[{"file":[{"date_created":"2020-11-18T07:26:10Z","date_updated":"2020-11-18T07:26:10Z","success":1,"file_name":"2020_PlosCompBio_Kaveh.pdf","checksum":"555456dd0e47bcf9e0994bcb95577e88","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8768","creator":"dernst","file_size":2498594}],"title":"The Moran process on 2-chromatic graphs","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Kaveh, Kamran","first_name":"Kamran","last_name":"Kaveh"},{"full_name":"McAvoy, Alex","last_name":"McAvoy","first_name":"Alex"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"publisher":"Public Library of Science","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"article_processing_charge":"No","quality_controlled":"1","_id":"8767","file_date_updated":"2020-11-18T07:26:10Z","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Resources are rarely distributed uniformly within a population. Heterogeneity in the concentration of a drug, the quality of breeding sites, or wealth can all affect evolutionary dynamics. In this study, we represent a collection of properties affecting the fitness at a given location using a color. A green node is rich in resources while a red node is poorer. More colors can represent a broader spectrum of resource qualities. For a population evolving according to the birth-death Moran model, the first question we address is which structures, identified by graph connectivity and graph coloring, are evolutionarily equivalent. We prove that all properly two-colored, undirected, regular graphs are evolutionarily equivalent (where “properly colored” means that no two neighbors have the same color). We then compare the effects of background heterogeneity on properly two-colored graphs to those with alternative schemes in which the colors are permuted. Finally, we discuss dynamic coloring as a model for spatiotemporal resource fluctuations, and we illustrate that random dynamic colorings often diminish the effects of background heterogeneity relative to a proper two-coloring."}],"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"citation":{"ieee":"K. Kaveh, A. McAvoy, K. Chatterjee, and M. A. Nowak, “The Moran process on 2-chromatic graphs,” <i>PLOS Computational Biology</i>, vol. 16, no. 11. Public Library of Science, 2020.","short":"K. Kaveh, A. McAvoy, K. Chatterjee, M.A. Nowak, PLOS Computational Biology 16 (2020).","ista":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. 2020. The Moran process on 2-chromatic graphs. PLOS Computational Biology. 16(11), e1008402.","ama":"Kaveh K, McAvoy A, Chatterjee K, Nowak MA. The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. 2020;16(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>","chicago":"Kaveh, Kamran, Alex McAvoy, Krishnendu Chatterjee, and Martin A. Nowak. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>.","apa":"Kaveh, K., McAvoy, A., Chatterjee, K., &#38; Nowak, M. A. (2020). The Moran process on 2-chromatic graphs. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">https://doi.org/10.1371/journal.pcbi.1008402</a>","mla":"Kaveh, Kamran, et al. “The Moran Process on 2-Chromatic Graphs.” <i>PLOS Computational Biology</i>, vol. 16, no. 11, e1008402, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008402\">10.1371/journal.pcbi.1008402</a>."},"publication_status":"published","issue":"11","oa":1,"date_updated":"2023-08-22T12:49:18Z","keyword":["Ecology","Modelling and Simulation","Computational Theory and Mathematics","Genetics","Ecology","Evolution","Behavior and Systematics","Molecular Biology","Cellular and Molecular Neuroscience"],"acknowledgement":"We thank Igor Erovenko for many helpful comments on an earlier version of this paper. : Army Research Laboratory (grant W911NF-18-2-0265) (M.A.N.); the Bill & Melinda Gates Foundation (grant OPP1148627) (M.A.N.); the NVIDIA Corporation (A.M.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","article_number":"e1008402","intvolume":"        16","month":"11","date_published":"2020-11-05T00:00:00Z","year":"2020","license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"isi":["000591317200004"]},"status":"public","day":"05","date_created":"2020-11-18T07:20:23Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"volume":16,"isi":1,"oa_version":"Published Version","doi":"10.1371/journal.pcbi.1008402","publication":"PLOS Computational Biology"},{"publisher":"American Physical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Yakaboylu, Enderalp","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"first_name":"D.","last_name":"Lundholm","full_name":"Lundholm, D."},{"full_name":"Rougerie, N.","first_name":"N.","last_name":"Rougerie"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"title":"Quantum impurity model for anyons","article_processing_charge":"No","department":[{"_id":"MiLe"},{"_id":"RoSe"}],"language":[{"iso":"eng"}],"article_type":"original","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"citation":{"mla":"Yakaboylu, Enderalp, et al. “Quantum Impurity Model for Anyons.” <i>Physical Review B</i>, vol. 102, no. 14, 144109, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.102.144109\">10.1103/physrevb.102.144109</a>.","apa":"Yakaboylu, E., Ghazaryan, A., Lundholm, D., Rougerie, N., Lemeshko, M., &#38; Seiringer, R. (2020). Quantum impurity model for anyons. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.102.144109\">https://doi.org/10.1103/physrevb.102.144109</a>","chicago":"Yakaboylu, Enderalp, Areg Ghazaryan, D. Lundholm, N. Rougerie, Mikhail Lemeshko, and Robert Seiringer. “Quantum Impurity Model for Anyons.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevb.102.144109\">https://doi.org/10.1103/physrevb.102.144109</a>.","ama":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. Quantum impurity model for anyons. <i>Physical Review B</i>. 2020;102(14). doi:<a href=\"https://doi.org/10.1103/physrevb.102.144109\">10.1103/physrevb.102.144109</a>","ieee":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, and R. Seiringer, “Quantum impurity model for anyons,” <i>Physical Review B</i>, vol. 102, no. 14. American Physical Society, 2020.","short":"E. Yakaboylu, A. Ghazaryan, D. Lundholm, N. Rougerie, M. Lemeshko, R. Seiringer, Physical Review B 102 (2020).","ista":"Yakaboylu E, Ghazaryan A, Lundholm D, Rougerie N, Lemeshko M, Seiringer R. 2020. Quantum impurity model for anyons. Physical Review B. 102(14), 144109."},"scopus_import":"1","abstract":[{"text":"One of the hallmarks of quantum statistics, tightly entwined with the concept of topological phases of matter, is the prediction of anyons. Although anyons are predicted to be realized in certain fractional quantum Hall systems, they have not yet been unambiguously detected in experiment. Here we introduce a simple quantum impurity model, where bosonic or fermionic impurities turn into anyons as a consequence of their interaction with the surrounding many-particle bath. A cloud of phonons dresses each impurity in such a way that it effectively attaches fluxes or vortices to it and thereby converts it into an Abelian anyon. The corresponding quantum impurity model, first, provides a different approach to the numerical solution of the many-anyon problem, along with a concrete perspective of anyons as emergent quasiparticles built from composite bosons or fermions. More importantly, the model paves the way toward realizing anyons using impurities in crystal lattices as well as ultracold gases. In particular, we consider two heavy electrons interacting with a two-dimensional lattice crystal in a magnetic field, and show that when the impurity-bath system is rotated at the cyclotron frequency, impurities behave as anyons as a consequence of the angular momentum exchange between the impurities and the bath. A possible experimental realization is proposed by identifying the statistics parameter in terms of the mean-square distance of the impurities and the magnetization of the impurity-bath system, both of which are accessible to experiment. Another proposed application is impurities immersed in a two-dimensional weakly interacting Bose gas.","lang":"eng"}],"arxiv":1,"type":"journal_article","_id":"8769","quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020"}],"publication_status":"published","date_published":"2020-10-01T00:00:00Z","month":"10","intvolume":"       102","acknowledgement":"We are grateful to M. Correggi, A. Deuchert, and P. Schmelcher for valuable discussions. We also thank the anonymous referees for helping to clarify a few important points in the experimental realization. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement\r\nNo 754411. D.L. acknowledges financial support from the Goran Gustafsson Foundation (grant no. 1804) and LMU Munich. R.S., M.L., and N.R. gratefully acknowledge financial support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 694227, No 801770, and No 758620, respectively).","article_number":"144109","date_updated":"2023-09-05T12:12:30Z","oa":1,"issue":"14","external_id":{"isi":["000582563300001"],"arxiv":["1912.07890"]},"year":"2020","volume":102,"date_created":"2020-11-18T07:34:17Z","day":"01","status":"public","publication":"Physical Review B","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.07890"}],"doi":"10.1103/physrevb.102.144109","ec_funded":1,"oa_version":"Preprint","isi":1},{"publisher":"Springer Nature","has_accepted_license":"1","file":[{"file_id":"8798","content_type":"application/pdf","creator":"dernst","file_size":7035340,"access_level":"open_access","relation":"main_file","checksum":"485b7b6cf30198ba0ce126491a28f125","success":1,"file_name":"2020_NatureComm_Nicolai.pdf","date_created":"2020-11-23T13:29:49Z","date_updated":"2020-11-23T13:29:49Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Vascular surveillance by haptotactic blood platelets in inflammation and infection","author":[{"full_name":"Nicolai, Leo","last_name":"Nicolai","first_name":"Leo"},{"full_name":"Schiefelbein, Karin","first_name":"Karin","last_name":"Schiefelbein"},{"full_name":"Lipsky, Silvia","last_name":"Lipsky","first_name":"Silvia"},{"first_name":"Alexander","last_name":"Leunig","full_name":"Leunig, Alexander"},{"full_name":"Hoffknecht, Marie","last_name":"Hoffknecht","first_name":"Marie"},{"first_name":"Kami","last_name":"Pekayvaz","full_name":"Pekayvaz, Kami"},{"last_name":"Raude","first_name":"Ben","full_name":"Raude, Ben"},{"full_name":"Marx, Charlotte","last_name":"Marx","first_name":"Charlotte"},{"full_name":"Ehrlich, Andreas","last_name":"Ehrlich","first_name":"Andreas"},{"full_name":"Pircher, Joachim","last_name":"Pircher","first_name":"Joachim"},{"full_name":"Zhang, Zhe","first_name":"Zhe","last_name":"Zhang"},{"last_name":"Saleh","first_name":"Inas","full_name":"Saleh, Inas"},{"last_name":"Marel","first_name":"Anna-Kristina","full_name":"Marel, Anna-Kristina"},{"full_name":"Löf, Achim","last_name":"Löf","first_name":"Achim"},{"first_name":"Tobias","last_name":"Petzold","full_name":"Petzold, Tobias"},{"full_name":"Lorenz, Michael","first_name":"Michael","last_name":"Lorenz"},{"last_name":"Stark","first_name":"Konstantin","full_name":"Stark, Konstantin"},{"first_name":"Robert","last_name":"Pick","full_name":"Pick, Robert"},{"full_name":"Rosenberger, Gerhild","first_name":"Gerhild","last_name":"Rosenberger"},{"first_name":"Ludwig","last_name":"Weckbach","full_name":"Weckbach, Ludwig"},{"last_name":"Uhl","first_name":"Bernd","full_name":"Uhl, Bernd"},{"full_name":"Xia, Sheng","last_name":"Xia","first_name":"Sheng"},{"full_name":"Reichel, Christoph Andreas","last_name":"Reichel","first_name":"Christoph Andreas"},{"first_name":"Barbara","last_name":"Walzog","full_name":"Walzog, Barbara"},{"full_name":"Schulz, Christian","last_name":"Schulz","first_name":"Christian"},{"full_name":"Zheden, Vanessa","last_name":"Zheden","orcid":"0000-0002-9438-4783","first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bender, Markus","last_name":"Bender","first_name":"Markus"},{"full_name":"Li, Rong","last_name":"Li","first_name":"Rong"},{"first_name":"Steffen","last_name":"Massberg","full_name":"Massberg, Steffen"},{"orcid":"0000-0001-6120-3723","last_name":"Gärtner","first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","full_name":"Gärtner, Florian R"}],"department":[{"_id":"MiSi"},{"_id":"EM-Fac"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2020-11-23T13:29:49Z","type":"journal_article","abstract":[{"text":"Breakdown of vascular barriers is a major complication of inflammatory diseases. Anucleate platelets form blood-clots during thrombosis, but also play a crucial role in inflammation. While spatio-temporal dynamics of clot formation are well characterized, the cell-biological mechanisms of platelet recruitment to inflammatory micro-environments remain incompletely understood. Here we identify Arp2/3-dependent lamellipodia formation as a prominent morphological feature of immune-responsive platelets. Platelets use lamellipodia to scan for fibrin(ogen) deposited on the inflamed vasculature and to directionally spread, to polarize and to govern haptotactic migration along gradients of the adhesive ligand. Platelet-specific abrogation of Arp2/3 interferes with haptotactic repositioning of platelets to microlesions, thus impairing vascular sealing and provoking inflammatory microbleeding. During infection, haptotaxis promotes capture of bacteria and prevents hematogenic dissemination, rendering platelets gate-keepers of the inflamed microvasculature. Consequently, these findings identify haptotaxis as a key effector function of immune-responsive platelets.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["20411723"]},"citation":{"chicago":"Nicolai, Leo, Karin Schiefelbein, Silvia Lipsky, Alexander Leunig, Marie Hoffknecht, Kami Pekayvaz, Ben Raude, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-19515-0\">https://doi.org/10.1038/s41467-020-19515-0</a>.","ama":"Nicolai L, Schiefelbein K, Lipsky S, et al. Vascular surveillance by haptotactic blood platelets in inflammation and infection. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-19515-0\">10.1038/s41467-020-19515-0</a>","ieee":"L. Nicolai <i>et al.</i>, “Vascular surveillance by haptotactic blood platelets in inflammation and infection,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","ista":"Nicolai L, Schiefelbein K, Lipsky S, Leunig A, Hoffknecht M, Pekayvaz K, Raude B, Marx C, Ehrlich A, Pircher J, Zhang Z, Saleh I, Marel A-K, Löf A, Petzold T, Lorenz M, Stark K, Pick R, Rosenberger G, Weckbach L, Uhl B, Xia S, Reichel CA, Walzog B, Schulz C, Zheden V, Bender M, Li R, Massberg S, Gärtner FR. 2020. Vascular surveillance by haptotactic blood platelets in inflammation and infection. Nature Communications. 11, 5778.","short":"L. Nicolai, K. Schiefelbein, S. Lipsky, A. Leunig, M. Hoffknecht, K. Pekayvaz, B. Raude, C. Marx, A. Ehrlich, J. Pircher, Z. Zhang, I. Saleh, A.-K. Marel, A. Löf, T. Petzold, M. Lorenz, K. Stark, R. Pick, G. Rosenberger, L. Weckbach, B. Uhl, S. Xia, C.A. Reichel, B. Walzog, C. Schulz, V. Zheden, M. Bender, R. Li, S. Massberg, F.R. Gärtner, Nature Communications 11 (2020).","mla":"Nicolai, Leo, et al. “Vascular Surveillance by Haptotactic Blood Platelets in Inflammation and Infection.” <i>Nature Communications</i>, vol. 11, 5778, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-19515-0\">10.1038/s41467-020-19515-0</a>.","apa":"Nicolai, L., Schiefelbein, K., Lipsky, S., Leunig, A., Hoffknecht, M., Pekayvaz, K., … Gärtner, F. R. (2020). Vascular surveillance by haptotactic blood platelets in inflammation and infection. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-19515-0\">https://doi.org/10.1038/s41467-020-19515-0</a>"},"quality_controlled":"1","_id":"8787","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We thank Sebastian Helmer, Nicole Blount, Christine Mann, and Beate Jantz for technical assistance; Hellen Ishikawa-Ankerhold for help and advice; Michael Sixt for critical\r\ndiscussions. This study was supported by the DFG SFB 914 (S.M. [B02 and Z01], K.Sch.\r\n[B02], B.W. [A02 and Z03], C.A.R. [B03], C.S. [A10], J.P. [Gerok position]), the DFG\r\nSFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Center for\r\nCardiovascular Research (DZHK) (Clinician Scientist Program [L.N.], MHA 1.4VD\r\n[S.M.], Postdoc Start-up Grant, 81×3600213 [F.G.]), FP7 program (project 260309,\r\nPRESTIGE [S.M.]), FöFoLe project 1015/1009 (L.N.), FöFoLe project 947 (F.G.), the\r\nFriedrich-Baur-Stiftung project 41/16 (F.G.), and LMUexcellence NFF (F.G.). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no.\r\n833440) (S.M.). F.G. received funding from the European Union’s Horizon 2020 research\r\nand innovation program under the Marie Skłodowska-Curie grant agreement no.\r\n747687.","article_number":"5778","month":"11","intvolume":"        11","date_published":"2020-11-13T00:00:00Z","oa":1,"date_updated":"2023-08-22T13:26:26Z","external_id":{"isi":["000594648000014"],"pmid":["33188196"]},"year":"2020","pmid":1,"volume":11,"status":"public","day":"13","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-11-22T23:01:23Z","doi":"10.1038/s41467-020-19515-0","publication":"Nature Communications","isi":1,"oa_version":"Published Version","ec_funded":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-31310-7"}]}},{"author":[{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"full_name":"Schaumberger, Nico","first_name":"Nico","last_name":"Schaumberger"},{"last_name":"Schmid","first_name":"Ulrich","full_name":"Schmid, Ulrich"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"title":"Precedence-aware automated competitive analysis of real-time scheduling","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"IEEE","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"article_processing_charge":"No","quality_controlled":"1","_id":"8788","type":"journal_article","scopus_import":"1","abstract":[{"text":"We consider a real-time setting where an environment releases sequences of firm-deadline tasks, and an online scheduler chooses on-the-fly the ones to execute on a single processor so as to maximize cumulated utility. The competitive ratio is a well-known performance measure for the scheduler: it gives the worst-case ratio, among all possible choices for the environment, of the cumulated utility of the online scheduler versus an offline scheduler that knows these choices in advance. Traditionally, competitive analysis is performed by hand, while automated techniques are rare and only handle static environments with independent tasks. We present a quantitative-verification framework for precedence-aware competitive analysis, where task releases may depend on preceding scheduling choices, i.e., the environment can respond to scheduling decisions dynamically . We consider two general classes of precedences: 1) follower precedences force the release of a dependent task upon the completion of a set of precursor tasks, while and 2) pairing precedences modify the characteristics of a dependent task provided the completion of a set of precursor tasks. Precedences make competitive analysis challenging, as the online and offline schedulers operate on diverging sequences. We make a formal presentation of our framework, and use a GPU-based implementation to analyze ten well-known schedulers on precedence-based application examples taken from the existing literature: 1) a handshake protocol (HP); 2) network packet-switching; 3) query scheduling (QS); and 4) a sporadic-interrupt setting. Our experimental results show that precedences and task parameters can vary drastically the best scheduler. Our framework thus supports application designers in choosing the best scheduler among a given set automatically.","lang":"eng"}],"publication_identifier":{"issn":["02780070"],"eissn":["19374151"]},"citation":{"mla":"Pavlogiannis, Andreas, et al. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11, IEEE, 2020, pp. 3981–92, doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012803\">10.1109/TCAD.2020.3012803</a>.","apa":"Pavlogiannis, A., Schaumberger, N., Schmid, U., &#38; Chatterjee, K. (2020). Precedence-aware automated competitive analysis of real-time scheduling. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE. <a href=\"https://doi.org/10.1109/TCAD.2020.3012803\">https://doi.org/10.1109/TCAD.2020.3012803</a>","chicago":"Pavlogiannis, Andreas, Nico Schaumberger, Ulrich Schmid, and Krishnendu Chatterjee. “Precedence-Aware Automated Competitive Analysis of Real-Time Scheduling.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TCAD.2020.3012803\">https://doi.org/10.1109/TCAD.2020.3012803</a>.","ama":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. Precedence-aware automated competitive analysis of real-time scheduling. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. 2020;39(11):3981-3992. doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012803\">10.1109/TCAD.2020.3012803</a>","short":"A. Pavlogiannis, N. Schaumberger, U. Schmid, K. Chatterjee, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 3981–3992.","ista":"Pavlogiannis A, Schaumberger N, Schmid U, Chatterjee K. 2020. Precedence-aware automated competitive analysis of real-time scheduling. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 3981–3992.","ieee":"A. Pavlogiannis, N. Schaumberger, U. Schmid, and K. Chatterjee, “Precedence-aware automated competitive analysis of real-time scheduling,” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11. IEEE, pp. 3981–3992, 2020."},"publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"}],"issue":"11","date_updated":"2023-08-22T13:27:05Z","acknowledgement":"This work was supported by the Austrian Science Foundation (FWF) under the NFN RiSE/SHiNE under Grant S11405 and Grant S11407. This article was presented in the International Conference on Embedded Software 2020 and appears as part of the ESWEEK-TCAD special issue. ","intvolume":"        39","month":"11","date_published":"2020-11-01T00:00:00Z","year":"2020","external_id":{"isi":["000587712700069"]},"page":"3981-3992","status":"public","day":"01","date_created":"2020-11-22T23:01:24Z","volume":39,"isi":1,"oa_version":"None","doi":"10.1109/TCAD.2020.3012803","publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems"},{"publication":"Mathematics","doi":"10.3390/math8111945","oa_version":"Published Version","ec_funded":1,"isi":1,"volume":8,"day":"04","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_created":"2020-11-22T23:01:24Z","external_id":{"isi":["000593962100001"]},"year":"2020","acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411, the Australian Research Council Discovery Grants DP160101236 and DP150100618, and the European Research Council Consolidator Grant 863818 (FoRM-SMArt).\r\nAuthors would like to thank Patrick McKinlay for his work on the preliminary results for this paper.","article_number":"1945","date_published":"2020-11-04T00:00:00Z","intvolume":"         8","month":"11","oa":1,"issue":"11","date_updated":"2025-07-14T09:09:49Z","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"abstract":[{"lang":"eng","text":"Cooperation is a ubiquitous and beneficial behavioural trait despite being prone to exploitation by free-riders. Hence, cooperative populations are prone to invasions by selfish individuals. However, a population consisting of only free-riders typically does not survive. Thus, cooperators and free-riders often coexist in some proportion. An evolutionary version of a Snowdrift Game proved its efficiency in analysing this phenomenon. However, what if the system has already reached its stable state but was perturbed due to a change in environmental conditions? Then, individuals may have to re-learn their effective strategies. To address this, we consider behavioural mistakes in strategic choice execution, which we refer to as incompetence. Parametrising the propensity to make such mistakes allows for a mathematical description of learning. We compare strategies based on their relative strategic advantage relying on both fitness and learning factors. When strategies are learned at distinct rates, allowing learning according to a prescribed order is optimal. Interestingly, the strategy with the lowest strategic advantage should be learnt first if we are to optimise fitness over the learning path. Then, the differences between strategies are balanced out in order to minimise the effect of behavioural uncertainty."}],"scopus_import":"1","file_date_updated":"2020-11-23T13:06:30Z","type":"journal_article","publication_identifier":{"eissn":["22277390"]},"citation":{"apa":"Kleshnina, M., Streipert, S., Filar, J., &#38; Chatterjee, K. (2020). Prioritised learning in snowdrift-type games. <i>Mathematics</i>. MDPI. <a href=\"https://doi.org/10.3390/math8111945\">https://doi.org/10.3390/math8111945</a>","mla":"Kleshnina, Maria, et al. “Prioritised Learning in Snowdrift-Type Games.” <i>Mathematics</i>, vol. 8, no. 11, 1945, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/math8111945\">10.3390/math8111945</a>.","ama":"Kleshnina M, Streipert S, Filar J, Chatterjee K. Prioritised learning in snowdrift-type games. <i>Mathematics</i>. 2020;8(11). doi:<a href=\"https://doi.org/10.3390/math8111945\">10.3390/math8111945</a>","ieee":"M. Kleshnina, S. Streipert, J. Filar, and K. Chatterjee, “Prioritised learning in snowdrift-type games,” <i>Mathematics</i>, vol. 8, no. 11. MDPI, 2020.","ista":"Kleshnina M, Streipert S, Filar J, Chatterjee K. 2020. Prioritised learning in snowdrift-type games. Mathematics. 8(11), 1945.","short":"M. Kleshnina, S. Streipert, J. Filar, K. Chatterjee, Mathematics 8 (2020).","chicago":"Kleshnina, Maria, Sabrina Streipert, Jerzy Filar, and Krishnendu Chatterjee. “Prioritised Learning in Snowdrift-Type Games.” <i>Mathematics</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/math8111945\">https://doi.org/10.3390/math8111945</a>."},"quality_controlled":"1","_id":"8789","department":[{"_id":"KrCh"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"MDPI","has_accepted_license":"1","author":[{"last_name":"Kleshnina","first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","full_name":"Kleshnina, Maria"},{"last_name":"Streipert","first_name":"Sabrina","full_name":"Streipert, Sabrina"},{"first_name":"Jerzy","last_name":"Filar","full_name":"Filar, Jerzy"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"title":"Prioritised learning in snowdrift-type games","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":565191,"creator":"dernst","content_type":"application/pdf","file_id":"8797","relation":"main_file","access_level":"open_access","checksum":"61cfcc3b35760656ce7a9385a4ace5d2","file_name":"2020_Mathematics_Kleshnina.pdf","success":1,"date_updated":"2020-11-23T13:06:30Z","date_created":"2020-11-23T13:06:30Z"}]},{"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8287"}]},"ec_funded":1,"oa_version":"Preprint","isi":1,"publication":"IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.02458"}],"doi":"10.1109/TCAD.2020.3012859","date_created":"2020-11-22T23:01:25Z","day":"01","status":"public","volume":39,"year":"2020","page":"4018-4029","external_id":{"isi":["000587712700072"],"arxiv":["1905.02458"]},"date_updated":"2023-08-22T13:27:33Z","oa":1,"issue":"11","date_published":"2020-11-01T00:00:00Z","month":"11","intvolume":"        39","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, and the Air Force Office of Scientific Research under award number FA2386-17-1-4065. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the United States Air Force. ","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"publication_status":"published","_id":"8790","quality_controlled":"1","publication_identifier":{"issn":["02780070"],"eissn":["19374151"]},"citation":{"apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., &#38; Schilling, C. (2020). Reachability analysis of linear hybrid systems via block decomposition. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE. <a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">https://doi.org/10.1109/TCAD.2020.3012859</a>","mla":"Bogomolov, Sergiy, et al. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11, IEEE, 2020, pp. 4018–29, doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">10.1109/TCAD.2020.3012859</a>.","ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. Reachability analysis of linear hybrid systems via block decomposition. <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. 2020;39(11):4018-4029. doi:<a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">10.1109/TCAD.2020.3012859</a>","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 39 (2020) 4018–4029.","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “Reachability analysis of linear hybrid systems via block decomposition,” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>, vol. 39, no. 11. IEEE, pp. 4018–4029, 2020.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2020. Reachability analysis of linear hybrid systems via block decomposition. IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 39(11), 4018–4029.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “Reachability Analysis of Linear Hybrid Systems via Block Decomposition.” <i>IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TCAD.2020.3012859\">https://doi.org/10.1109/TCAD.2020.3012859</a>."},"arxiv":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this article, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks."}],"type":"journal_article","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"ToHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Bogomolov","orcid":"0000-0002-0686-0365","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy"},{"full_name":"Forets, Marcelo","first_name":"Marcelo","last_name":"Forets"},{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"full_name":"Potomkin, Kostiantyn","last_name":"Potomkin","first_name":"Kostiantyn"},{"first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","last_name":"Schilling","full_name":"Schilling, Christian"}],"title":"Reachability analysis of linear hybrid systems via block decomposition","publisher":"IEEE"},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7995"}]},"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.qrfj6q5cn"}],"doi":"10.5061/dryad.qrfj6q5cn","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"_id":"8809","date_created":"2020-11-25T11:07:25Z","day":"01","status":"public","citation":{"mla":"Perini, Samuel, et al. <i>Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>.","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>.","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>."},"abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"type":"research_data_reference","year":"2020","article_processing_charge":"No","department":[{"_id":"NiBa"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","date_updated":"2023-08-22T07:13:37Z","title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Perini, Samuel","last_name":"Perini","first_name":"Samuel"},{"full_name":"Rafajlovic, Marina","last_name":"Rafajlovic","first_name":"Marina"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"oa":1,"date_published":"2020-07-01T00:00:00Z","has_accepted_license":"1","month":"07","publisher":"Dryad"},{"year":"2020","language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"article_processing_charge":"No","external_id":{"pmid":["PPR234457 "]},"oa":1,"title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Laura","last_name":"Santini","full_name":"Santini, Laura"},{"full_name":"Halbritter, Florian","first_name":"Florian","last_name":"Halbritter"},{"first_name":"Fabian","last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian"},{"full_name":"Suzuki, Toru","first_name":"Toru","last_name":"Suzuki"},{"first_name":"Maki","last_name":"Asami","full_name":"Asami, Maki"},{"full_name":"Ramesmayer, Julia","first_name":"Julia","last_name":"Ramesmayer"},{"full_name":"Ma, Xiaoyan","first_name":"Xiaoyan","last_name":"Ma"},{"full_name":"Lackner, Andreas","last_name":"Lackner","first_name":"Andreas"},{"full_name":"Warr, Nick","first_name":"Nick","last_name":"Warr"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"full_name":"Laue, Ernest","first_name":"Ernest","last_name":"Laue"},{"last_name":"Farlik","first_name":"Matthias","full_name":"Farlik, Matthias"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"last_name":"Beyer","first_name":"Andreas","full_name":"Beyer, Andreas"},{"full_name":"Perry, Anthony C. F.","first_name":"Anthony C. F.","last_name":"Perry"},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"}],"date_updated":"2023-09-12T11:05:28Z","publisher":"Cold Spring Harbor Laboratory","month":"11","date_published":"2020-11-05T00:00:00Z","oa_version":"Preprint","publication_status":"submitted","doi":"10.1101/2020.11.03.366948","main_file_link":[{"url":"https://doi.org/10.1101/2020.11.03.366948","open_access":"1"}],"publication":"bioRxiv","day":"05","status":"public","_id":"8813","date_created":"2020-11-26T07:17:19Z","type":"preprint","abstract":[{"text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation.","lang":"eng"}],"citation":{"chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>.","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, <a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","ieee":"L. Santini <i>et al.</i>, “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2020.11.03.366948\">10.1101/2020.11.03.366948</a>.","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.11.03.366948\">https://doi.org/10.1101/2020.11.03.366948</a>"},"pmid":1},{"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"citation":{"ieee":"J. Hajny, “Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration,” Institute of Science and Technology Austria, 2020.","short":"J. Hajny, Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration, Institute of Science and Technology Austria, 2020.","ista":"Hajny J. 2020. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. Institute of Science and Technology Austria.","ama":"Hajny J. Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8822\">10.15479/AT:ISTA:8822</a>","chicago":"Hajny, Jakub. “Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8822\">https://doi.org/10.15479/AT:ISTA:8822</a>.","apa":"Hajny, J. (2020). <i>Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8822\">https://doi.org/10.15479/AT:ISTA:8822</a>","mla":"Hajny, Jakub. <i>Identification and Characterization of the Molecular Machinery of Auxin-Dependent Canalization during Vasculature Formation and Regeneration</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8822\">10.15479/AT:ISTA:8822</a>."},"abstract":[{"lang":"eng","text":"Self-organization is a hallmark of plant development manifested e.g. by intricate leaf vein patterns, flexible formation of vasculature during organogenesis or its regeneration following wounding. Spontaneously arising channels transporting the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED 1 (PIN1) auxin exporter, provide positional cues for these as well as other plant patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB auxin signaling pathway essential for PIN1 coordinated polarization during auxin canalization, we performed microarray experiments. Besides the known components of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified and characterized a new regulator of auxin canalization, the transcription factor WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23 involved in the regulation of auxin-mediated PIN repolarization. We identified a novel and crucial part of the molecular machinery underlying auxin canalization. The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated repolarization leading to defects in auxin transport, ultimately to leaf venation and vasculature regeneration defects. Our results describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back on its own transport and thus for coordinated tissue polarization during auxin canalization."}],"type":"dissertation","file_date_updated":"2021-12-08T23:30:03Z","_id":"8822","article_processing_charge":"No","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","author":[{"orcid":"0000-0003-2140-7195","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","first_name":"Jakub","full_name":"Hajny, Jakub"}],"title":"Identification and characterization of the molecular machinery of auxin-dependent canalization during vasculature formation and regeneration","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"8919","embargo_to":"open_access","creator":"jhajny","file_size":91279806,"relation":"source_file","checksum":"210a9675af5e4c78b0b56d920ac82866","access_level":"closed","file_name":"Jakub Hajný IST Austria final_JH.docx","date_updated":"2021-07-16T22:30:03Z","date_created":"2020-12-04T07:27:52Z"},{"date_created":"2020-12-09T15:04:41Z","date_updated":"2021-12-08T23:30:03Z","file_name":"Jakub Hajný IST Austria final_JH-merged without Science.pdf","embargo":"2021-12-07","access_level":"open_access","checksum":"1781385b4aa73eba89cc76c6172f71d2","relation":"main_file","file_id":"8933","content_type":"application/pdf","file_size":68707697,"creator":"jhajny"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8822","related_material":{"record":[{"id":"7427","status":"public","relation":"part_of_dissertation"},{"id":"6260","status":"public","relation":"part_of_dissertation"},{"id":"7500","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"449"},{"status":"public","relation":"part_of_dissertation","id":"191"}]},"oa_version":"Published Version","date_created":"2020-12-01T12:38:18Z","ddc":["580"],"status":"public","day":"01","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"page":"249","year":"2020","date_published":"2020-12-01T00:00:00Z","alternative_title":["ISTA Thesis"],"month":"12","date_updated":"2025-05-07T11:12:31Z","oa":1},{"language":[{"iso":"eng"}],"department":[{"_id":"GeKa"}],"article_processing_charge":"No","file":[{"relation":"main_file","checksum":"22a612e206232fa94b138b2c2f957582","access_level":"open_access","file_size":1697939,"creator":"gkatsaro","content_type":"application/pdf","file_id":"8832","date_created":"2020-12-02T10:42:31Z","date_updated":"2020-12-02T10:42:31Z","file_name":"Superconducting_2D_Ge.pdf"}],"author":[{"first_name":"Kushagra","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","orcid":"0000-0001-9985-9293","last_name":"Aggarwal","full_name":"Aggarwal, Kushagra"},{"last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C","full_name":"Hofmann, Andrea C"},{"first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","last_name":"Jirovec","full_name":"Jirovec, Daniel"},{"full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","orcid":"0000-0002-7370-5357","last_name":"Prieto Gonzalez"},{"last_name":"Sammak","first_name":"Amir","full_name":"Sammak, Amir"},{"last_name":"Botifoll","first_name":"Marc","full_name":"Botifoll, Marc"},{"first_name":"Sara","last_name":"Marti-Sanchez","full_name":"Marti-Sanchez, Sara"},{"last_name":"Veldhorst","first_name":"Menno","full_name":"Veldhorst, Menno"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"full_name":"Scappucci, Giordano","first_name":"Giordano","last_name":"Scappucci"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","full_name":"Katsaros, Georgios"}],"title":"Enhancement of proximity induced superconductivity in planar Germanium","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publication_status":"submitted","project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"844511"},{"grant_number":"862046","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"}],"_id":"8831","type":"preprint","file_date_updated":"2020-12-02T10:42:31Z","abstract":[{"text":"Holes in planar Ge have high mobilities, strong spin-orbit interaction and electrically tunable g-factors, and are therefore emerging as a promising candidate for hybrid superconductorsemiconductor devices. This is further motivated by the observation of supercurrent transport in planar Ge Josephson Field effect transistors (JoFETs). A key challenge towards hybrid germanium quantum technology is the design of high quality interfaces and superconducting contacts that are robust against magnetic fields. By combining the assets of Al, which has a long superconducting coherence, and Nb, which has a significant superconducting gap, we form low-disordered JoFETs with large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip.","lang":"eng"}],"arxiv":1,"citation":{"chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” <i>ArXiv</i>, n.d.","ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity induced superconductivity in planar Germanium. <i>arXiv</i>.","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros, ArXiv (n.d.).","ieee":"K. Aggarwal <i>et al.</i>, “Enhancement of proximity induced superconductivity in planar Germanium,” <i>arXiv</i>. .","ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. arXiv, 2012.00322.","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” <i>ArXiv</i>, 2012.00322.","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity in planar Germanium. <i>arXiv</i>."},"year":"2020","external_id":{"arxiv":["2012.00322"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa":1,"date_updated":"2024-03-25T23:30:14Z","acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement #844511 and the Grant Agreement #862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Aut`onoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from\r\nthe European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 – ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. GS and MV acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO).","article_number":"2012.00322","month":"12","date_published":"2020-12-02T00:00:00Z","oa_version":"Submitted 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supplementary material of \"Enhancement of Proximity Induced Superconductivity in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).\r\n","lang":"eng"}],"citation":{"chicago":"Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">https://doi.org/10.15479/AT:ISTA:8834</a>.","ama":"Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>","ista":"Katsaros G. 2020. Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>.","short":"G. Katsaros, (2020).","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","mla":"Katsaros, Georgios. <i>Enhancement of Proximity Induced Superconductivity in Planar Germanium</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8834\">10.15479/AT:ISTA:8834</a>.","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8834\">https://doi.org/10.15479/AT:ISTA:8834</a>"},"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10559"},{"id":"8831","status":"public","relation":"used_in_publication"}]},"contributor":[{"contributor_type":"project_member","last_name":"Aggarwal","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","first_name":"Kushagra"},{"contributor_type":"project_member","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C","last_name":"Hofmann"},{"last_name":"Jirovec","first_name":"Daniel","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member"},{"contributor_type":"project_member","last_name":"Prieto Gonzalez","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amir","last_name":"Sammak","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Marc","last_name":"Botifoll"},{"last_name":"Marti-Sanchez","first_name":"Sara","contributor_type":"project_member"},{"contributor_type":"project_member","last_name":"Veldhorst","first_name":"Menno"},{"last_name":"Arbiol","first_name":"Jordi","contributor_type":"project_member"},{"last_name":"Scappucci","first_name":"Giordano","contributor_type":"project_member"},{"last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","contributor_type":"project_leader"}],"doi":"10.15479/AT:ISTA:8834"},{"file":[{"relation":"main_file","checksum":"da7413c819e079720669c82451b49294","access_level":"open_access","content_type":"application/pdf","file_id":"8915","creator":"dernst","file_size":4071247,"date_updated":"2020-12-03T11:45:26Z","date_created":"2020-12-03T11:45:26Z","success":1,"file_name":"2020_Neuroscience_Salamatina.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Differential loss of spinal interneurons in a mouse model of ALS","author":[{"full_name":"Salamatina, Alina","last_name":"Salamatina","first_name":"Alina"},{"full_name":"Yang, Jerry H","last_name":"Yang","first_name":"Jerry H"},{"full_name":"Brenner-Morton, Susan","last_name":"Brenner-Morton","first_name":"Susan"},{"full_name":"Bikoff, Jay B ","first_name":"Jay B ","last_name":"Bikoff"},{"last_name":"Fang","first_name":"Linjing","full_name":"Fang, Linjing"},{"full_name":"Kintner, Christopher R","first_name":"Christopher R","last_name":"Kintner"},{"full_name":"Jessell, Thomas M","last_name":"Jessell","first_name":"Thomas M"},{"orcid":"0000-0001-9242-5601","last_name":"Sweeney","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425","first_name":"Lora Beatrice Jaeger","full_name":"Sweeney, Lora Beatrice Jaeger"}],"has_accepted_license":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"LoSw"}],"_id":"8914","quality_controlled":"1","publication_identifier":{"issn":["0306-4522"]},"citation":{"ama":"Salamatina A, Yang JH, Brenner-Morton S, et al. Differential loss of spinal interneurons in a mouse model of ALS. <i>Neuroscience</i>. 2020;450:81-95. doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">10.1016/j.neuroscience.2020.08.011</a>","ieee":"A. Salamatina <i>et al.</i>, “Differential loss of spinal interneurons in a mouse model of ALS,” <i>Neuroscience</i>, vol. 450. Elsevier, pp. 81–95, 2020.","ista":"Salamatina A, Yang JH, Brenner-Morton S, Bikoff JB, Fang L, Kintner CR, Jessell TM, Sweeney LB. 2020. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 450, 81–95.","short":"A. Salamatina, J.H. Yang, S. Brenner-Morton, J.B. Bikoff, L. Fang, C.R. Kintner, T.M. Jessell, L.B. Sweeney, Neuroscience 450 (2020) 81–95.","chicago":"Salamatina, Alina, Jerry H Yang, Susan Brenner-Morton, Jay B  Bikoff, Linjing Fang, Christopher R Kintner, Thomas M Jessell, and Lora B. Sweeney. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” <i>Neuroscience</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">https://doi.org/10.1016/j.neuroscience.2020.08.011</a>.","apa":"Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner, C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a mouse model of ALS. <i>Neuroscience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">https://doi.org/10.1016/j.neuroscience.2020.08.011</a>","mla":"Salamatina, Alina, et al. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” <i>Neuroscience</i>, vol. 450, Elsevier, 2020, pp. 81–95, doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">10.1016/j.neuroscience.2020.08.011</a>."},"file_date_updated":"2020-12-03T11:45:26Z","type":"journal_article","abstract":[{"text":"Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron populations in the spinal cord and cortex. Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord.","lang":"eng"}],"scopus_import":"1","publication_status":"published","date_updated":"2024-01-31T10:15:34Z","oa":1,"month":"12","intvolume":"       450","date_published":"2020-12-01T00:00:00Z","acknowledgement":"This work was made possible by the generous support of Project ALS. Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. This manuscript is dedicated to Tom Jessell, an inspirational scientist, friend and mentor.","year":"2020","page":"81-95","external_id":{"pmid":["32858144"],"isi":["000595588700008"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2020-12-03T11:47:31Z","day":"01","status":"public","pmid":1,"volume":450,"isi":1,"oa_version":"Published Version","doi":"10.1016/j.neuroscience.2020.08.011","publication":"Neuroscience"},{"oa":1,"date_updated":"2023-08-24T10:50:00Z","acknowledgement":"CN, DD, NF-F, and JD were funded by the BBSRC (grant number BB/M009459/1). NK and AM were funded through the ERASMUS+Program. NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna.","article_number":"586870","date_published":"2020-11-10T00:00:00Z","intvolume":"        11","month":"11","year":"2020","external_id":{"isi":["000591637000001"]},"day":"10","status":"public","date_created":"2020-12-06T23:01:14Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"volume":11,"oa_version":"Published Version","isi":1,"publication":"Frontiers in Plant Science","doi":"10.3389/fpls.2020.586870","title":"A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"first_name":"Despoina","last_name":"Dadarou","full_name":"Dadarou, Despoina"},{"first_name":"Nestoras","last_name":"Kargios","full_name":"Kargios, Nestoras"},{"full_name":"Mallioura, Areti","first_name":"Areti","last_name":"Mallioura"},{"full_name":"Fernandez-Fuentes, Narcis","first_name":"Narcis","last_name":"Fernandez-Fuentes"},{"full_name":"Cavallari, Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola"},{"last_name":"Doonan","first_name":"John H.","full_name":"Doonan, John H."}],"file":[{"date_updated":"2020-12-09T09:14:19Z","date_created":"2020-12-09T09:14:19Z","file_name":"2020_Frontiers_Nibau.pdf","success":1,"access_level":"open_access","relation":"main_file","checksum":"1c0ee6ce9950aa665d6a5cc64aa6b752","creator":"dernst","file_size":1833244,"content_type":"application/pdf","file_id":"8929"}],"publisher":"Frontiers","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"article_processing_charge":"No","quality_controlled":"1","_id":"8924","abstract":[{"lang":"eng","text":"Maintaining fertility in a fluctuating environment is key to the reproductive success of flowering plants. Meiosis and pollen formation are particularly sensitive to changes in growing conditions, especially temperature. We have previously identified cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent meiosis and this may involve the regulation of alternative splicing (AS), including of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain which may be involved in co-factor interaction. In leaves, both isoforms have distinct temperature-dependent functions on target mRNA processing, but their role in pollen development is unknown. In the present study, we characterize the role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the long (L) form is necessary and sufficient to rescue the fertility defects of the cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of the ATP binding pocket of the kinase indicates that kinase activity is necessary for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore, we show that there is partial functional overlap between CDKG1 and its paralog CDKG2 that could in part be explained by overlapping gene expression."}],"scopus_import":"1","file_date_updated":"2020-12-09T09:14:19Z","type":"journal_article","publication_identifier":{"eissn":["1664-462X"]},"citation":{"apa":"Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N., Cavallari, N., &#38; Doonan, J. H. (2020). A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2020.586870\">https://doi.org/10.3389/fpls.2020.586870</a>","mla":"Nibau, Candida, et al. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” <i>Frontiers in Plant Science</i>, vol. 11, 586870, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2020.586870\">10.3389/fpls.2020.586870</a>.","ama":"Nibau C, Dadarou D, Kargios N, et al. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fpls.2020.586870\">10.3389/fpls.2020.586870</a>","ieee":"C. Nibau <i>et al.</i>, “A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020.","short":"C. Nibau, D. Dadarou, N. Kargios, A. Mallioura, N. Fernandez-Fuentes, N. Cavallari, J.H. Doonan, Frontiers in Plant Science 11 (2020).","ista":"Nibau C, Dadarou D, Kargios N, Mallioura A, Fernandez-Fuentes N, Cavallari N, Doonan JH. 2020. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 11, 586870.","chicago":"Nibau, Candida, Despoina Dadarou, Nestoras Kargios, Areti Mallioura, Narcis Fernandez-Fuentes, Nicola Cavallari, and John H. Doonan. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” <i>Frontiers in Plant Science</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fpls.2020.586870\">https://doi.org/10.3389/fpls.2020.586870</a>."},"publication_status":"published"},{"_id":"8926","quality_controlled":"1","citation":{"chicago":"Irtem, Erdem, Daniel Arenas Esteban, Miguel Duarte, Daniel Choukroun, Seungho Lee, Maria Ibáñez, Sara Bals, and Tom Breugelmans. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” <i>ACS Catalysis</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acscatal.0c03210\">https://doi.org/10.1021/acscatal.0c03210</a>.","short":"E. Irtem, D. Arenas Esteban, M. Duarte, D. Choukroun, S. Lee, M. Ibáñez, S. Bals, T. Breugelmans, ACS Catalysis 10 (2020) 13468–13478.","ieee":"E. Irtem <i>et al.</i>, “Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction,” <i>ACS Catalysis</i>, vol. 10, no. 22. American Chemical Society, pp. 13468–13478, 2020.","ista":"Irtem E, Arenas Esteban D, Duarte M, Choukroun D, Lee S, Ibáñez M, Bals S, Breugelmans T. 2020. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 10(22), 13468–13478.","ama":"Irtem E, Arenas Esteban D, Duarte M, et al. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. <i>ACS Catalysis</i>. 2020;10(22):13468-13478. doi:<a href=\"https://doi.org/10.1021/acscatal.0c03210\">10.1021/acscatal.0c03210</a>","mla":"Irtem, Erdem, et al. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” <i>ACS Catalysis</i>, vol. 10, no. 22, American Chemical Society, 2020, pp. 13468–78, doi:<a href=\"https://doi.org/10.1021/acscatal.0c03210\">10.1021/acscatal.0c03210</a>.","apa":"Irtem, E., Arenas Esteban, D., Duarte, M., Choukroun, D., Lee, S., Ibáñez, M., … Breugelmans, T. (2020). Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. <i>ACS Catalysis</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acscatal.0c03210\">https://doi.org/10.1021/acscatal.0c03210</a>"},"publication_identifier":{"eissn":["21555435"]},"abstract":[{"text":"Bimetallic nanoparticles with tailored size and specific composition have shown promise as stable and selective catalysts for electrochemical reduction of CO2 (CO2R) in batch systems. Yet, limited effort was devoted to understand the effect of ligand coverage and postsynthesis treatments on CO2 reduction, especially under industrially applicable conditions, such as at high currents (>100 mA/cm2) using gas diffusion electrodes (GDE) and flow reactors. In this work, Cu–Ag core–shell nanoparticles (11 ± 2 nm) were prepared with three different surface modes: (i) capped with oleylamine, (ii) capped with monoisopropylamine, and (iii) surfactant-free with a reducing borohydride agent; Cu–Ag (OAm), Cu–Ag (MIPA), and Cu–Ag (NaBH4), respectively. The ligand exchange and removal was evidenced by infrared spectroscopy (ATR-FTIR) analysis, whereas high-resolution scanning transmission electron microscopy (HAADF-STEM) showed their effect on the interparticle distance and nanoparticle rearrangement. Later on, we developed a process-on-substrate method to track these effects on CO2R. Cu–Ag (OAm) gave a lower on-set potential for hydrocarbon production, whereas Cu–Ag (MIPA) and Cu–Ag (NaBH4) promoted syngas production. The electrochemical impedance and surface area analysis on the well-controlled electrodes showed gradual increases in the electrical conductivity and active surface area after each surface treatment. We found that the increasing amount of the triple phase boundaries (the meeting point for the electron–electrolyte–CO2 reactant) affect the required electrode potential and eventually the C+2e̅/C2e̅ product ratio. This study highlights the importance of the electron transfer to those active sites affected by the capping agents—particularly on larger substrates that are crucial for their industrial application.","lang":"eng"}],"scopus_import":"1","type":"journal_article","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","author":[{"full_name":"Irtem, Erdem","last_name":"Irtem","first_name":"Erdem"},{"full_name":"Arenas Esteban, Daniel","first_name":"Daniel","last_name":"Arenas Esteban"},{"full_name":"Duarte, Miguel","last_name":"Duarte","first_name":"Miguel"},{"full_name":"Choukroun, Daniel","last_name":"Choukroun","first_name":"Daniel"},{"full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"first_name":"Sara","last_name":"Bals","full_name":"Bals, Sara"},{"full_name":"Breugelmans, Tom","last_name":"Breugelmans","first_name":"Tom"}],"title":"Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Chemical Society","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"MaIb"}],"date_created":"2020-12-06T23:01:15Z","status":"public","day":"20","volume":10,"ec_funded":1,"oa_version":"None","isi":1,"publication":"ACS Catalysis","doi":"10.1021/acscatal.0c03210","date_updated":"2023-08-24T10:52:32Z","issue":"22","date_published":"2020-11-20T00:00:00Z","month":"11","intvolume":"        10","acknowledgement":"The authors also acknowledge financial support from the University Research Fund (BOF-GOA-PS ID No. 33928). S.L. has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2020","page":"13468-13478","external_id":{"isi":["000592978900031"]}},{"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","month":"12","date_published":"2020-12-10T00:00:00Z","file":[{"success":1,"file_name":"PLoSCompBiol2020_datarep.zip","date_updated":"2020-12-09T15:00:19Z","date_created":"2020-12-09T15:00:19Z","content_type":"application/zip","file_id":"8932","file_size":315494370,"creator":"bkavcic","relation":"main_file","access_level":"open_access","checksum":"60a818edeffaa7da1ebf5f8fbea9ba18"}],"oa":1,"author":[{"full_name":"Kavcic, Bor","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","orcid":"0000-0001-6041-254X"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","date_updated":"2024-02-21T12:41:42Z","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"department":[{"_id":"GaTk"}],"article_processing_charge":"No","year":"2020","file_date_updated":"2020-12-09T15:00:19Z","type":"research_data","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"citation":{"chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>.","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>.","short":"B. Kavcic, (2020).","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>","mla":"Kavcic, Bor. <i>Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>"},"day":"10","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8930","date_created":"2020-12-09T15:04:02Z","ddc":["570"],"doi":"10.15479/AT:ISTA:8930","oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8997"}]},"contributor":[{"contributor_type":"supervisor","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","contributor_type":"supervisor"}]},{"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship"}],"publication_status":"published","citation":{"apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>, vol. 33, no. 9, 108463, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>.","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","ieee":"S. Tan <i>et al.</i>, “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” <i>Cell Reports</i>, vol. 33, no. 9. Elsevier, 2020.","ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. 2020;33(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>","chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>."},"publication_identifier":{"eissn":["22111247"]},"type":"journal_article","file_date_updated":"2020-12-14T07:33:39Z","abstract":[{"lang":"eng","text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds."}],"scopus_import":"1","_id":"8943","quality_controlled":"1","article_processing_charge":"Yes","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"article_type":"original","has_accepted_license":"1","publisher":"Elsevier","file":[{"file_name":"2020_CellReports_Tan.pdf","success":1,"date_updated":"2020-12-14T07:33:39Z","date_created":"2020-12-14T07:33:39Z","file_size":8056434,"creator":"dernst","content_type":"application/pdf","file_id":"8948","checksum":"ed18cba0fb48ed2e789381a54cc21904","relation":"main_file","access_level":"open_access"}],"title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","author":[{"full_name":"Tan, Shutang","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"full_name":"Di Donato, Martin","last_name":"Di Donato","first_name":"Martin"},{"full_name":"Glanc, Matous","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","last_name":"Glanc"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang"},{"full_name":"Klíma, Petr","first_name":"Petr","last_name":"Klíma"},{"full_name":"Liu, Jie","last_name":"Liu","first_name":"Jie"},{"last_name":"Bailly","first_name":"Aurélien","full_name":"Bailly, Aurélien"},{"first_name":"Noel","last_name":"Ferro","full_name":"Ferro, Noel"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.celrep.2020.108463","publication":"Cell Reports","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/plants-on-aspirin/","relation":"press_release"}]},"isi":1,"ec_funded":1,"oa_version":"Published Version","pmid":1,"volume":33,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-12-13T23:01:21Z","ddc":["580"],"day":"01","status":"public","external_id":{"pmid":["33264621"],"isi":["000595658100018"]},"year":"2020","intvolume":"        33","month":"12","date_published":"2020-12-01T00:00:00Z","acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","article_number":"108463","date_updated":"2023-11-16T13:03:31Z","issue":"9","oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}]},{"article_processing_charge":"No","department":[{"_id":"JoFi"}],"language":[{"iso":"eng"}],"article_type":"original","publisher":"American Physical Society","title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","author":[{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kopčík, M.","last_name":"Kopčík","first_name":"M."},{"last_name":"Szabó","first_name":"P.","full_name":"Szabó, P."},{"first_name":"T.","last_name":"Samuely","full_name":"Samuely, T."},{"last_name":"Kačmarčík","first_name":"J.","full_name":"Kačmarčík, J."},{"first_name":"P.","last_name":"Neilinger","full_name":"Neilinger, P."},{"full_name":"Grajcar, M.","last_name":"Grajcar","first_name":"M."},{"first_name":"P.","last_name":"Samuely","full_name":"Samuely, P."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"citation":{"chicago":"Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>.","ama":"Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. 2020;102(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>","ista":"Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508.","ieee":"M. Zemlicka <i>et al.</i>, “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” <i>Physical Review B</i>, vol. 102, no. 18. American Physical Society, 2020.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020).","mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>.","apa":"Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>"},"abstract":[{"lang":"eng","text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2."}],"scopus_import":"1","arxiv":1,"type":"journal_article","_id":"8944","quality_controlled":"1","external_id":{"arxiv":["2011.04329"],"isi":["000591509900003"]},"year":"2020","date_published":"2020-11-01T00:00:00Z","intvolume":"       102","month":"11","acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ","article_number":"180508","date_updated":"2023-08-24T10:53:36Z","oa":1,"issue":"18","publication":"Physical Review B","main_file_link":[{"url":"https://arxiv.org/abs/2011.04329","open_access":"1"}],"doi":"10.1103/PhysRevB.102.180508","oa_version":"Preprint","isi":1,"volume":102,"date_created":"2020-12-13T23:01:21Z","day":"01","status":"public"},{"year":"2020","external_id":{"isi":["000601787300001"]},"date_updated":"2023-08-24T10:57:48Z","issue":"12","oa":1,"month":"12","intvolume":"         9","date_published":"2020-12-11T00:00:00Z","article_number":"2662","acknowledgement":"This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript.","isi":1,"oa_version":"Published Version","ec_funded":1,"doi":"10.3390/cells9122662","publication":"Cells","date_created":"2020-12-14T08:04:03Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"day":"11","status":"public","volume":9,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"SiHi"}],"file":[{"success":1,"file_name":"2020_Cells_Zhang.pdf","date_created":"2020-12-14T08:09:43Z","date_updated":"2020-12-14T08:09:43Z","file_id":"8950","content_type":"application/pdf","creator":"dernst","file_size":3504525,"relation":"main_file","access_level":"open_access","checksum":"5095cbdc728c9a510c5761cf60a8861c"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Zhang, Xuying","last_name":"Zhang","first_name":"Xuying"},{"first_name":"Christine V.","last_name":"Mennicke","full_name":"Mennicke, Christine V."},{"last_name":"Xiao","first_name":"Guanxi","full_name":"Xiao, Guanxi"},{"full_name":"Beattie, Robert J","last_name":"Beattie","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"last_name":"Haider","first_name":"Mansoor","full_name":"Haider, Mansoor"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"full_name":"Ghashghaei, H. Troy","first_name":"H. Troy","last_name":"Ghashghaei"}],"title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","has_accepted_license":"1","publisher":"MDPI","project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02416"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020"}],"publication_status":"published","_id":"8949","quality_controlled":"1","publication_identifier":{"issn":["2073-4409"]},"citation":{"chicago":"Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>.","ieee":"X. Zhang <i>et al.</i>, “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” <i>Cells</i>, vol. 9, no. 12. MDPI, 2020.","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020).","ista":"Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662.","ama":"Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. 2020;9(12). doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>","mla":"Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>, vol. 9, no. 12, 2662, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>.","apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., &#38; Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>"},"type":"journal_article","file_date_updated":"2020-12-14T08:09:43Z","abstract":[{"text":"<jats:p>Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.</jats:p>","lang":"eng"}]},{"status":"public","day":"21","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8951","date_created":"2020-12-20T10:00:26Z","ddc":["570"],"type":"research_data","file_date_updated":"2020-12-20T22:01:44Z","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}],"citation":{"apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>","mla":"Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","short":"A.A. Nagy-Staron, (2020).","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>."},"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9283"}]},"contributor":[{"contributor_type":"project_member","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","last_name":"Nagy-Staron"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","last_name":"Tomasek","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Caroline","last_name":"Caruso Carter"},{"contributor_type":"project_member","first_name":"Elisabeth","last_name":"Sonnleitner"},{"contributor_type":"project_member","last_name":"Kavcic","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"},{"contributor_type":"project_member","first_name":"Tiago","last_name":"Paixão"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","contributor_type":"project_manager"}],"doi":"10.15479/AT:ISTA:8951","file":[{"date_updated":"2020-12-20T09:52:52Z","date_created":"2020-12-20T09:52:52Z","success":1,"file_name":"readme.txt","access_level":"open_access","relation":"main_file","checksum":"f57862aeee1690c7effd2b1117d40ed1","file_id":"8952","content_type":"text/plain","file_size":523,"creator":"bkavcic"},{"file_name":"GRNs Research depository.gb","success":1,"date_created":"2020-12-20T22:01:44Z","date_updated":"2020-12-20T22:01:44Z","creator":"bkavcic","file_size":379228,"file_id":"8954","content_type":"application/octet-stream","access_level":"open_access","checksum":"f2c6d5232ec6d551b6993991e8689e9f","relation":"main_file"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Nagy-Staron, Anna A","first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1391-8377","last_name":"Nagy-Staron"}],"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","date_updated":"2024-02-21T12:41:57Z","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"publisher":"Institute of Science and Technology Austria","month":"12","has_accepted_license":"1","date_published":"2020-12-21T00:00:00Z","year":"2020","department":[{"_id":"CaGu"}],"article_processing_charge":"No"},{"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2020-12-20T23:01:18Z","ddc":["570"],"status":"public","day":"26","pmid":1,"volume":11,"isi":1,"oa_version":"Published Version","ec_funded":1,"doi":"10.3389/fphys.2020.558070","publication":"Frontiers in Physiology","date_updated":"2023-08-24T11:00:45Z","oa":1,"intvolume":"        11","month":"11","date_published":"2020-11-26T00:00:00Z","acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","article_number":"558070","year":"2020","external_id":{"pmid":["33324233"],"isi":["000596849400001"]},"_id":"8955","quality_controlled":"1","citation":{"apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., &#38; Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>, vol. 11, 558070, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” <i>Frontiers in Physiology</i>, vol. 11. Frontiers, 2020.","short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).","ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.","chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>."},"publication_identifier":{"eissn":["1664042X"]},"type":"journal_article","file_date_updated":"2020-12-21T10:37:50Z","abstract":[{"text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies.","lang":"eng"}],"scopus_import":"1","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","file":[{"date_updated":"2020-12-21T10:37:50Z","date_created":"2020-12-21T10:37:50Z","success":1,"file_name":"2020_Frontiers_Rizzo.pdf","relation":"main_file","access_level":"open_access","checksum":"ef9515b28c5619b7126c0f347958bcb3","content_type":"application/pdf","file_id":"8961","file_size":13380030,"creator":"dernst"}],"title":"Network physiology of cortico–muscular interactions","author":[{"full_name":"Rizzo, Rossella","first_name":"Rossella","last_name":"Rizzo"},{"last_name":"Zhang","first_name":"Xiyun","full_name":"Zhang, Xiyun"},{"first_name":"Jilin W.J.L.","last_name":"Wang","full_name":"Wang, Jilin W.J.L."},{"full_name":"Lombardi, Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio"},{"full_name":"Ivanov, Plamen Ch","last_name":"Ivanov","first_name":"Plamen Ch"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","publisher":"Frontiers","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","department":[{"_id":"GaTk"}]}]