to detect inputs from novel classes and retrain the classifier on an augmented dataset. However, not only the classifier but also the detection mechanism needs to adapt in order to distinguish between newly learned and yet unknown input classes. To address this challenge, we introduce an algorithmic framework for active monitoring of a neural network. A monitor wrapped in our framework operates in parallel with the neural network and interacts with a human user via a series of interpretable labeling queries for incremental adaptation. In addition, we propose an adaptive quantitative monitor to improve precision. An experimental evaluation on a diverse set of benchmarks with varying numbers of classes confirms the benefits of our active monitoring framework in dynamic scenarios.","lang":"eng"}],"date_published":"2021-10-06T00:00:00Z","status":"public","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/2009.06429","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1007/978-3-030-88494-9_3","oa_version":"Preprint","alternative_title":["LNCS"],"date_updated":"2025-04-15T06:26:14Z","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"ec_funded":1,"day":"06","corr_author":"1"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       209","type":"conference","citation":{"chicago":"Chatterjee, Bapi, Sathya Peri, and Muktikanta Sa. “Brief Announcement: Non-Blocking Dynamic Unbounded Graphs with Worst-Case Amortized Bounds.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">https://doi.org/10.4230/LIPIcs.DISC.2021.52</a>.","apa":"Chatterjee, B., Peri, S., &#38; Sa, M. (2021). Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">https://doi.org/10.4230/LIPIcs.DISC.2021.52</a>","short":"B. Chatterjee, S. Peri, M. Sa, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","ama":"Chatterjee B, Peri S, Sa M. Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">10.4230/LIPIcs.DISC.2021.52</a>","mla":"Chatterjee, Bapi, et al. “Brief Announcement: Non-Blocking Dynamic Unbounded Graphs with Worst-Case Amortized Bounds.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 52, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">10.4230/LIPIcs.DISC.2021.52</a>.","ieee":"B. Chatterjee, S. Peri, and M. Sa, “Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","ista":"Chatterjee B, Peri S, Sa M. 2021. Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds. 35th International Symposium on Distributed Computing. DISC: Distributed Computing, LIPIcs, vol. 209, 52."},"has_accepted_license":"1","article_number":"52","scopus_import":"1","quality_controlled":"1","author":[{"full_name":"Chatterjee, Bapi","first_name":"Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-2742-4028"},{"first_name":"Sathya","last_name":"Peri","full_name":"Peri, Sathya"},{"first_name":"Muktikanta","last_name":"Sa","full_name":"Sa, Muktikanta"}],"_id":"10216","file_date_updated":"2021-11-12T09:23:22Z","publication_identifier":{"isbn":["9-783-9597-7210-5"],"issn":["1868-8969"]},"date_created":"2021-11-07T23:01:23Z","acknowledgement":"This work was partially funded by National Supercomputing Mission, Govt. of India under the project “Concurrent and Distributed Programming primitives and algorithms for Temporal Graphs”(DST/NSM/R&D_Exascale/2021/16).\r\n","article_processing_charge":"No","department":[{"_id":"DaAl"}],"conference":{"location":"Freiburg, Germany","start_date":"2021-10-04","end_date":"2021-10-08","name":"DISC: Distributed Computing"},"year":"2021","publication":"35th International Symposium on Distributed Computing","external_id":{"arxiv":["2003.01697"]},"title":"Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds","volume":209,"day":"04","file":[{"creator":"cchlebak","access_level":"open_access","date_updated":"2021-11-12T09:23:22Z","content_type":"application/pdf","relation":"main_file","checksum":"76546df112a0ba1166c864d33d7834e2","date_created":"2021-11-12T09:23:22Z","file_id":"10276","success":1,"file_size":795860,"file_name":"2021_LIPIcsDISC_BChatterjee.pdf"}],"arxiv":1,"oa_version":"Published Version","date_updated":"2025-05-14T10:54:39Z","alternative_title":["LIPIcs"],"language":[{"iso":"eng"}],"oa":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","doi":"10.4230/LIPIcs.DISC.2021.52","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"This paper reports a new concurrent graph data structure that supports updates of both edges and vertices and queries: Breadth-first search, Single-source shortest-path, and Betweenness centrality. The operations are provably linearizable and non-blocking.","lang":"eng"}],"publication_status":"published","ddc":["000"],"status":"public","date_published":"2021-10-04T00:00:00Z"},{"title":"Lower bounds for shared-memory leader election under bounded write contention","volume":209,"year":"2021","project":[{"name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223"}],"publication":"35th International Symposium on Distributed Computing","date_created":"2021-11-07T23:01:23Z","acknowledgement":"Dan Alistarh: Supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Giorgi Nadiradze: Supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). The authors would like to thank the DISC anonymous reviewers for their useful\r\nfeedback and comments.","article_processing_charge":"No","publication_identifier":{"issn":["1868-8969"],"isbn":["9-783-9597-7210-5"]},"conference":{"location":"Freiburg, Germany","start_date":"2021-10-04","end_date":"2021-10-08","name":"DISC: Distributed Computing"},"department":[{"_id":"DaAl"}],"has_accepted_license":"1","article_number":"4","scopus_import":"1","quality_controlled":"1","citation":{"chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Giorgi Nadiradze. “Lower Bounds for Shared-Memory Leader Election under Bounded Write Contention.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">https://doi.org/10.4230/LIPIcs.DISC.2021.4</a>.","apa":"Alistarh, D.-A., Gelashvili, R., &#38; Nadiradze, G. (2021). Lower bounds for shared-memory leader election under bounded write contention. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">https://doi.org/10.4230/LIPIcs.DISC.2021.4</a>","short":"D.-A. Alistarh, R. Gelashvili, G. Nadiradze, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","ama":"Alistarh D-A, Gelashvili R, Nadiradze G. Lower bounds for shared-memory leader election under bounded write contention. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">10.4230/LIPIcs.DISC.2021.4</a>","ieee":"D.-A. Alistarh, R. Gelashvili, and G. Nadiradze, “Lower bounds for shared-memory leader election under bounded write contention,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","mla":"Alistarh, Dan-Adrian, et al. “Lower Bounds for Shared-Memory Leader Election under Bounded Write Contention.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 4, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">10.4230/LIPIcs.DISC.2021.4</a>.","ista":"Alistarh D-A, Gelashvili R, Nadiradze G. 2021. Lower bounds for shared-memory leader election under bounded write contention. 35th International Symposium on Distributed Computing. DISC: Distributed Computing, LIPIcs, vol. 209, 4."},"author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","first_name":"Giorgi"}],"_id":"10217","file_date_updated":"2021-11-12T09:33:26Z","intvolume":"       209","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","type":"conference","abstract":[{"text":"This paper gives tight logarithmic lower bounds on the solo step complexity of leader election in an asynchronous shared-memory model with single-writer multi-reader (SWMR) registers, for both deterministic and randomized obstruction-free algorithms. The approach extends to lower bounds for deterministic and randomized obstruction-free algorithms using multi-writer registers under bounded write concurrency, showing a trade-off between the solo step complexity of a leader election algorithm, and the worst-case number of stalls incurred by a processor in an execution.","lang":"eng"}],"publication_status":"published","ddc":["000"],"date_published":"2021-10-04T00:00:00Z","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","doi":"10.4230/LIPIcs.DISC.2021.4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-05-14T10:54:30Z","alternative_title":["LIPIcs"],"oa_version":"Published Version","ec_funded":1,"oa":1,"language":[{"iso":"eng"}],"day":"04","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2021-11-12T09:33:26Z","access_level":"open_access","creator":"cchlebak","file_size":706791,"file_name":"2021_LIPIcsDISC_Alistarh.pdf","success":1,"file_id":"10277","date_created":"2021-11-12T09:33:26Z","checksum":"b4cdc6668c899a601c5e6a96b8ca54d9"}]},{"date_created":"2021-11-07T23:01:24Z","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 840605.","article_processing_charge":"No","publication_identifier":{"issn":["1868-8969"],"isbn":["9-783-9597-7210-5"]},"conference":{"location":"Freiburg, Germany","start_date":"2021-10-04","end_date":"2021-10-08","name":"DISC: Distributed Computing "},"department":[{"_id":"DaAl"}],"external_id":{"arxiv":["2102.08808"]},"title":"Brief announcement: Fast graphical population protocols","volume":209,"year":"2021","project":[{"call_identifier":"H2020","grant_number":"840605","name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425"}],"publication":"35th International Symposium on Distributed Computing","intvolume":"       209","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","type":"conference","has_accepted_license":"1","scopus_import":"1","article_number":"43","quality_controlled":"1","citation":{"apa":"Alistarh, D.-A., Gelashvili, R., &#38; Rybicki, J. (2021). Brief announcement: Fast graphical population protocols. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">https://doi.org/10.4230/LIPIcs.DISC.2021.43</a>","short":"D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Brief Announcement: Fast Graphical Population Protocols.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">https://doi.org/10.4230/LIPIcs.DISC.2021.43</a>.","ista":"Alistarh D-A, Gelashvili R, Rybicki J. 2021. Brief announcement: Fast graphical population protocols. 35th International Symposium on Distributed Computing. DISC: Distributed Computing , LIPIcs, vol. 209, 43.","ieee":"D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Brief announcement: Fast graphical population protocols,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","mla":"Alistarh, Dan-Adrian, et al. “Brief Announcement: Fast Graphical Population Protocols.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 43, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">10.4230/LIPIcs.DISC.2021.43</a>.","ama":"Alistarh D-A, Gelashvili R, Rybicki J. Brief announcement: Fast graphical population protocols. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">10.4230/LIPIcs.DISC.2021.43</a>"},"author":[{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel","full_name":"Rybicki, Joel"}],"_id":"10218","file_date_updated":"2021-11-12T08:16:44Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","doi":"10.4230/LIPIcs.DISC.2021.43","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","abstract":[{"lang":"eng","text":"Let G be a graph on n nodes. In the stochastic population protocol model, a collection of n indistinguishable, resource-limited nodes collectively solve tasks via pairwise interactions. In each interaction, two randomly chosen neighbors first read each other’s states, and then update their local states. A rich line of research has established tight upper and lower bounds on the complexity of fundamental tasks, such as majority and leader election, in this model, when G is a clique. Specifically, in the clique, these tasks can be solved fast, i.e., in n polylog n pairwise interactions, with high probability, using at most polylog n states per node. In this work, we consider the more general setting where G is an arbitrary graph, and present a technique for simulating protocols designed for fully-connected networks in any connected regular graph. Our main result is a simulation that is efficient on many interesting graph families: roughly, the simulation overhead is polylogarithmic in the number of nodes, and quadratic in the conductance of the graph. As an example, this implies that, in any regular graph with conductance φ, both leader election and exact majority can be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability, using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast and space-efficient population protocols for leader election and exact majority on graphs with good expansion properties."}],"ddc":["000"],"date_published":"2021-10-04T00:00:00Z","status":"public","day":"04","file":[{"date_updated":"2021-11-12T08:16:44Z","creator":"cchlebak","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2021-11-12T08:16:44Z","file_id":"10274","checksum":"fd2a690f6856d21247e9aa952b0e2885","success":1,"file_name":"2021_LIPIcsDISC_Alistarh.pdf","file_size":534219}],"date_updated":"2025-04-14T07:50:55Z","oa_version":"Published Version","alternative_title":["LIPIcs"],"arxiv":1,"oa":1,"ec_funded":1,"language":[{"iso":"eng"}]},{"doi":"10.4230/LIPIcs.DISC.2021.58","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","date_published":"2021-10-04T00:00:00Z","status":"public","publication_status":"published","abstract":[{"text":"We show that any algorithm that solves the sinkless orientation problem in the supported LOCAL model requires Ω(log n) rounds, and this is tight. The supported LOCAL is at least as strong as the usual LOCAL model, and as a corollary this also gives a new, short and elementary proof that shows that the round complexity of the sinkless orientation problem in the deterministic LOCAL model is Ω(log n).","lang":"eng"}],"ddc":["000"],"file":[{"date_updated":"2021-11-12T08:27:42Z","access_level":"open_access","creator":"cchlebak","relation":"main_file","content_type":"application/pdf","file_id":"10275","date_created":"2021-11-12T08:27:42Z","checksum":"c43188dc2070bbd2bf5fd6fdaf9ce36d","file_name":"2021_LIPIcsDISC_Korhonen.pdf","file_size":474242,"success":1}],"day":"04","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"oa_version":"Published Version","date_updated":"2025-05-14T10:54:13Z","alternative_title":["LIPIcs"],"arxiv":1,"conference":{"location":"Freiburg, Germany","start_date":"2021-10-04","end_date":"2021-10-08","name":"DISC: Distributed Computing "},"department":[{"_id":"DaAl"}],"acknowledgement":"Janne H. Korhonen: Project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Ami Paz: We acknowledge the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N. Stefan Schmid: Research supported by the Austrian Science Fund (FWF) project ADVISE, I 4800-N, 2020-2023.\r\n","date_created":"2021-11-07T23:01:24Z","article_processing_charge":"No","publication_identifier":{"isbn":["9-783-9597-7210-5"],"issn":["1868-8969"]},"title":"Brief announcement: Sinkless orientation is hard also in the supported LOCAL model","external_id":{"arxiv":["2108.02655"]},"volume":209,"year":"2021","publication":"35th International Symposium on Distributed Computing","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020"}],"type":"conference","intvolume":"       209","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Korhonen","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne","full_name":"Korhonen, Janne"},{"full_name":"Paz, Ami","first_name":"Ami","last_name":"Paz"},{"full_name":"Rybicki, Joel","first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","orcid":"0000-0002-6432-6646"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"}],"file_date_updated":"2021-11-12T08:27:42Z","_id":"10219","has_accepted_license":"1","quality_controlled":"1","article_number":"58","scopus_import":"1","citation":{"apa":"Korhonen, J., Paz, A., Rybicki, J., Schmid, S., &#38; Suomela, J. (2021). Brief announcement: Sinkless orientation is hard also in the supported LOCAL model. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">https://doi.org/10.4230/LIPIcs.DISC.2021.58</a>","short":"J. Korhonen, A. Paz, J. Rybicki, S. Schmid, J. Suomela, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","chicago":"Korhonen, Janne, Ami Paz, Joel Rybicki, Stefan Schmid, and Jukka Suomela. “Brief Announcement: Sinkless Orientation Is Hard Also in the Supported LOCAL Model.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">https://doi.org/10.4230/LIPIcs.DISC.2021.58</a>.","ista":"Korhonen J, Paz A, Rybicki J, Schmid S, Suomela J. 2021. Brief announcement: Sinkless orientation is hard also in the supported LOCAL model. 35th International Symposium on Distributed Computing. DISC: Distributed Computing , LIPIcs, vol. 209, 58.","ieee":"J. Korhonen, A. Paz, J. Rybicki, S. Schmid, and J. Suomela, “Brief announcement: Sinkless orientation is hard also in the supported LOCAL model,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","mla":"Korhonen, Janne, et al. “Brief Announcement: Sinkless Orientation Is Hard Also in the Supported LOCAL Model.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 58, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">10.4230/LIPIcs.DISC.2021.58</a>.","ama":"Korhonen J, Paz A, Rybicki J, Schmid S, Suomela J. Brief announcement: Sinkless orientation is hard also in the supported LOCAL model. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">10.4230/LIPIcs.DISC.2021.58</a>"}},{"oa_version":"Preprint","date_updated":"2025-07-02T10:54:52Z","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"day":"30","corr_author":"1","publication_status":"published","abstract":[{"lang":"eng","text":"We study conditions under which a finite simplicial complex K can be mapped to ℝd without higher-multiplicity intersections. An almost r-embedding is a map f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on previous constructions of counterexamples (for d ≥ 3r) based on a series of papers by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite 2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection number of the f-images of any r pairwise disjoint simplices of K is zero. This result can be restated in terms of a cohomological obstruction and extends an analogous codimension 3 criterion by the second and fourth authors. As another application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for r = 2 is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample."}],"date_published":"2021-10-30T00:00:00Z","status":"public","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1511.03501","open_access":"1"}],"doi":"10.1007/s11856-021-2216-z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","scopus_import":"1","citation":{"ama":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity intersections. III. Codimension 2. <i>Israel Journal of Mathematics</i>. 2021;245:501–534. doi:<a href=\"https://doi.org/10.1007/s11856-021-2216-z\">10.1007/s11856-021-2216-z</a>","ieee":"S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections. III. Codimension 2,” <i>Israel Journal of Mathematics</i>, vol. 245. Springer Nature, pp. 501–534, 2021.","ista":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534.","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” <i>Israel Journal of Mathematics</i>, vol. 245, Springer Nature, 2021, pp. 501–534, doi:<a href=\"https://doi.org/10.1007/s11856-021-2216-z\">10.1007/s11856-021-2216-z</a>.","chicago":"Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” <i>Israel Journal of Mathematics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11856-021-2216-z\">https://doi.org/10.1007/s11856-021-2216-z</a>.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A. B., &#38; Wagner, U. (2021). Eliminating higher-multiplicity intersections. III. Codimension 2. <i>Israel Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11856-021-2216-z\">https://doi.org/10.1007/s11856-021-2216-z</a>","short":"S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 501–534."},"author":[{"first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7840-5062","full_name":"Avvakumov, Sergey"},{"first_name":"Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"},{"first_name":"Arkadiy B.","last_name":"Skopenkov","full_name":"Skopenkov, Arkadiy B."},{"last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","full_name":"Wagner, Uli"}],"_id":"10220","intvolume":"       245","publisher":"Springer Nature","type":"journal_article","isi":1,"page":"501–534 ","related_material":{"record":[{"relation":"earlier_version","id":"9308","status":"public"},{"relation":"earlier_version","id":"8183","status":"public"}]},"external_id":{"isi":["000712942100013"],"arxiv":["1511.03501"]},"title":"Eliminating higher-multiplicity intersections. III. Codimension 2","article_type":"original","volume":245,"year":"2021","publication":"Israel Journal of Mathematics","project":[{"call_identifier":"FWF","grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory","_id":"26611F5C-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"Research supported by the Swiss National Science Foundation (Project SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169), by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful comments and discussions.","date_created":"2021-11-07T23:01:24Z","article_processing_charge":"No","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"department":[{"_id":"UlWa"}]},{"author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio","full_name":"Cipolloni, Giorgio"},{"orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László"},{"orcid":"0000-0002-2904-1856","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"_id":"10221","file_date_updated":"2022-02-02T10:19:55Z","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Eigenstate thermalization hypothesis for Wigner matrices. <i>Communications in Mathematical Physics</i>. 2021;388(2):1005–1048. doi:<a href=\"https://doi.org/10.1007/s00220-021-04239-z\">10.1007/s00220-021-04239-z</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis for Wigner matrices,” <i>Communications in Mathematical Physics</i>, vol. 388, no. 2. Springer Nature, pp. 1005–1048, 2021.","mla":"Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” <i>Communications in Mathematical Physics</i>, vol. 388, no. 2, Springer Nature, 2021, pp. 1005–1048, doi:<a href=\"https://doi.org/10.1007/s00220-021-04239-z\">10.1007/s00220-021-04239-z</a>.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00220-021-04239-z\">https://doi.org/10.1007/s00220-021-04239-z</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Eigenstate thermalization hypothesis for Wigner matrices. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-021-04239-z\">https://doi.org/10.1007/s00220-021-04239-z</a>","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048."},"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","type":"journal_article","isi":1,"publisher":"Springer Nature","intvolume":"       388","year":"2021","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication":"Communications in Mathematical Physics","article_type":"original","external_id":{"arxiv":["2012.13215"],"isi":["000712232700001"]},"title":"Eigenstate thermalization hypothesis for Wigner matrices","volume":388,"page":"1005–1048","department":[{"_id":"LaEr"}],"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"date_created":"2021-11-07T23:01:25Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","article_processing_charge":"Yes (via OA deal)","oa":1,"language":[{"iso":"eng"}],"arxiv":1,"issue":"2","date_updated":"2025-04-15T06:53:08Z","oa_version":"Published Version","file":[{"checksum":"a2c7b6f5d23b5453cd70d1261272283b","file_id":"10715","date_created":"2022-02-02T10:19:55Z","file_name":"2021_CommunMathPhys_Cipolloni.pdf","file_size":841426,"success":1,"access_level":"open_access","creator":"cchlebak","date_updated":"2022-02-02T10:19:55Z","relation":"main_file","content_type":"application/pdf"}],"corr_author":"1","day":"29","status":"public","date_published":"2021-10-29T00:00:00Z","abstract":[{"text":"We prove that any deterministic matrix is approximately the identity in the eigenbasis of a large random Wigner matrix with very high probability and with an optimal error inversely proportional to the square root of the dimension. Our theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch (Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity (QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278, 2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020).","lang":"eng"}],"publication_status":"published","ddc":["510"],"doi":"10.1007/s00220-021-04239-z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10"},{"arxiv":1,"date_updated":"2025-04-15T07:45:32Z","oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"day":"25","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2023-08-14T11:55:10Z","file_name":"2023_ExperimentalMath_Akopyan.pdf","file_size":1966019,"success":1,"checksum":"3514382e3a1eb87fa6c61ad622874415","file_id":"14053","date_created":"2023-08-14T11:55:10Z"}],"corr_author":"1","abstract":[{"text":"Consider a random set of points on the unit sphere in ℝd, which can be either uniformly sampled or a Poisson point process. Its convex hull is a random inscribed polytope, whose boundary approximates the sphere. We focus on the case d = 3, for which there are elementary proofs and fascinating formulas for metric properties. In particular, we study the fraction of acute facets, the expected intrinsic volumes, the total edge length, and the distance to a fixed point. Finally we generalize the results to the ellipsoid with homeoid density.","lang":"eng"}],"publication_status":"published","ddc":["510"],"status":"public","date_published":"2021-10-25T00:00:00Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10","doi":"10.1080/10586458.2021.1980459","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed in the 2-sphere. <i>Experimental Mathematics</i>. 2021:1-15. doi:<a href=\"https://doi.org/10.1080/10586458.2021.1980459\">10.1080/10586458.2021.1980459</a>","ista":"Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics., 1–15.","mla":"Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” <i>Experimental Mathematics</i>, Taylor and Francis, 2021, pp. 1–15, doi:<a href=\"https://doi.org/10.1080/10586458.2021.1980459\">10.1080/10586458.2021.1980459</a>.","ieee":"A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes inscribed in the 2-sphere,” <i>Experimental Mathematics</i>. Taylor and Francis, pp. 1–15, 2021.","chicago":"Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” <i>Experimental Mathematics</i>. Taylor and Francis, 2021. <a href=\"https://doi.org/10.1080/10586458.2021.1980459\">https://doi.org/10.1080/10586458.2021.1980459</a>.","short":"A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021) 1–15.","apa":"Akopyan, A., Edelsbrunner, H., &#38; Nikitenko, A. (2021). The beauty of random polytopes inscribed in the 2-sphere. <i>Experimental Mathematics</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/10586458.2021.1980459\">https://doi.org/10.1080/10586458.2021.1980459</a>"},"has_accepted_license":"1","quality_controlled":"1","scopus_import":"1","author":[{"full_name":"Akopyan, Arseniy","first_name":"Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton"}],"_id":"10222","file_date_updated":"2023-08-14T11:55:10Z","publisher":"Taylor and Francis","type":"journal_article","isi":1,"page":"1-15","year":"2021","project":[{"call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended"},{"call_identifier":"FWF","grant_number":"Z00342","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Persistent Homology, Algorithms and Stochastic Geometry","grant_number":"I4887"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF"}],"publication":"Experimental Mathematics","article_type":"original","external_id":{"isi":["000710893500001"],"arxiv":["2007.07783"]},"title":"The beauty of random polytopes inscribed in the 2-sphere","publication_identifier":{"issn":["1058-6458"],"eissn":["1944-950X"]},"date_created":"2021-11-07T23:01:25Z","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and for directing us to relevant references. We also thank to Anton Mellit for a useful discussion on Bessel functions.","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"HeEd"}]},{"publication_status":"published","abstract":[{"text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments.","lang":"eng"}],"status":"public","date_published":"2021-11-11T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1038/s41586-021-04037-6","pmid":1,"date_updated":"2025-07-10T11:49:46Z","oa_version":"Preprint","issue":"7884","oa":1,"ec_funded":1,"language":[{"iso":"eng"}],"day":"11","corr_author":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10095"}],"link":[{"url":"https://ist.ac.at/en/news/stop-and-grow/","description":"News on IST Webpage","relation":"press_release"}]},"page":"273-277","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"},{"call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"publication":"Nature","year":"2021","volume":599,"title":"Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth","article_type":"original","external_id":{"isi":["000713338100006"],"pmid":["34707283"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"article_processing_charge":"No","date_created":"2021-11-07T23:01:25Z","acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"keyword":["Multidisciplinary"],"citation":{"chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. 2021;599(7884):273-277. doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth,” <i>Nature</i>, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. Nature. 599(7884), 273–277.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>."},"quality_controlled":"1","scopus_import":"1","_id":"10223","author":[{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia"},{"full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"full_name":"Chen, Jian","last_name":"Chen","first_name":"Jian"},{"full_name":"Shabala, Lana","first_name":"Lana","last_name":"Shabala"},{"full_name":"Smet, Wouter","last_name":"Smet","first_name":"Wouter"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Shabala","first_name":"Sergey","full_name":"Shabala, Sergey"},{"last_name":"De Rybel","first_name":"Bert","full_name":"De Rybel, Bert"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"last_name":"Kinoshita","first_name":"Toshinori","full_name":"Kinoshita, Toshinori"},{"first_name":"William M.","last_name":"Gray","full_name":"Gray, William M."},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","full_name":"Friml, Jiří"}],"publisher":"Springer Nature","intvolume":"       599","isi":1,"type":"journal_article"},{"author":[{"last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530","first_name":"Dario","full_name":"Feliciangeli, Dario"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert"}],"_id":"10224","file_date_updated":"2021-12-14T08:35:42Z","has_accepted_license":"1","scopus_import":"1","quality_controlled":"1","citation":{"chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00205-021-01715-7\">https://doi.org/10.1007/s00205-021-01715-7</a>.","apa":"Feliciangeli, D., &#38; Seiringer, R. (2021). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-021-01715-7\">https://doi.org/10.1007/s00205-021-01715-7</a>","short":"D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906.","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>Archive for Rational Mechanics and Analysis</i>. 2021;242(3):1835–1906. doi:<a href=\"https://doi.org/10.1007/s00205-021-01715-7\">10.1007/s00205-021-01715-7</a>","ieee":"D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.","ista":"Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 242(3), 1835–1906.","mla":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906, doi:<a href=\"https://doi.org/10.1007/s00205-021-01715-7\">10.1007/s00205-021-01715-7</a>."},"type":"journal_article","isi":1,"intvolume":"       242","publisher":"Springer Nature","title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","external_id":{"arxiv":["2101.12566"],"isi":["000710850600001"]},"article_type":"original","volume":242,"year":"2021","publication":"Archive for Rational Mechanics and Analysis","project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"page":"1835–1906","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9787"}]},"department":[{"_id":"RoSe"}],"date_created":"2021-11-07T23:01:26Z","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.7.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"language":[{"iso":"eng"}],"ec_funded":1,"oa":1,"issue":"3","oa_version":"Published Version","date_updated":"2025-04-14T09:11:09Z","arxiv":1,"file":[{"creator":"alisjak","access_level":"open_access","date_updated":"2021-12-14T08:35:42Z","content_type":"application/pdf","relation":"main_file","checksum":"672e9c21b20f1a50854b7c821edbb92f","date_created":"2021-12-14T08:35:42Z","file_id":"10544","success":1,"file_size":990529,"file_name":"2021_Springer_Feliciangeli.pdf"}],"day":"25","date_published":"2021-10-25T00:00:00Z","status":"public","publication_status":"published","abstract":[{"text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.","lang":"eng"}],"ddc":["530"],"doi":"10.1007/s00205-021-01715-7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"10"},{"abstract":[{"text":"Tropisms are among the most important growth responses for plant adaptation to the surrounding environment. One of the most common tropisms is root gravitropism. Root gravitropism enables the plant to anchor securely to the soil enabling the absorption of water and nutrients. Most of the knowledge related to the plant gravitropism has been acquired from the flowering plants, due to limited research in non-seed plants. Limited research on non-seed plants is due in large part to the lack of standard research methods. Here, we describe the experimental methods to evaluate gravitropism in representative non-seed plant species, including the non-vascular plant moss Physcomitrium patens, the early diverging extant vascular plant lycophyte Selaginella moellendorffii and fern Ceratopteris richardii. In addition, we introduce the methods used for statistical analysis of the root gravitropism in non-seed plant species.","lang":"eng"}],"publication_status":"published","date_published":"2021-10-14T00:00:00Z","status":"public","month":"10","pmid":1,"doi":"10.1007/978-1-0716-1677-2_2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","series_title":"MIMB","date_updated":"2025-04-14T07:45:00Z","oa_version":"None","alternative_title":["Methods in Molecular Biology"],"ec_funded":1,"language":[{"iso":"eng"}],"day":"14","corr_author":"1","page":"43-51","title":"Evaluation of gravitropism in non-seed plants","external_id":{"pmid":["34647246"]},"volume":2368,"year":"2021","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"publication":"Plant Gravitropism","date_created":"2021-11-11T09:26:10Z","acknowledgement":"The Ceratopteris richardii spores were obtained from the lab of Jo Ann Banks at Purdue University. This work was supported by funding from the European Union’s Horizon 2020 research and innovation program (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), IST Fellow program and DOC Fellowship of the Austrian Academy of Sciences.","article_processing_charge":"No","publication_identifier":{"isbn":["978-1-0716-1676-5"],"eisbn":["978-1-0716-1677-2"]},"department":[{"_id":"JiFr"}],"scopus_import":"1","quality_controlled":"1","citation":{"chicago":"Zhang, Yuzhou, Lanxin Li, and Jiří Friml. “Evaluation of Gravitropism in Non-Seed Plants.” In <i>Plant Gravitropism</i>, edited by Elison B Blancaflor, 2368:43–51. MIMB. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">https://doi.org/10.1007/978-1-0716-1677-2_2</a>.","apa":"Zhang, Y., Li, L., &#38; Friml, J. (2021). Evaluation of gravitropism in non-seed plants. In E. B. Blancaflor (Ed.), <i>Plant Gravitropism</i> (Vol. 2368, pp. 43–51). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">https://doi.org/10.1007/978-1-0716-1677-2_2</a>","short":"Y. Zhang, L. Li, J. Friml, in:, E.B. Blancaflor (Ed.), Plant Gravitropism, Springer Nature, 2021, pp. 43–51.","ama":"Zhang Y, Li L, Friml J. Evaluation of gravitropism in non-seed plants. In: Blancaflor EB, ed. <i>Plant Gravitropism</i>. Vol 2368. MIMB. Springer Nature; 2021:43-51. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">10.1007/978-1-0716-1677-2_2</a>","ieee":"Y. Zhang, L. Li, and J. Friml, “Evaluation of gravitropism in non-seed plants,” in <i>Plant Gravitropism</i>, vol. 2368, E. B. Blancaflor, Ed. Springer Nature, 2021, pp. 43–51.","mla":"Zhang, Yuzhou, et al. “Evaluation of Gravitropism in Non-Seed Plants.” <i>Plant Gravitropism</i>, edited by Elison B Blancaflor, vol. 2368, Springer Nature, 2021, pp. 43–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">10.1007/978-1-0716-1677-2_2</a>.","ista":"Zhang Y, Li L, Friml J. 2021.Evaluation of gravitropism in non-seed plants. In: Plant Gravitropism. Methods in Molecular Biology, vol. 2368, 43–51."},"author":[{"full_name":"Zhang, Yuzhou","first_name":"Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang"},{"full_name":"Li, Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Lanxin"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"_id":"10267","intvolume":"      2368","editor":[{"full_name":"Blancaflor, Elison B","last_name":"Blancaflor","first_name":"Elison B"}],"publisher":"Springer Nature","type":"book_chapter"},{"author":[{"full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","orcid":"0000-0003-0619-7783","first_name":"Matous"}],"_id":"10268","citation":{"ieee":"L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,” in <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–114.","ista":"Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.","mla":"Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–14, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>.","ama":"Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: <i>Plant Cell Division</i>. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>","apa":"Hörmayer, L., Friml, J., &#38; Glanc, M. (2021). Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In <i>Plant Cell Division</i> (Vol. 2382, pp. 105–114). Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>","short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114.","chicago":"Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” In <i>Plant Cell Division</i>, 2382:105–14. MIMB. Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>."},"quality_controlled":"1","scopus_import":"1","type":"book_chapter","publisher":"Humana Press","intvolume":"      2382","year":"2021","publication":"Plant Cell Division","external_id":{"pmid":["34705235"]},"title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","volume":2382,"page":"105-114","department":[{"_id":"JiFr"}],"acknowledged_ssus":[{"_id":"Bio"}],"publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"eisbn":["978-1-0716-1744-1"],"isbn":["978-1-0716-1743-4"]},"date_created":"2021-11-11T10:03:30Z","acknowledgement":"We thank B. De Rybel for allowing M.G. to work on this manuscript during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading and correcting the manuscript.","article_processing_charge":"No","language":[{"iso":"eng"}],"series_title":"MIMB","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","date_updated":"2022-06-03T06:47:06Z","day":"28","status":"public","date_published":"2021-10-28T00:00:00Z","publication_status":"published","abstract":[{"text":"The analysis of dynamic cellular processes such as plant cytokinesis stands and falls with live-cell time-lapse confocal imaging. Conventional approaches to time-lapse imaging of cell division in Arabidopsis root tips are tedious and have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous imaging of multiple root tips on a vertical-stage confocal microscope with automated root tracking. We also provide modifications of the basic protocol to implement this imaging method in the analysis of genetic, pharmacological or laser ablation wounding-mediated experimental manipulations. Our method dramatically improves the efficiency of cell division time-lapse imaging by increasing the throughput, while reducing the person-hour requirements of such experiments.","lang":"eng"}],"pmid":1,"doi":"10.1007/978-1-0716-1744-1_6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10"}]