[{"month":"07","has_accepted_license":"1","external_id":{"isi":["000443861300016"],"pmid":["30061750"]},"oa_version":"Submitted Version","day":"30","file_date_updated":"2020-07-14T12:44:56Z","publist_id":"7777","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/","description":"News on IST Homepage","relation":"press_release"}]},"publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity."}],"year":"2018","oa":1,"date_published":"2018-07-30T00:00:00Z","volume":4,"_id":"146","publisher":"Nature Publishing Group","file":[{"date_created":"2019-11-18T16:24:07Z","file_name":"2018_NaturePlants_Shi.pdf","creator":"dernst","date_updated":"2020-07-14T12:44:56Z","file_size":226829,"access_level":"open_access","content_type":"application/pdf","file_id":"7043","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","relation":"main_file"}],"type":"journal_article","intvolume":"         4","date_created":"2018-12-11T11:44:52Z","author":[{"full_name":"Shi, Chun Lin","last_name":"Shi","first_name":"Chun Lin"},{"full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim"},{"first_name":"Ullrich","last_name":"Herrmann","full_name":"Herrmann, Ullrich"},{"full_name":"Wildhagen, Mari","first_name":"Mari","last_name":"Wildhagen"},{"first_name":"Ivan","last_name":"Kulik","full_name":"Kulik, Ivan","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB"},{"full_name":"Kopf, Andreas","last_name":"Kopf","first_name":"Andreas"},{"full_name":"Ishida, Takashi","last_name":"Ishida","first_name":"Takashi"},{"full_name":"Olsson, Vilde","last_name":"Olsson","first_name":"Vilde"},{"full_name":"Anker, Mari Kristine","last_name":"Anker","first_name":"Mari Kristine"},{"full_name":"Albert, Markus","last_name":"Albert","first_name":"Markus"},{"full_name":"Butenko, Melinka A","last_name":"Butenko","first_name":"Melinka A"},{"full_name":"Felix, Georg","first_name":"Georg","last_name":"Felix"},{"full_name":"Sawa, Shinichiro","first_name":"Shinichiro","last_name":"Sawa"},{"full_name":"Claassen, Manfred","last_name":"Claassen","first_name":"Manfred"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí"},{"last_name":"Aalen","first_name":"Reidunn B","full_name":"Aalen, Reidunn B"}],"doi":"10.1038/s41477-018-0212-z","pmid":1,"department":[{"_id":"JiFr"}],"issue":"8","ddc":["580"],"publication":"Nature Plants","page":"596 - 604","citation":{"ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604.","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>.","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","ieee":"C. L. Shi <i>et al.</i>, “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. 2018;4(8):596-604. doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>"},"scopus_import":"1","isi":1,"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","date_updated":"2023-09-19T10:08:45Z"},{"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","date_updated":"2026-06-18T17:36:26Z","publication_identifier":{"issn":["1040-4651"]},"article_processing_charge":"No","ddc":["580"],"corr_author":"1","issue":"10","pmid":1,"department":[{"_id":"JiFr"}],"status":"public","citation":{"chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. 2018;30(10):2553-2572. doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>","apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>","ieee":"U. Kania <i>et al.</i>, “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” <i>The Plant Cell</i>, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018."},"page":"2553 - 2572","publication":"The Plant Cell","isi":1,"scopus_import":"1","_id":"147","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.18.00127"}],"publisher":"Oxford University Press","author":[{"first_name":"Urszula","last_name":"Kania","full_name":"Kania, Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"first_name":"Qing","last_name":"Lu","full_name":"Lu, Qing"},{"last_name":"Hicks","first_name":"Glenn R","full_name":"Hicks, Glenn R"},{"full_name":"Nerinckx, Wim","last_name":"Nerinckx","first_name":"Wim"},{"full_name":"Mishev, Kiril","first_name":"Kiril","last_name":"Mishev"},{"full_name":"Peurois, Francois","last_name":"Peurois","first_name":"Francois"},{"last_name":"Cherfils","first_name":"Jacqueline","full_name":"Cherfils, Jacqueline"},{"first_name":"Rycke Riet Maria","last_name":"De","full_name":"De, Rycke Riet Maria"},{"full_name":"Grones, Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","first_name":"Peter"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"date_created":"2018-12-11T11:44:52Z","doi":"10.1105/tpc.18.00127","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"intvolume":"        30","type":"journal_article","oa_version":"Published Version","external_id":{"pmid":["30018156"],"isi":["000450000500023"]},"ec_funded":1,"day":"12","month":"11","date_published":"2018-11-12T00:00:00Z","volume":30,"year":"2018","oa":1,"publist_id":"7776","abstract":[{"lang":"eng","text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development."}],"article_type":"original","publication_status":"published"},{"month":"07","ec_funded":1,"external_id":{"isi":["000438482800019"],"pmid":["30007417"]},"oa_version":"Published Version","day":"12","publist_id":"7774","publication_status":"published","abstract":[{"lang":"eng","text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote."}],"year":"2018","oa":1,"volume":174,"date_published":"2018-07-12T00:00:00Z","_id":"148","publisher":"Cell Press","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417"}],"intvolume":"       174","type":"journal_article","date_created":"2018-12-11T11:44:53Z","author":[{"full_name":"Nishiyama, Tomoaki","first_name":"Tomoaki","last_name":"Nishiyama"},{"last_name":"Sakayama","first_name":"Hidetoshi","full_name":"Sakayama, Hidetoshi"},{"full_name":"De Vries, Jan","first_name":"Jan","last_name":"De Vries"},{"last_name":"Buschmann","first_name":"Henrik","full_name":"Buschmann, Henrik"},{"first_name":"Denis","last_name":"Saint Marcoux","full_name":"Saint Marcoux, Denis"},{"full_name":"Ullrich, Kristian","first_name":"Kristian","last_name":"Ullrich"},{"full_name":"Haas, Fabian","last_name":"Haas","first_name":"Fabian"},{"full_name":"Vanderstraeten, Lisa","first_name":"Lisa","last_name":"Vanderstraeten"},{"first_name":"Dirk","last_name":"Becker","full_name":"Becker, Dirk"},{"full_name":"Lang, Daniel","last_name":"Lang","first_name":"Daniel"},{"last_name":"Vosolsobě","first_name":"Stanislav","full_name":"Vosolsobě, Stanislav"},{"full_name":"Rombauts, Stephane","last_name":"Rombauts","first_name":"Stephane"},{"first_name":"Per","last_name":"Wilhelmsson","full_name":"Wilhelmsson, Per"},{"last_name":"Janitza","first_name":"Philipp","full_name":"Janitza, Philipp"},{"first_name":"Ramona","last_name":"Kern","full_name":"Kern, Ramona"},{"full_name":"Heyl, Alexander","first_name":"Alexander","last_name":"Heyl"},{"full_name":"Rümpler, Florian","first_name":"Florian","last_name":"Rümpler"},{"last_name":"Calderón Villalobos","first_name":"Luz","full_name":"Calderón Villalobos, Luz"},{"full_name":"Clay, John","first_name":"John","last_name":"Clay"},{"full_name":"Skokan, Roman","last_name":"Skokan","first_name":"Roman"},{"full_name":"Toyoda, Atsushi","last_name":"Toyoda","first_name":"Atsushi"},{"full_name":"Suzuki, Yutaka","first_name":"Yutaka","last_name":"Suzuki"},{"full_name":"Kagoshima, Hiroshi","first_name":"Hiroshi","last_name":"Kagoshima"},{"full_name":"Schijlen, Elio","last_name":"Schijlen","first_name":"Elio"},{"last_name":"Tajeshwar","first_name":"Navindra","full_name":"Tajeshwar, Navindra"},{"full_name":"Catarino, Bruno","first_name":"Bruno","last_name":"Catarino"},{"first_name":"Alexander","last_name":"Hetherington","full_name":"Hetherington, Alexander"},{"full_name":"Saltykova, Assia","first_name":"Assia","last_name":"Saltykova"},{"full_name":"Bonnot, Clemence","first_name":"Clemence","last_name":"Bonnot"},{"first_name":"Holger","last_name":"Breuninger","full_name":"Breuninger, Holger"},{"full_name":"Symeonidi, Aikaterini","first_name":"Aikaterini","last_name":"Symeonidi"},{"first_name":"Guru","last_name":"Radhakrishnan","full_name":"Radhakrishnan, Guru"},{"first_name":"Filip","last_name":"Van Nieuwerburgh","full_name":"Van Nieuwerburgh, Filip"},{"first_name":"Dieter","last_name":"Deforce","full_name":"Deforce, Dieter"},{"first_name":"Caren","last_name":"Chang","full_name":"Chang, Caren"},{"last_name":"Karol","first_name":"Kenneth","full_name":"Karol, Kenneth"},{"first_name":"Rainer","last_name":"Hedrich","full_name":"Hedrich, Rainer"},{"first_name":"Peter","last_name":"Ulvskov","full_name":"Ulvskov, Peter"},{"full_name":"Glöckner, Gernot","last_name":"Glöckner","first_name":"Gernot"},{"full_name":"Delwiche, Charles","first_name":"Charles","last_name":"Delwiche"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Van De Peer, Yves","last_name":"Van De Peer","first_name":"Yves"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"last_name":"Beilby","first_name":"Mary","full_name":"Beilby, Mary"},{"last_name":"Dolan","first_name":"Liam","full_name":"Dolan, Liam"},{"last_name":"Kohara","first_name":"Yuji","full_name":"Kohara, Yuji"},{"last_name":"Sugano","first_name":"Sumio","full_name":"Sugano, Sumio"},{"full_name":"Fujiyama, Asao","last_name":"Fujiyama","first_name":"Asao"},{"last_name":"Delaux","first_name":"Pierre Marc","full_name":"Delaux, Pierre Marc"},{"last_name":"Quint","first_name":"Marcel","full_name":"Quint, Marcel"},{"last_name":"Theissen","first_name":"Gunter","full_name":"Theissen, Gunter"},{"first_name":"Martin","last_name":"Hagemann","full_name":"Hagemann, Martin"},{"first_name":"Jesper","last_name":"Harholt","full_name":"Harholt, Jesper"},{"first_name":"Christophe","last_name":"Dunand","full_name":"Dunand, Christophe"},{"last_name":"Zachgo","first_name":"Sabine","full_name":"Zachgo, Sabine"},{"full_name":"Langdale, Jane","first_name":"Jane","last_name":"Langdale"},{"full_name":"Maumus, Florian","first_name":"Florian","last_name":"Maumus"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"full_name":"Gould, Sven B","last_name":"Gould","first_name":"Sven B"},{"first_name":"Stefan","last_name":"Rensing","full_name":"Rensing, Stefan"}],"doi":"10.1016/j.cell.2018.06.033","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"pmid":1,"department":[{"_id":"JiFr"}],"issue":"2","ddc":["580"],"publication":"Cell","citation":{"short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>.","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. 2018;174(2):448-464.e24. doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>","ieee":"T. Nishiyama <i>et al.</i>, “The Chara genome: Secondary complexity and implications for plant terrestrialization,” <i>Cell</i>, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018."},"page":"448 - 464.e24","scopus_import":"1","isi":1,"status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","article_processing_charge":"No","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","date_updated":"2026-06-18T17:39:09Z","acknowledgement":"In-Data-Review"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Inositol phosphates are assembly co-factors for HIV-1","publication_identifier":{"eissn":["1476-4687"]},"date_updated":"2023-09-12T07:44:37Z","article_processing_charge":"No","issue":"7719","department":[{"_id":"FlSc"}],"pmid":1,"status":"public","publication":"Nature","citation":{"ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>.","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512."},"page":"509–512","scopus_import":"1","isi":1,"_id":"150","publisher":"Nature Publishing Group","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/"}],"author":[{"full_name":"Dick, Robert","first_name":"Robert","last_name":"Dick"},{"full_name":"Zadrozny, Kaneil K","last_name":"Zadrozny","first_name":"Kaneil K"},{"first_name":"Chaoyi","last_name":"Xu","full_name":"Xu, Chaoyi"},{"first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078"},{"first_name":"Terri D","last_name":"Lyddon","full_name":"Lyddon, Terri D"},{"last_name":"Ricana","first_name":"Clifton L","full_name":"Ricana, Clifton L"},{"full_name":"Wagner, Jonathan M","first_name":"Jonathan M","last_name":"Wagner"},{"full_name":"Perilla, Juan R","first_name":"Juan R","last_name":"Perilla"},{"full_name":"Ganser, Pornillos Barbie K","last_name":"Ganser","first_name":"Pornillos Barbie K"},{"full_name":"Johnson, Marc C","last_name":"Johnson","first_name":"Marc C"},{"full_name":"Pornillos, Owen","last_name":"Pornillos","first_name":"Owen"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"}],"date_created":"2018-12-11T11:44:53Z","doi":"10.1038/s41586-018-0396-4","intvolume":"       560","type":"journal_article","external_id":{"isi":["000442483400046"],"pmid":["30158708"]},"oa_version":"Submitted Version","day":"29","month":"08","year":"2018","oa":1,"date_published":"2018-08-29T00:00:00Z","volume":560,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"publication_status":"published","article_type":"original","abstract":[{"text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.","lang":"eng"}]},{"oa":1,"year":"2018","volume":28,"date_published":"2018-07-26T00:00:00Z","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context."}],"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"7769","day":"26","external_id":{"isi":["000445118200007"]},"oa_version":"Submitted Version","month":"07","has_accepted_license":"1","doi":"10.1016/j.tcb.2018.06.006","date_created":"2018-12-11T11:44:54Z","author":[{"id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk","first_name":"Karol"},{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"intvolume":"        28","type":"journal_article","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":2185385,"checksum":"ef6d2b4e1fd63948539639242610bfa6","relation":"main_file","file_id":"6994","date_updated":"2020-07-14T12:45:00Z","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","date_created":"2019-11-07T12:55:20Z","creator":"lsazanov"}],"publisher":"Elsevier","_id":"152","status":"public","scopus_import":"1","isi":1,"publication":"Trends in Cell Biology","page":"835 - 867","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"citation":{"chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>.","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. 2018;28(10):835-867. doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>","apa":"Fiedorczuk, K., &#38; Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” <i>Trends in Cell Biology</i>, vol. 28, no. 10. Elsevier, pp. 835–867, 2018."},"issue":"10","ddc":["572"],"department":[{"_id":"LeSa"}],"date_updated":"2023-09-13T08:51:56Z","title":"Mammalian mitochondrial complex I structure and disease causing mutations","article_processing_charge":"No","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}]},{"pmid":1,"department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"publication":"Methods in Cell Biology","citation":{"ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91.","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In <i>Methods in Cell Biology</i> (Vol. 147, pp. 79–91). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: <i>Methods in Cell Biology</i>. Vol 147. Academic Press; 2018:79-91. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>.","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In <i>Methods in Cell Biology</i>, 147:79–91. Academic Press, 2018. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91."},"page":"79 - 91","scopus_import":"1","isi":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","publication_identifier":{"issn":["0091-679X"]},"date_updated":"2025-07-10T11:51:09Z","month":"07","external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"oa_version":"None","day":"27","publist_id":"7768","publication_status":"published","abstract":[{"text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters.","lang":"eng"}],"year":"2018","volume":147,"date_published":"2018-07-27T00:00:00Z","_id":"153","publisher":"Academic Press","type":"book_chapter","intvolume":"       147","date_created":"2018-12-11T11:44:54Z","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz"},{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","first_name":"Anne","last_name":"Reversat"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","first_name":"Alexander F","last_name":"Leithner"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"doi":"10.1016/bs.mcb.2018.07.004"},{"main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"publisher":"SPIE","_id":"155","doi":"10.1117/12.2309928","date_created":"2018-12-11T11:44:55Z","editor":[{"first_name":"D L","last_name":"Andrews","full_name":"Andrews, D L"},{"full_name":"Ostendorf, A","first_name":"A","last_name":"Ostendorf"},{"full_name":"Bain, A J","first_name":"A J","last_name":"Bain"},{"last_name":"Nunzi","first_name":"J M","full_name":"Nunzi, J M"}],"author":[{"full_name":"Xuereb, André","first_name":"André","last_name":"Xuereb"},{"full_name":"Aquilina, Matteo","last_name":"Aquilina","first_name":"Matteo"},{"first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423"}],"intvolume":"     10672","type":"conference","day":"04","external_id":{"isi":["000453298500019"],"arxiv":["1806.01000"]},"oa_version":"Preprint","month":"05","oa":1,"year":"2018","volume":10672,"date_published":"2018-05-04T00:00:00Z","arxiv":1,"alternative_title":["Proceedings of SPIE"],"publication_status":"published","abstract":[{"text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource.","lang":"eng"}],"publist_id":"7766","quality_controlled":"1","conference":{"start_date":"2018-04-22","name":"SPIE: The international society for optical engineering","end_date":"2018-04-26","location":"Strasbourg, France"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-18T08:12:24Z","title":"Routing thermal noise through quantum networks","article_number":"106721N","article_processing_charge":"No","department":[{"_id":"JoFi"}],"status":"public","scopus_import":"1","isi":1,"citation":{"short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","mla":"Xuereb, André, et al. <i>Routing Thermal Noise through Quantum Networks</i>. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>.","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.","chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>.","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","apa":"Xuereb, A., Aquilina, M., &#38; Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, &#38; J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>"}},{"has_accepted_license":"1","month":"07","oa_version":"Submitted Version","external_id":{"isi":["000489765800009"]},"day":"12","publist_id":"7765","file_date_updated":"2020-10-09T06:22:41Z","abstract":[{"lang":"eng","text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost."}],"publication_status":"published","alternative_title":["LNCS"],"volume":10951,"date_published":"2018-07-12T00:00:00Z","oa":1,"year":"2018","_id":"156","publisher":"Springer","file":[{"creator":"dernst","date_created":"2020-10-09T06:22:41Z","file_name":"2018_LNCS_Ferrere.pdf","date_updated":"2020-10-09T06:22:41Z","access_level":"open_access","file_size":485576,"content_type":"application/pdf","file_id":"8637","success":1,"relation":"main_file","checksum":"a045c213c42c445f1889326f8db82a0a"}],"intvolume":"     10951","type":"conference","author":[{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"}],"date_created":"2018-12-11T11:44:55Z","doi":"10.1007/978-3-319-95582-7_9","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"department":[{"_id":"ToHe"}],"ddc":["000"],"citation":{"ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: Formal Methods, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>.","mla":"Ferrere, Thomas. <i>The Compound Interest in Relaxing Punctuality</i>. Vol. 10951, Springer, 2018, pp. 147–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>.","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: Formal Methods, LNCS, vol. 10951, 147–164.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164."},"page":"147 - 164","isi":1,"scopus_import":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"conference":{"start_date":"2018-07-15","end_date":"2018-07-17","location":"Oxford, UK","name":"FM: Formal Methods"},"quality_controlled":"1","article_processing_charge":"No","title":"The compound interest in relaxing punctuality","date_updated":"2025-07-10T11:51:10Z"},{"article_processing_charge":"No","date_updated":"2025-04-15T06:30:08Z","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","title":"Evolution of cooperation in stochastic games","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"scopus_import":"1","citation":{"mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>.","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” <i>Nature</i>, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. <i>Nature</i>. 2018;559(7713):246-249. doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., &#38; Nowak, M. (2018). Evolution of cooperation in stochastic games. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>"},"page":"246 - 249","publication":"Nature","status":"public","department":[{"_id":"KrCh"}],"ddc":["000"],"issue":"7713","intvolume":"       559","type":"journal_article","project":[{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41586-018-0277-x","author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"last_name":"Šimsa","first_name":"Štepán","full_name":"Šimsa, Štepán"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"date_created":"2018-12-11T11:44:56Z","publisher":"Nature Publishing Group","_id":"157","file":[{"checksum":"011ab905cf9a410bc2b96f15174d654d","relation":"main_file","file_id":"7049","content_type":"application/pdf","access_level":"open_access","file_size":2834442,"date_updated":"2020-07-14T12:45:02Z","date_created":"2019-11-19T08:09:57Z","file_name":"2018_Nature_Hilbe.pdf","creator":"dernst"}],"abstract":[{"text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas.","lang":"eng"}],"publication_status":"published","publist_id":"7764","related_material":{"link":[{"url":"https://ist.ac.at/en/news/engineering-cooperation/","relation":"press_release","description":"News on IST Homepage"}]},"file_date_updated":"2020-07-14T12:45:02Z","volume":559,"date_published":"2018-07-04T00:00:00Z","oa":1,"year":"2018","has_accepted_license":"1","month":"07","day":"04","oa_version":"Submitted Version","ec_funded":1,"external_id":{"isi":["000438240900054"]}},{"date_created":"2018-12-11T11:44:56Z","author":[{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"full_name":"Park, Chulmin","last_name":"Park","first_name":"Chulmin"},{"last_name":"Gutièrrez","first_name":"Carla","full_name":"Gutièrrez, Carla"},{"full_name":"Wójcikowska, Barbara","last_name":"Wójcikowska","first_name":"Barbara"},{"first_name":"Aleš","last_name":"Pěnčík","full_name":"Pěnčík, Aleš"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"first_name":"Junyi","last_name":"Chen","full_name":"Chen, Junyi"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"first_name":"Thomas","last_name":"Dresselhaus","full_name":"Dresselhaus, Thomas"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"},{"full_name":"Laux, Thomas","last_name":"Laux","first_name":"Thomas"}],"project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"doi":"10.1038/s41477-018-0204-z","intvolume":"         4","type":"journal_article","_id":"158","publisher":"Nature Publishing Group","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211","open_access":"1"}],"year":"2018","oa":1,"date_published":"2018-07-16T00:00:00Z","volume":4,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/","relation":"press_release","description":"News on IST Homepage"}]},"publist_id":"7763","publication_status":"published","abstract":[{"lang":"eng","text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development."}],"external_id":{"isi":["000443861300011"],"pmid":["30013211"]},"ec_funded":1,"oa_version":"Submitted Version","day":"16","month":"07","title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","date_updated":"2025-04-15T07:48:03Z","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","publication":"Nature Plants","citation":{"short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>.","ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.","chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>.","ieee":"H. Robert <i>et al.</i>, “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. 2018;4(8):548-553. doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>"},"page":"548 - 553","scopus_import":"1","isi":1,"issue":"8","pmid":1,"department":[{"_id":"JiFr"}]},{"file_date_updated":"2020-07-14T12:45:03Z","related_material":{"link":[{"url":"https://doi.org/10.1038/s41589-021-00744-3","relation":"erratum"}]},"publist_id":"7762","publication_status":"published","article_type":"original","abstract":[{"text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control.","lang":"eng"}],"oa":1,"year":"2018","date_published":"2018-07-16T00:00:00Z","volume":14,"month":"07","has_accepted_license":"1","external_id":{"isi":["000438970200010"]},"oa_version":"Submitted Version","day":"16","intvolume":"        14","type":"journal_article","date_created":"2018-12-11T11:44:56Z","author":[{"last_name":"Fehrentz","first_name":"Timm","full_name":"Fehrentz, Timm"},{"first_name":"Florian","last_name":"Huber","full_name":"Huber, Florian"},{"first_name":"Nina","last_name":"Hartrampf","full_name":"Hartrampf, Nina"},{"full_name":"Bruegmann, Tobias","first_name":"Tobias","last_name":"Bruegmann"},{"full_name":"Frank, James","last_name":"Frank","first_name":"James"},{"first_name":"Nicholas","last_name":"Fine","full_name":"Fine, Nicholas"},{"full_name":"Malan, Daniela","first_name":"Daniela","last_name":"Malan"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tikhonov, Denis","first_name":"Denis","last_name":"Tikhonov"},{"full_name":"Sumser, Maritn","last_name":"Sumser","first_name":"Maritn"},{"first_name":"Philipp","last_name":"Sasse","full_name":"Sasse, Philipp"},{"last_name":"Hodson","first_name":"David","full_name":"Hodson, David"},{"full_name":"Zhorov, Boris","last_name":"Zhorov","first_name":"Boris"},{"full_name":"Klocker, Nikolaj","last_name":"Klocker","first_name":"Nikolaj"},{"full_name":"Trauner, Dirk","last_name":"Trauner","first_name":"Dirk"}],"doi":"10.1038/s41589-018-0090-8","_id":"159","publisher":"Nature Publishing Group","file":[{"creator":"dernst","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","date_created":"2020-05-14T12:14:09Z","date_updated":"2020-07-14T12:45:03Z","access_level":"open_access","file_size":6321000,"content_type":"application/pdf","file_id":"7832","checksum":"d42935094ec845f54a0688bf12986d62","relation":"main_file"}],"publication":"Nature Chemical Biology","page":"764 - 767","citation":{"ieee":"T. Fehrentz <i>et al.</i>, “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” <i>Nature Chemical Biology</i>, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018.","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. <i>Nature Chemical Biology</i>. 2018;14(8):764-767. doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>","ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:<a href=\"https://doi.org/10.1038/s41589-018-0090-8\">10.1038/s41589-018-0090-8</a>.","chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41589-018-0090-8\">https://doi.org/10.1038/s41589-018-0090-8</a>.","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767."},"scopus_import":"1","isi":1,"status":"public","department":[{"_id":"JoDa"}],"issue":"8","ddc":["570"],"article_processing_charge":"No","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","date_updated":"2023-09-13T09:36:35Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1"},{"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"doi":"10.1103/PhysRevFluids.3.103303","date_created":"2018-12-11T11:44:10Z","author":[{"first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"type":"journal_article","intvolume":"         3","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":1838431,"checksum":"7fc0a2322214d1c04debef36d5bf2e8a","relation":"main_file","file_id":"5043","date_updated":"2020-07-14T12:45:04Z","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","date_created":"2018-12-12T10:13:56Z","creator":"system"}],"publisher":"American Physical Society","_id":"16","volume":3,"date_published":"2018-10-16T00:00:00Z","year":"2018","oa":1,"abstract":[{"text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives.","lang":"eng"}],"publication_status":"published","article_type":"original","publist_id":"8039","file_date_updated":"2020-07-14T12:45:04Z","day":"16","oa_version":"Submitted Version","external_id":{"isi":["000447469200001"]},"ec_funded":1,"has_accepted_license":"1","month":"10","acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","date_updated":"2025-04-14T07:44:02Z","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","article_number":"103303","article_processing_charge":"No","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"status":"public","pubrep_id":"1062","isi":1,"scopus_import":"1","citation":{"short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>.","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>.","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","apa":"Varshney, A., &#38; Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">https://doi.org/10.1103/PhysRevFluids.3.103303</a>","ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103303\">10.1103/PhysRevFluids.3.103303</a>"},"publication":"Physical Review Fluids","ddc":["532"],"issue":"10","department":[{"_id":"BjHo"}]},{"date_created":"2018-12-11T11:44:57Z","author":[{"last_name":"Kragl","first_name":"Bernhard","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"doi":"10.1007/978-3-319-96145-3_5","intvolume":"     10981","type":"conference","file":[{"content_type":"application/pdf","file_size":1603844,"access_level":"open_access","checksum":"c64fff560fe5a7532ec10626ad1c215e","relation":"main_file","file_id":"5705","date_updated":"2020-07-14T12:45:04Z","date_created":"2018-12-17T12:52:12Z","file_name":"2018_LNCS_Kragl.pdf","creator":"dernst"}],"_id":"160","publisher":"Springer","alternative_title":["LNCS"],"date_published":"2018-07-18T00:00:00Z","volume":10981,"oa":1,"year":"2018","related_material":{"record":[{"status":"public","id":"8332","relation":"dissertation_contains"}]},"publist_id":"7761","file_date_updated":"2020-07-14T12:45:04Z","abstract":[{"text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs.","lang":"eng"}],"publication_status":"published","oa_version":"Published Version","external_id":{"isi":["000491481600005"]},"day":"18","has_accepted_license":"1","month":"07","title":"Layered Concurrent Programs","date_updated":"2026-04-08T07:23:52Z","article_processing_charge":"No","conference":{"end_date":"2018-07-17","location":"Oxford, UK","name":"CAV: Computer Aided Verification","start_date":"2018-07-14"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"page":"79 - 102","citation":{"apa":"Kragl, B., &#38; Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>.","mla":"Kragl, Bernhard, and Shaz Qadeer. <i>Layered Concurrent Programs</i>. Vol. 10981, Springer, 2018, pp. 79–102, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102."},"isi":1,"scopus_import":"1","ddc":["000"],"department":[{"_id":"ToHe"}]},{"oa_version":"Published Version","ec_funded":1,"external_id":{"isi":["000440149300021"]},"day":"30","has_accepted_license":"1","month":"07","volume":9,"date_published":"2018-07-30T00:00:00Z","year":"2018","oa":1,"related_material":{"record":[{"relation":"popular_science","id":"5587","status":"public"}]},"publist_id":"7760","file_date_updated":"2020-07-14T12:45:06Z","abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"publication_status":"published","file":[{"file_size":1043205,"access_level":"open_access","content_type":"application/pdf","file_id":"5728","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","relation":"main_file","date_created":"2018-12-17T16:44:28Z","file_name":"2018_NatureComm_DeMartino.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:06Z"}],"_id":"161","publisher":"Springer Nature","author":[{"first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706"},{"first_name":"Andersson Anna","last_name":"Mc","full_name":"Mc, Andersson Anna"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"date_created":"2018-12-11T11:44:57Z","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"doi":"10.1038/s41467-018-05417-9","type":"journal_article","intvolume":"         9","ddc":["570"],"issue":"1","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"status":"public","citation":{"ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” <i>Nature Communications</i>, vol. 9, no. 1. Springer Nature, 2018.","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &#38; Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>.","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018)."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"Nature Communications","isi":1,"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Statistical mechanics for metabolic networks during steady state growth","date_updated":"2025-04-15T06:50:08Z","article_processing_charge":"No","article_number":"2988"},{"title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","date_updated":"2025-04-14T07:27:30Z","article_processing_charge":"No","article_number":"e34465","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","citation":{"ieee":"M. Kaucka <i>et al.</i>, “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>, vol. 7, e34465, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465.","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018)."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"eLife","isi":1,"scopus_import":"1","ddc":["571"],"department":[{"_id":"AnKi"}],"date_created":"2018-12-11T11:44:57Z","author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"full_name":"Petersen, Julian","first_name":"Julian","last_name":"Petersen"},{"first_name":"Marketa","last_name":"Tesarova","full_name":"Tesarova, Marketa"},{"full_name":"Szarowska, Bara","first_name":"Bara","last_name":"Szarowska"},{"full_name":"Kastriti, Maria","first_name":"Maria","last_name":"Kastriti"},{"full_name":"Xie, Meng","last_name":"Xie","first_name":"Meng"},{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"first_name":"Karl","last_name":"Annusver","full_name":"Annusver, Karl"},{"full_name":"Kasper, Maria","first_name":"Maria","last_name":"Kasper"},{"last_name":"Symmons","first_name":"Orsolya","full_name":"Symmons, Orsolya"},{"last_name":"Pan","first_name":"Leslie","full_name":"Pan, Leslie"},{"full_name":"Spitz, Francois","first_name":"Francois","last_name":"Spitz"},{"full_name":"Kaiser, Jozef","last_name":"Kaiser","first_name":"Jozef"},{"full_name":"Hovorakova, Maria","last_name":"Hovorakova","first_name":"Maria"},{"full_name":"Zikmund, Tomas","first_name":"Tomas","last_name":"Zikmund"},{"full_name":"Sunadome, Kazunori","last_name":"Sunadome","first_name":"Kazunori"},{"last_name":"Matise","first_name":"Michael P","full_name":"Matise, Michael P"},{"full_name":"Wang, Hui","last_name":"Wang","first_name":"Hui"},{"last_name":"Marklund","first_name":"Ulrika","full_name":"Marklund, Ulrika"},{"full_name":"Abdo, Hind","last_name":"Abdo","first_name":"Hind"},{"full_name":"Ernfors, Patrik","last_name":"Ernfors","first_name":"Patrik"},{"full_name":"Maire, Pascal","first_name":"Pascal","last_name":"Maire"},{"first_name":"Maud","last_name":"Wurmser","full_name":"Wurmser, Maud"},{"last_name":"Chagin","first_name":"Andrei S","full_name":"Chagin, Andrei S"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"full_name":"Adameyko, Igor","first_name":"Igor","last_name":"Adameyko"}],"project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"doi":"10.7554/eLife.34465","type":"journal_article","intvolume":"         7","file":[{"content_type":"application/pdf","file_size":9816484,"access_level":"open_access","relation":"main_file","checksum":"da2378cdcf6b5461dcde194e4d608343","file_id":"5727","date_updated":"2020-07-14T12:45:07Z","file_name":"2018_eLife_Kaucka.pdf","date_created":"2018-12-17T16:41:58Z","creator":"dernst"}],"_id":"162","publisher":"eLife Sciences Publications","volume":7,"date_published":"2018-06-13T00:00:00Z","oa":1,"year":"2018","related_material":{"record":[{"relation":"research_data","status":"public","id":"9838"}]},"publist_id":"7759","file_date_updated":"2020-07-14T12:45:07Z","abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"publication_status":"published","oa_version":"Published Version","external_id":{"isi":["000436227500001"]},"ec_funded":1,"day":"13","has_accepted_license":"1","month":"06"},{"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["0022-1554"]},"date_updated":"2026-06-18T17:50:00Z","title":"Agitation modules: Flexible means to accelerate automated freeze substitution","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"pmid":1,"issue":"12","ddc":["570"],"scopus_import":"1","isi":1,"publication":"Journal of Histochemistry and Cytochemistry","page":"903-921","citation":{"chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications, 2018. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>.","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921.","mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>.","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. 2018;66(12):903-921. doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>","ieee":"S. Reipert <i>et al.</i>, “Agitation modules: Flexible means to accelerate automated freeze substitution,” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018."},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1369/0022155418786698"}],"publisher":"SAGE Publications","_id":"163","type":"journal_article","intvolume":"        66","doi":"10.1369/0022155418786698","date_created":"2018-12-11T11:44:57Z","author":[{"first_name":"Siegfried","last_name":"Reipert","full_name":"Reipert, Siegfried"},{"full_name":"Goldammer, Helmuth","last_name":"Goldammer","first_name":"Helmuth"},{"full_name":"Richardson, Christine","first_name":"Christine","last_name":"Richardson"},{"last_name":"Goldberg","first_name":"Martin","full_name":"Goldberg, Martin"},{"last_name":"Hawkins","first_name":"Timothy","full_name":"Hawkins, Timothy"},{"last_name":"Hollergschwandtner","first_name":"Elena","full_name":"Hollergschwandtner, Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Antreich, Sebastian","first_name":"Sebastian","last_name":"Antreich"},{"full_name":"Stierhof, York","last_name":"Stierhof","first_name":"York"}],"month":"12","day":"01","external_id":{"isi":["000452277700005"],"pmid":["29969056"]},"oa_version":"Published Version","article_type":"original","publication_status":"published","abstract":[{"text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches.","lang":"eng"}],"oa":1,"year":"2018","date_published":"2018-12-01T00:00:00Z","volume":66},{"title":"Drag enhancement and drag reduction in viscoelastic flow","date_updated":"2025-04-14T07:43:59Z","article_processing_charge":"No","article_number":"103302 ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","pubrep_id":"1061","status":"public","citation":{"short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302.","mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>.","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>.","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","apa":"Varshney, A., &#38; Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>"},"publication":"Physical Review Fluids","isi":1,"scopus_import":"1","ddc":["532"],"issue":"10","department":[{"_id":"BjHo"}],"author":[{"first_name":"Atul","last_name":"Varshney","full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999"},{"last_name":"Steinberg","first_name":"Victor","full_name":"Steinberg, Victor"}],"date_created":"2018-12-11T11:44:11Z","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"doi":"10.1103/PhysRevFluids.3.103302","type":"journal_article","intvolume":"         3","file":[{"date_updated":"2020-07-14T12:45:12Z","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","date_created":"2018-12-12T10:10:14Z","creator":"system","content_type":"application/pdf","access_level":"open_access","file_size":1409040,"relation":"main_file","checksum":"e1445be33e8165114e96246275600750","file_id":"4800"}],"_id":"17","publisher":"American Physical Society","volume":3,"date_published":"2018-10-15T00:00:00Z","year":"2018","oa":1,"publist_id":"8038","file_date_updated":"2020-07-14T12:45:12Z","abstract":[{"text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow.","lang":"eng"}],"publication_status":"published","oa_version":"Published Version","external_id":{"isi":["000447311500001"]},"ec_funded":1,"day":"15","has_accepted_license":"1","month":"10"},{"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","end_date":"2018-06-14"},"quality_controlled":"1","article_number":"39","title":"Hanani-Tutte for approximating maps of graphs","date_updated":"2021-01-12T06:53:36Z","publication_identifier":{"isbn":["978-3-95977-066-8"]},"department":[{"_id":"UlWa"}],"ddc":["510"],"citation":{"mla":"Fulek, Radoslav, and Jan Kynčl. <i>Hanani-Tutte for Approximating Maps of Graphs</i>. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>.","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>","apa":"Fulek, R., &#38; Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"scopus_import":1,"status":"public","_id":"185","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file":[{"date_updated":"2020-07-14T12:45:19Z","creator":"dernst","date_created":"2018-12-17T12:33:52Z","file_name":"2018_LIPIcs_Fulek.pdf","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","relation":"main_file","file_id":"5701","content_type":"application/pdf","access_level":"open_access","file_size":718857}],"type":"conference","intvolume":"        99","author":[{"first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"}],"date_created":"2018-12-11T11:45:04Z","doi":"10.4230/LIPIcs.SoCG.2018.39","project":[{"grant_number":"M02281","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","month":"01","oa_version":"Published Version","day":"01","publist_id":"7735","file_date_updated":"2020-07-14T12:45:19Z","abstract":[{"lang":"eng","text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint &quot;pipes&quot; corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once."}],"publication_status":"published","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"volume":99,"date_published":"2018-01-01T00:00:00Z","oa":1,"year":"2018"},{"doi":"10.4230/LIPIcs.SoCG.2018.40","project":[{"grant_number":"M02281","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"}],"date_created":"2018-12-11T11:45:05Z","type":"conference","intvolume":"        99","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"186","year":"2018","oa":1,"date_published":"2018-06-11T00:00:00Z","volume":99,"arxiv":1,"alternative_title":["LIPIcs"],"publication_status":"published","abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.","lang":"eng"}],"related_material":{"record":[{"id":"11593","status":"public","relation":"later_version"}]},"publist_id":"7734","day":"11","external_id":{"arxiv":["1803.05085"]},"oa_version":"Submitted Version","month":"06","date_updated":"2025-04-14T13:52:37Z","title":"The ℤ2-Genus of Kuratowski minors","article_processing_charge":"No","quality_controlled":"1","conference":{"start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","page":"40.1 - 40.14","citation":{"apa":"Fulek, R., &#38; Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>.","mla":"Fulek, Radoslav, and Jan Kynčl. <i>The ℤ2-Genus of Kuratowski Minors</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>.","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14."},"department":[{"_id":"UlWa"}]},{"ddc":["516"],"department":[{"_id":"HeEd"}],"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. <i>The Multi-Cover Persistence of Euclidean Balls</i>. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>."},"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"location":"Budapest, Hungary","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11"},"language":[{"iso":"eng"}],"quality_controlled":"1","title":"The multi-cover persistence of Euclidean balls","date_updated":"2026-04-08T07:01:29Z","acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","article_number":"34","oa_version":"Published Version","day":"11","month":"06","has_accepted_license":"1","alternative_title":["LIPIcs"],"oa":1,"year":"2018","date_published":"2018-06-11T00:00:00Z","volume":99,"file_date_updated":"2020-07-14T12:45:19Z","related_material":{"record":[{"relation":"later_version","id":"9317","status":"public"},{"id":"9056","status":"public","relation":"dissertation_contains"}]},"publist_id":"7732","publication_status":"published","abstract":[{"lang":"eng","text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. "}],"file":[{"date_updated":"2020-07-14T12:45:19Z","creator":"dernst","file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","date_created":"2018-12-18T09:27:22Z","content_type":"application/pdf","file_size":528018,"access_level":"open_access","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","relation":"main_file","file_id":"5738"}],"_id":"187","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"first_name":"Georg F","last_name":"Osang","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116"}],"date_created":"2018-12-11T11:45:05Z","project":[{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"doi":"10.4230/LIPIcs.SoCG.2018.34","type":"conference","intvolume":"        99"}]