[{"department":[{"_id":"FrLo"}],"external_id":{"arxiv":["1804.11130"]},"doi":"10.48550/arXiv.1804.11130","extern":"1","oa_version":"Preprint","day":"30","oa":1,"citation":{"apa":"Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., &#38; Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>","mla":"Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, 1804.11130, doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>.","ama":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” <i>arXiv</i>. .","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>.","ista":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130."},"abstract":[{"text":"A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples.","lang":"eng"}],"date_updated":"2023-09-13T12:23:03Z","month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"submitted","date_published":"2018-04-30T00:00:00Z","author":[{"first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"last_name":"Vincent","first_name":"Damien","full_name":"Vincent, Damien"},{"full_name":"Tolstikhin, Ilya","first_name":"Ilya","last_name":"Tolstikhin"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"}],"status":"public","date_created":"2023-09-13T12:20:49Z","article_number":"1804.11130","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1804.11130","open_access":"1"}],"type":"preprint","year":"2018","_id":"14327","language":[{"iso":"eng"}],"publication":"arXiv","arxiv":1,"title":"Competitive training of mixtures of independent deep generative models","article_processing_charge":"No"},{"scopus_import":"1","department":[{"_id":"ToHe"}],"external_id":{"isi":["000545262800041"]},"conference":{"end_date":"2018-07-12","location":"Oxford, UK","start_date":"2018-07-09","name":"LICS: Logic in Computer Science"},"doi":"10.1145/3209108.3209194","publisher":"IEEE","oa_version":"None","day":"09","citation":{"short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.","ieee":"T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.","ama":"Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>.","apa":"Ferrere, T., Henzinger, T. A., &#38; Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>","mla":"Ferrere, Thomas, et al. <i>A Theory of Register Monitors</i>. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>.","ista":"Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403."},"volume":"Part F138033","page":"394 - 403","abstract":[{"text":"The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines.","lang":"eng"}],"date_updated":"2023-09-08T11:49:13Z","quality_controlled":"1","publist_id":"7779","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"month":"07","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-09T00:00:00Z","publication_status":"published","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","last_name":"Ferrere","first_name":"Thomas","full_name":"Ferrere, Thomas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Ege","last_name":"Saraç","full_name":"Saraç, Ege"}],"status":"public","date_created":"2018-12-11T11:44:52Z","type":"conference","_id":"144","year":"2018","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"A theory of register monitors"},{"publication_identifier":{"issn":["0261-4189"]},"file":[{"file_id":"5710","checksum":"a540feb6c9af6aefc78de531461a8835","access_level":"open_access","date_updated":"2020-07-14T12:44:56Z","relation":"main_file","content_type":"application/pdf","file_name":"2018_EMBO_Truckenbrodt.pdf","file_size":2846470,"date_created":"2018-12-17T14:17:29Z","creator":"dernst"}],"external_id":{"isi":["000440416900005"],"pmid":["29950309"]},"scopus_import":"1","issue":"15","oa_version":"Published Version","doi":"10.15252/embj.201798044","oa":1,"day":"01","acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","date_published":"2018-08-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"original","status":"public","ddc":["570"],"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:44:56Z","publication":"The EMBO Journal","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","department":[{"_id":"JoDa"}],"pmid":1,"publisher":"Wiley","volume":37,"citation":{"ieee":"S. M. Truckenbrodt <i>et al.</i>, “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” <i>The EMBO Journal</i>, vol. 37, no. 15. Wiley, 2018.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>. Wiley, 2018. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>.","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. 2018;37(15). doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>, vol. 37, no. 15, e98044, Wiley, 2018, doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>.","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. Wiley. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044."},"date_updated":"2023-09-13T09:02:48Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins.","lang":"eng"}],"has_accepted_license":"1","quality_controlled":"1","publist_id":"7778","publication_status":"published","month":"08","isi":1,"author":[{"last_name":"Truckenbrodt","first_name":"Sven M","full_name":"Truckenbrodt, Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Viplav","first_name":"Abhiyan","full_name":"Viplav, Abhiyan"},{"full_name":"Jähne, Sebsatian","last_name":"Jähne","first_name":"Sebsatian"},{"full_name":"Vogts, Angela","first_name":"Angela","last_name":"Vogts"},{"full_name":"Denker, Annette","last_name":"Denker","first_name":"Annette"},{"first_name":"Hanna","last_name":"Wildhagen","full_name":"Wildhagen, Hanna"},{"last_name":"Fornasiero","first_name":"Eugenio","full_name":"Fornasiero, Eugenio"},{"full_name":"Rizzoli, Silvio","last_name":"Rizzoli","first_name":"Silvio"}],"intvolume":"        37","date_created":"2018-12-11T11:44:52Z","type":"journal_article","article_number":"e98044","_id":"145","year":"2018"},{"file_date_updated":"2020-07-14T12:44:56Z","language":[{"iso":"eng"}],"publication":"Nature Plants","article_processing_charge":"No","title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-30T00:00:00Z","article_type":"original","status":"public","ddc":["580"],"day":"30","oa":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:44:56Z","file_id":"7043","checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","file_name":"2018_NaturePlants_Shi.pdf","date_created":"2019-11-18T16:24:07Z","file_size":226829,"creator":"dernst"}],"issue":"8","scopus_import":"1","external_id":{"isi":["000443861300016"],"pmid":["30061750"]},"doi":"10.1038/s41477-018-0212-z","oa_version":"Submitted Version","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/","description":"News on IST Homepage","relation":"press_release"}]},"type":"journal_article","year":"2018","_id":"146","isi":1,"month":"07","publication_status":"published","author":[{"last_name":"Shi","first_name":"Chun Lin","full_name":"Shi, Chun Lin"},{"last_name":"Von Wangenheim","first_name":"Daniel","full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247"},{"last_name":"Herrmann","first_name":"Ullrich","full_name":"Herrmann, Ullrich"},{"last_name":"Wildhagen","first_name":"Mari","full_name":"Wildhagen, Mari"},{"id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","full_name":"Kulik, Ivan","first_name":"Ivan","last_name":"Kulik"},{"full_name":"Kopf, Andreas","first_name":"Andreas","last_name":"Kopf"},{"full_name":"Ishida, Takashi","first_name":"Takashi","last_name":"Ishida"},{"first_name":"Vilde","last_name":"Olsson","full_name":"Olsson, Vilde"},{"last_name":"Anker","first_name":"Mari Kristine","full_name":"Anker, Mari Kristine"},{"full_name":"Albert, Markus","last_name":"Albert","first_name":"Markus"},{"full_name":"Butenko, Melinka A","last_name":"Butenko","first_name":"Melinka A"},{"first_name":"Georg","last_name":"Felix","full_name":"Felix, Georg"},{"full_name":"Sawa, Shinichiro","first_name":"Shinichiro","last_name":"Sawa"},{"last_name":"Claassen","first_name":"Manfred","full_name":"Claassen, Manfred"},{"first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Reidunn B","last_name":"Aalen","full_name":"Aalen, Reidunn B"}],"intvolume":"         4","date_created":"2018-12-11T11:44:52Z","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.","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>","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>.","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>","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."},"volume":4,"page":"596 - 604","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-09-19T10:08:45Z","has_accepted_license":"1","publist_id":"7777","quality_controlled":"1","department":[{"_id":"JiFr"}],"pmid":1,"publisher":"Nature Publishing Group"},{"day":"12","oa":1,"doi":"10.1105/tpc.18.00127","oa_version":"Published Version","publication_identifier":{"issn":["1040-4651"]},"scopus_import":"1","issue":"10","external_id":{"pmid":["30018156"],"isi":["000450000500023"]},"language":[{"iso":"eng"}],"publication":"The Plant Cell","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1105/tpc.18.00127","open_access":"1"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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_published":"2018-11-12T00:00:00Z","article_type":"original","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."}],"date_updated":"2025-05-07T11:12:30Z","publist_id":"7776","quality_controlled":"1","citation":{"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>","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>.","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.","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>.","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.","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>","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."},"page":"2553 - 2572","volume":30,"pmid":1,"publisher":"Oxford University Press","department":[{"_id":"JiFr"}],"type":"journal_article","year":"2018","_id":"147","intvolume":"        30","date_created":"2018-12-11T11:44:52Z","isi":1,"ec_funded":1,"month":"11","publication_status":"published","project":[{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"}],"author":[{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula","last_name":"Kania","first_name":"Urszula"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"full_name":"Lu, Qing","first_name":"Qing","last_name":"Lu"},{"last_name":"Hicks","first_name":"Glenn R","full_name":"Hicks, Glenn R"},{"full_name":"Nerinckx, Wim","first_name":"Wim","last_name":"Nerinckx"},{"first_name":"Kiril","last_name":"Mishev","full_name":"Mishev, Kiril"},{"last_name":"Peurois","first_name":"Francois","full_name":"Peurois, Francois"},{"full_name":"Cherfils, Jacqueline","last_name":"Cherfils","first_name":"Jacqueline"},{"last_name":"De","first_name":"Rycke Riet Maria","full_name":"De, Rycke Riet Maria"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"},{"first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}]},{"type":"journal_article","_id":"148","year":"2018","intvolume":"       174","date_created":"2018-12-11T11:44:53Z","month":"07","isi":1,"ec_funded":1,"project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","author":[{"last_name":"Nishiyama","first_name":"Tomoaki","full_name":"Nishiyama, Tomoaki"},{"last_name":"Sakayama","first_name":"Hidetoshi","full_name":"Sakayama, Hidetoshi"},{"first_name":"Jan","last_name":"De Vries","full_name":"De Vries, Jan"},{"first_name":"Henrik","last_name":"Buschmann","full_name":"Buschmann, Henrik"},{"last_name":"Saint Marcoux","first_name":"Denis","full_name":"Saint Marcoux, Denis"},{"last_name":"Ullrich","first_name":"Kristian","full_name":"Ullrich, Kristian"},{"full_name":"Haas, Fabian","first_name":"Fabian","last_name":"Haas"},{"first_name":"Lisa","last_name":"Vanderstraeten","full_name":"Vanderstraeten, Lisa"},{"first_name":"Dirk","last_name":"Becker","full_name":"Becker, Dirk"},{"first_name":"Daniel","last_name":"Lang","full_name":"Lang, Daniel"},{"last_name":"Vosolsobě","first_name":"Stanislav","full_name":"Vosolsobě, Stanislav"},{"last_name":"Rombauts","first_name":"Stephane","full_name":"Rombauts, Stephane"},{"full_name":"Wilhelmsson, Per","first_name":"Per","last_name":"Wilhelmsson"},{"first_name":"Philipp","last_name":"Janitza","full_name":"Janitza, Philipp"},{"full_name":"Kern, Ramona","last_name":"Kern","first_name":"Ramona"},{"full_name":"Heyl, Alexander","last_name":"Heyl","first_name":"Alexander"},{"last_name":"Rümpler","first_name":"Florian","full_name":"Rümpler, Florian"},{"first_name":"Luz","last_name":"Calderón Villalobos","full_name":"Calderón Villalobos, Luz"},{"full_name":"Clay, John","last_name":"Clay","first_name":"John"},{"full_name":"Skokan, Roman","last_name":"Skokan","first_name":"Roman"},{"first_name":"Atsushi","last_name":"Toyoda","full_name":"Toyoda, Atsushi"},{"first_name":"Yutaka","last_name":"Suzuki","full_name":"Suzuki, Yutaka"},{"last_name":"Kagoshima","first_name":"Hiroshi","full_name":"Kagoshima, Hiroshi"},{"full_name":"Schijlen, Elio","first_name":"Elio","last_name":"Schijlen"},{"full_name":"Tajeshwar, Navindra","last_name":"Tajeshwar","first_name":"Navindra"},{"first_name":"Bruno","last_name":"Catarino","full_name":"Catarino, Bruno"},{"full_name":"Hetherington, Alexander","last_name":"Hetherington","first_name":"Alexander"},{"first_name":"Assia","last_name":"Saltykova","full_name":"Saltykova, Assia"},{"full_name":"Bonnot, Clemence","first_name":"Clemence","last_name":"Bonnot"},{"full_name":"Breuninger, Holger","last_name":"Breuninger","first_name":"Holger"},{"full_name":"Symeonidi, Aikaterini","first_name":"Aikaterini","last_name":"Symeonidi"},{"last_name":"Radhakrishnan","first_name":"Guru","full_name":"Radhakrishnan, Guru"},{"full_name":"Van Nieuwerburgh, Filip","first_name":"Filip","last_name":"Van Nieuwerburgh"},{"first_name":"Dieter","last_name":"Deforce","full_name":"Deforce, Dieter"},{"full_name":"Chang, Caren","last_name":"Chang","first_name":"Caren"},{"full_name":"Karol, Kenneth","last_name":"Karol","first_name":"Kenneth"},{"last_name":"Hedrich","first_name":"Rainer","full_name":"Hedrich, Rainer"},{"first_name":"Peter","last_name":"Ulvskov","full_name":"Ulvskov, Peter"},{"full_name":"Glöckner, Gernot","last_name":"Glöckner","first_name":"Gernot"},{"last_name":"Delwiche","first_name":"Charles","full_name":"Delwiche, Charles"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Van De Peer, Yves","last_name":"Van De Peer","first_name":"Yves"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mary","last_name":"Beilby","full_name":"Beilby, Mary"},{"first_name":"Liam","last_name":"Dolan","full_name":"Dolan, Liam"},{"full_name":"Kohara, Yuji","first_name":"Yuji","last_name":"Kohara"},{"last_name":"Sugano","first_name":"Sumio","full_name":"Sugano, Sumio"},{"full_name":"Fujiyama, Asao","last_name":"Fujiyama","first_name":"Asao"},{"first_name":"Pierre Marc","last_name":"Delaux","full_name":"Delaux, Pierre Marc"},{"full_name":"Quint, Marcel","first_name":"Marcel","last_name":"Quint"},{"full_name":"Theissen, Gunter","last_name":"Theissen","first_name":"Gunter"},{"last_name":"Hagemann","first_name":"Martin","full_name":"Hagemann, Martin"},{"full_name":"Harholt, Jesper","first_name":"Jesper","last_name":"Harholt"},{"last_name":"Dunand","first_name":"Christophe","full_name":"Dunand, Christophe"},{"first_name":"Sabine","last_name":"Zachgo","full_name":"Zachgo, Sabine"},{"full_name":"Langdale, Jane","first_name":"Jane","last_name":"Langdale"},{"full_name":"Maumus, Florian","first_name":"Florian","last_name":"Maumus"},{"full_name":"Van Der Straeten, Dominique","first_name":"Dominique","last_name":"Van Der Straeten"},{"full_name":"Gould, Sven B","last_name":"Gould","first_name":"Sven B"},{"first_name":"Stefan","last_name":"Rensing","full_name":"Rensing, Stefan"}],"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."}],"date_updated":"2023-09-19T10:02:47Z","publist_id":"7774","quality_controlled":"1","page":"448 - 464.e24","citation":{"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>","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>.","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.","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."},"volume":174,"pmid":1,"publisher":"Cell Press","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publication":"Cell","article_processing_charge":"No","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-12T00:00:00Z","acknowledgement":"In-Data-Review","day":"12","oa":1,"doi":"10.1016/j.cell.2018.06.033","oa_version":"Published Version","scopus_import":"1","issue":"2","external_id":{"pmid":["30007417"],"isi":["000438482800019"]}},{"_id":"149","year":"2018","related_material":{"record":[{"id":"1677","status":"public","relation":"part_of_dissertation"},{"id":"550","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"6183"},{"status":"public","id":"566","relation":"part_of_dissertation"},{"status":"public","id":"1010","relation":"part_of_dissertation"},{"status":"public","id":"6240","relation":"part_of_dissertation"},{"id":"6184","status":"public","relation":"part_of_dissertation"}]},"type":"dissertation","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes","first_name":"Johannes","last_name":"Alt"}],"ec_funded":1,"month":"07","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804"}],"publication_status":"published","date_created":"2018-12-11T11:44:53Z","page":"456","citation":{"apa":"Alt, J. (2018). <i>Dyson equation and eigenvalue statistics of random matrices</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">https://doi.org/10.15479/AT:ISTA:TH_1040</a>","mla":"Alt, Johannes. <i>Dyson Equation and Eigenvalue Statistics of Random Matrices</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">10.15479/AT:ISTA:TH_1040</a>.","ieee":"J. Alt, “Dyson equation and eigenvalue statistics of random matrices,” Institute of Science and Technology Austria, 2018.","chicago":"Alt, Johannes. “Dyson Equation and Eigenvalue Statistics of Random Matrices.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">https://doi.org/10.15479/AT:ISTA:TH_1040</a>.","short":"J. Alt, Dyson Equation and Eigenvalue Statistics of Random Matrices, Institute of Science and Technology Austria, 2018.","ama":"Alt J. Dyson equation and eigenvalue statistics of random matrices. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1040\">10.15479/AT:ISTA:TH_1040</a>","ista":"Alt J. 2018. Dyson equation and eigenvalue statistics of random matrices. Institute of Science and Technology Austria."},"pubrep_id":"1040","publist_id":"7772","has_accepted_license":"1","abstract":[{"lang":"eng","text":"The eigenvalue density of many large random matrices is well approximated by a deterministic measure, the self-consistent density of states. In the present work, we show this behaviour for several classes of random matrices. In fact, we establish that, in each of these classes, the self-consistent density of states approximates the eigenvalue density of the random matrix on all scales slightly above the typical eigenvalue spacing. For large classes of random matrices, the self-consistent density of states exhibits several universal features. We prove that, under suitable assumptions, random Gram matrices and Hermitian random matrices with decaying correlations have a 1/3-Hölder continuous self-consistent density of states ρ on R, which is analytic, where it is positive, and has either a square root edge or a cubic root cusp, where it vanishes. We, thus, extend the validity of the corresponding result for Wigner-type matrices from [4, 5, 7]. We show that ρ is determined as the inverse Stieltjes transform of the normalized trace of the unique solution m(z) to the Dyson equation −m(z) −1 = z − a + S[m(z)] on C N×N with the constraint Im m(z) ≥ 0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of C N×N and S is a positivity-preserving operator on C N×N encoding the first two moments of the random matrix. In order to analyze a possible limit of ρ for N → ∞ and address some applications in free probability theory, we also consider the Dyson equation on infinite dimensional von Neumann algebras. We present two applications to random matrices. We first establish that, under certain assumptions, large random matrices with independent entries have a rotationally symmetric self-consistent density of states which is supported on a centered disk in C. Moreover, it is infinitely often differentiable apart from a jump on the boundary of this disk. Second, we show edge universality at all regular (not necessarily extreme) spectral edges for Hermitian random matrices with decaying correlations."}],"supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2024-02-22T14:34:33Z","department":[{"_id":"LaEr"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:44:57Z","article_processing_charge":"No","title":"Dyson equation and eigenvalue statistics of random matrices","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"date_published":"2018-07-12T00:00:00Z","ddc":["515","519"],"status":"public","day":"12","oa":1,"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"file":[{"file_name":"2018_thesis_Alt.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:44:57Z","access_level":"open_access","checksum":"d4dad55a7513f345706aaaba90cb1bb8","file_id":"6241","creator":"dernst","date_created":"2019-04-08T13:55:20Z","file_size":5801709},{"file_id":"6242","checksum":"d73fcf46300dce74c403f2b491148ab4","date_updated":"2020-07-14T12:44:57Z","access_level":"closed","relation":"source_file","content_type":"application/zip","file_name":"2018_thesis_Alt_source.zip","file_size":3802059,"date_created":"2019-04-08T13:55:20Z","creator":"dernst"}],"doi":"10.15479/AT:ISTA:TH_1040","oa_version":"Published Version"},{"date_published":"2018-05-18T00:00:00Z","acknowledgement":"This work was funded by grants from the European Research Council (ERC StG 281556 and CoG 724373) and the Austrian Science Foundation (FWF) to M.S. and by Swiss National Foundation (SNF) project grants 31003A_135649, 31003A_153457 and CR23I3_156234 to J.V.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687, and J.R. was funded by an EMBO long-term fellowship (ALTF 1396-2014).","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29777221","open_access":"1"}],"title":"Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells","article_processing_charge":"No","publication":"Nature Immunology","language":[{"iso":"eng"}],"external_id":{"pmid":["29777221"],"isi":["000433041500026"]},"scopus_import":"1","issue":"6","oa_version":"Published Version","doi":"10.1038/s41590-018-0109-z","oa":1,"day":"18","author":[{"id":"4167FE56-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6625-3348","last_name":"Hons","first_name":"Miroslav","full_name":"Hons, Miroslav"},{"orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja","last_name":"Kopf","first_name":"Aglaja"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"first_name":"Alexander F","last_name":"Leithner","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner"},{"full_name":"Abe, Jun","last_name":"Abe","first_name":"Jun"},{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","first_name":"Jörg","last_name":"Renkawitz"},{"first_name":"Jens","last_name":"Stein","full_name":"Stein, Jens"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"publication_status":"published","acknowledged_ssus":[{"_id":"SSU"}],"project":[{"call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients"},{"grant_number":"747687","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014"},{"call_identifier":"FP7","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"ec_funded":1,"month":"05","isi":1,"date_created":"2018-12-11T11:44:10Z","intvolume":"        19","year":"2018","_id":"15","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","id":"6891","status":"public"}]},"department":[{"_id":"MiSi"},{"_id":"Bio"}],"publisher":"Nature Publishing Group","pmid":1,"volume":19,"citation":{"ista":"Hons M, Kopf A, Hauschild R, Leithner AF, Gärtner FR, Abe J, Renkawitz J, Stein J, Sixt MK. 2018. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. Nature Immunology. 19(6), 606–616.","ieee":"M. Hons <i>et al.</i>, “Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells,” <i>Nature Immunology</i>, vol. 19, no. 6. Nature Publishing Group, pp. 606–616, 2018.","short":"M. Hons, A. Kopf, R. Hauschild, A.F. Leithner, F.R. Gärtner, J. Abe, J. Renkawitz, J. Stein, M.K. Sixt, Nature Immunology 19 (2018) 606–616.","ama":"Hons M, Kopf A, Hauschild R, et al. Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. 2018;19(6):606-616. doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>","chicago":"Hons, Miroslav, Aglaja Kopf, Robert Hauschild, Alexander F Leithner, Florian R Gärtner, Jun Abe, Jörg Renkawitz, Jens Stein, and Michael K Sixt. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>.","mla":"Hons, Miroslav, et al. “Chemokines and Integrins Independently Tune Actin Flow and Substrate Friction during Intranodal Migration of T Cells.” <i>Nature Immunology</i>, vol. 19, no. 6, Nature Publishing Group, 2018, pp. 606–16, doi:<a href=\"https://doi.org/10.1038/s41590-018-0109-z\">10.1038/s41590-018-0109-z</a>.","apa":"Hons, M., Kopf, A., Hauschild, R., Leithner, A. F., Gärtner, F. R., Abe, J., … Sixt, M. K. (2018). Chemokines and integrins independently tune actin flow and substrate friction during intranodal migration of T cells. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41590-018-0109-z\">https://doi.org/10.1038/s41590-018-0109-z</a>"},"page":"606 - 616","publist_id":"8040","quality_controlled":"1","date_updated":"2024-03-25T23:30:22Z","abstract":[{"lang":"eng","text":"Although much is known about the physiological framework of T cell motility, and numerous rate-limiting molecules have been identified through loss-of-function approaches, an integrated functional concept of T cell motility is lacking. Here, we used in vivo precision morphometry together with analysis of cytoskeletal dynamics in vitro to deconstruct the basic mechanisms of T cell migration within lymphatic organs. We show that the contributions of the integrin LFA-1 and the chemokine receptor CCR7 are complementary rather than positioned in a linear pathway, as they are during leukocyte extravasation from the blood vasculature. Our data demonstrate that CCR7 controls cortical actin flows, whereas integrins mediate substrate friction that is sufficient to drive locomotion in the absence of considerable surface adhesions and plasma membrane flux."}]},{"status":"public","date_published":"2018-08-29T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"original","publication":"Nature","language":[{"iso":"eng"}],"title":"Inositol phosphates are assembly co-factors for HIV-1","article_processing_charge":"No","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"oa_version":"Submitted Version","doi":"10.1038/s41586-018-0396-4","publication_identifier":{"eissn":["1476-4687"]},"external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"scopus_import":"1","issue":"7719","oa":1,"day":"29","intvolume":"       560","date_created":"2018-12-11T11:44:53Z","publication_status":"published","month":"08","isi":1,"author":[{"last_name":"Dick","first_name":"Robert","full_name":"Dick, Robert"},{"full_name":"Zadrozny, Kaneil K","first_name":"Kaneil K","last_name":"Zadrozny"},{"full_name":"Xu, Chaoyi","first_name":"Chaoyi","last_name":"Xu"},{"full_name":"Schur, Florian","first_name":"Florian","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"},{"first_name":"Terri D","last_name":"Lyddon","full_name":"Lyddon, Terri D"},{"full_name":"Ricana, Clifton L","first_name":"Clifton L","last_name":"Ricana"},{"full_name":"Wagner, Jonathan M","last_name":"Wagner","first_name":"Jonathan M"},{"full_name":"Perilla, Juan R","last_name":"Perilla","first_name":"Juan R"},{"full_name":"Ganser, Pornillos Barbie K","last_name":"Ganser","first_name":"Pornillos Barbie K"},{"last_name":"Johnson","first_name":"Marc C","full_name":"Johnson, Marc C"},{"last_name":"Pornillos","first_name":"Owen","full_name":"Pornillos, Owen"},{"full_name":"Vogt, Volker","first_name":"Volker","last_name":"Vogt"}],"type":"journal_article","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-018-0505-4"}]},"year":"2018","_id":"150","pmid":1,"publisher":"Nature Publishing Group","department":[{"_id":"FlSc"}],"date_updated":"2023-09-12T07:44:37Z","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","volume":560,"citation":{"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>.","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>","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.","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>.","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>","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."},"page":"509–512"},{"oa":1,"day":"26","oa_version":"Submitted Version","doi":"10.1016/j.tcb.2018.06.006","file":[{"file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","content_type":"application/pdf","relation":"main_file","file_id":"6994","checksum":"ef6d2b4e1fd63948539639242610bfa6","date_updated":"2020-07-14T12:45:00Z","access_level":"open_access","creator":"lsazanov","date_created":"2019-11-07T12:55:20Z","file_size":2185385}],"external_id":{"isi":["000445118200007"]},"scopus_import":"1","issue":"10","publication":"Trends in Cell Biology","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Mammalian mitochondrial complex I structure and disease causing mutations","file_date_updated":"2020-07-14T12:45:00Z","status":"public","ddc":["572"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2018-07-26T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"original","date_updated":"2023-09-13T08:51:56Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","publist_id":"7769","has_accepted_license":"1","volume":28,"page":"835 - 867","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>.","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>","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.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","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>.","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>","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867."},"publisher":"Elsevier","department":[{"_id":"LeSa"}],"type":"journal_article","_id":"152","year":"2018","intvolume":"        28","date_created":"2018-12-11T11:44:54Z","publication_status":"published","isi":1,"month":"07","author":[{"id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol","first_name":"Karol","last_name":"Fiedorczuk"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}]},{"_id":"153","year":"2018","type":"book_chapter","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","first_name":"Jörg","last_name":"Renkawitz"},{"orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","last_name":"Reversat","full_name":"Reversat, Anne"},{"last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"publication_status":"published","isi":1,"month":"07","date_created":"2018-12-11T11:44:54Z","intvolume":"       147","volume":147,"citation":{"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.","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>","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>.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","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.","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>.","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>"},"page":"79 - 91","quality_controlled":"1","publist_id":"7768","date_updated":"2023-09-13T08:56:35Z","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"}],"department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"publisher":"Academic Press","pmid":1,"title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","article_processing_charge":"No","publication":"Methods in Cell Biology","language":[{"iso":"eng"}],"date_published":"2018-07-27T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","day":"27","external_id":{"isi":["000452412300006"],"pmid":["30165964"]},"scopus_import":"1","publication_identifier":{"issn":["0091679X"]},"oa_version":"None","doi":"10.1016/bs.mcb.2018.07.004"},{"file_date_updated":"2020-07-14T12:45:01Z","language":[{"iso":"eng"}],"publication":"Mathematical Physics Analysis and Geometry","title":"Stability of the 2+2 fermionic system with point interactions","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","date_published":"2018-09-01T00:00:00Z","article_type":"original","status":"public","ddc":["530"],"day":"01","oa":1,"file":[{"relation":"main_file","content_type":"application/pdf","file_id":"5729","checksum":"411c4db5700d7297c9cd8ebc5dd29091","access_level":"open_access","date_updated":"2020-07-14T12:45:01Z","file_name":"2018_MathPhysics_Moser.pdf","date_created":"2018-12-17T16:49:02Z","file_size":496973,"creator":"dernst"}],"publication_identifier":{"eissn":["15729656"],"issn":["13850172"]},"scopus_import":"1","issue":"3","external_id":{"isi":["000439639700001"]},"doi":"10.1007/s11040-018-9275-3","oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","id":"52","status":"public"}]},"article_number":"19","type":"journal_article","_id":"154","year":"2018","month":"09","isi":1,"ec_funded":1,"publication_status":"published","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"author":[{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas","first_name":"Thomas","last_name":"Moser"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"intvolume":"        21","date_created":"2018-12-11T11:44:55Z","citation":{"mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3, 19, Springer, 2018, doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>.","apa":"Moser, T., &#38; Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” <i>Mathematical Physics Analysis and Geometry</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11040-018-9275-3\">https://doi.org/10.1007/s11040-018-9275-3</a>.","ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” <i>Mathematical Physics Analysis and Geometry</i>, vol. 21, no. 3. Springer, 2018.","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. <i>Mathematical Physics Analysis and Geometry</i>. 2018;21(3). doi:<a href=\"https://doi.org/10.1007/s11040-018-9275-3\">10.1007/s11040-018-9275-3</a>","short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19."},"volume":21,"abstract":[{"text":"We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-09-19T09:31:15Z","publist_id":"7767","quality_controlled":"1","has_accepted_license":"1","department":[{"_id":"RoSe"}],"publisher":"Springer"},{"publisher":"SPIE","conference":{"location":"Strasbourg, France","start_date":"2018-04-22","end_date":"2018-04-26","name":"SPIE: The international society for optical engineering"},"department":[{"_id":"JoFi"}],"publist_id":"7766","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"date_updated":"2023-09-18T08:12:24Z","citation":{"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>","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>.","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>","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.","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","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>.","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."},"volume":10672,"date_created":"2018-12-11T11:44:55Z","intvolume":"     10672","author":[{"first_name":"André","last_name":"Xuereb","full_name":"Xuereb, André"},{"full_name":"Aquilina, Matteo","last_name":"Aquilina","first_name":"Matteo"},{"orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","first_name":"Shabir"}],"isi":1,"month":"05","publication_status":"published","year":"2018","_id":"155","article_number":"106721N","type":"conference","doi":"10.1117/12.2309928","oa_version":"Preprint","scopus_import":"1","external_id":{"isi":["000453298500019"],"arxiv":["1806.01000"]},"day":"04","oa":1,"status":"public","alternative_title":["Proceedings of SPIE"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-05-04T00:00:00Z","arxiv":1,"title":"Routing thermal noise through quantum networks","article_processing_charge":"No","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"editor":[{"full_name":"Andrews, D L","first_name":"D L","last_name":"Andrews"},{"full_name":"Ostendorf, A","last_name":"Ostendorf","first_name":"A"},{"last_name":"Bain","first_name":"A J","full_name":"Bain, A J"},{"full_name":"Nunzi, J M","first_name":"J M","last_name":"Nunzi"}]},{"file":[{"success":1,"creator":"dernst","date_created":"2020-10-09T06:22:41Z","file_size":485576,"file_name":"2018_LNCS_Ferrere.pdf","content_type":"application/pdf","relation":"main_file","checksum":"a045c213c42c445f1889326f8db82a0a","file_id":"8637","access_level":"open_access","date_updated":"2020-10-09T06:22:41Z"}],"scopus_import":"1","external_id":{"isi":["000489765800009"]},"doi":"10.1007/978-3-319-95582-7_9","oa_version":"Submitted Version","day":"12","oa":1,"alternative_title":["LNCS"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-12T00:00:00Z","status":"public","ddc":["000"],"file_date_updated":"2020-10-09T06:22:41Z","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"The compound interest in relaxing punctuality","department":[{"_id":"ToHe"}],"conference":{"name":"FM: International Symposium on Formal Methods","end_date":"2018-07-17","location":"Oxford, UK","start_date":"2018-07-15"},"publisher":"Springer","citation":{"short":"T. Ferrere, in:, Springer, 2018, 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>.","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>","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on 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>","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: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164."},"page":"147 - 164","volume":10951,"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."}],"date_updated":"2023-09-19T10:05:37Z","publist_id":"7765","quality_controlled":"1","has_accepted_license":"1","month":"07","isi":1,"publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas"}],"intvolume":"     10951","date_created":"2018-12-11T11:44:55Z","type":"conference","_id":"156","year":"2018"},{"page":"246 - 249","volume":559,"citation":{"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.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 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>.","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>","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>.","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>","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249."},"date_updated":"2023-09-11T13:43:22Z","abstract":[{"lang":"eng","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."}],"publist_id":"7764","has_accepted_license":"1","quality_controlled":"1","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","type":"journal_article","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/engineering-cooperation/","description":"News on IST Homepage"}]},"year":"2018","_id":"157","publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"isi":1,"month":"07","ec_funded":1,"author":[{"full_name":"Hilbe, Christian","first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Šimsa, Štepán","first_name":"Štepán","last_name":"Šimsa"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"intvolume":"       559","date_created":"2018-12-11T11:44:56Z","oa":1,"day":"04","file":[{"file_size":2834442,"date_created":"2019-11-19T08:09:57Z","creator":"dernst","file_id":"7049","checksum":"011ab905cf9a410bc2b96f15174d654d","date_updated":"2020-07-14T12:45:02Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2018_Nature_Hilbe.pdf"}],"external_id":{"isi":["000438240900054"]},"issue":"7713","scopus_import":"1","oa_version":"Submitted Version","doi":"10.1038/s41586-018-0277-x","file_date_updated":"2020-07-14T12:45:02Z","publication":"Nature","language":[{"iso":"eng"}],"title":"Evolution of cooperation in stochastic games","article_processing_charge":"No","date_published":"2018-07-04T00:00:00Z","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["000"]},{"scopus_import":"1","issue":"8","external_id":{"pmid":["30013211"],"isi":["000443861300011"]},"doi":"10.1038/s41477-018-0204-z","oa_version":"Submitted Version","day":"16","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","date_published":"2018-07-16T00:00:00Z","status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211","open_access":"1"}],"language":[{"iso":"eng"}],"publication":"Nature Plants","title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","article_processing_charge":"No","department":[{"_id":"JiFr"}],"pmid":1,"publisher":"Nature Publishing Group","volume":4,"page":"548 - 553","citation":{"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>.","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>","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.","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.","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>","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>.","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."},"abstract":[{"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.","lang":"eng"}],"date_updated":"2025-05-07T11:12:31Z","publist_id":"7763","quality_controlled":"1","ec_funded":1,"month":"07","isi":1,"publication_status":"published","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"author":[{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"last_name":"Park","first_name":"Chulmin","full_name":"Park, Chulmin"},{"full_name":"Gutièrrez, Carla","last_name":"Gutièrrez","first_name":"Carla"},{"full_name":"Wójcikowska, Barbara","last_name":"Wójcikowska","first_name":"Barbara"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"first_name":"Junyi","last_name":"Chen","full_name":"Chen, Junyi"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"last_name":"Dresselhaus","first_name":"Thomas","full_name":"Dresselhaus, Thomas"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Laux, Thomas","last_name":"Laux","first_name":"Thomas"}],"intvolume":"         4","date_created":"2018-12-11T11:44:56Z","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/","relation":"press_release"}]},"type":"journal_article","year":"2018","_id":"158"},{"day":"16","oa":1,"file":[{"date_created":"2020-05-14T12:14:09Z","file_size":6321000,"creator":"dernst","relation":"main_file","content_type":"application/pdf","file_id":"7832","checksum":"d42935094ec845f54a0688bf12986d62","access_level":"open_access","date_updated":"2020-07-14T12:45:03Z","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf"}],"issue":"8","scopus_import":"1","external_id":{"isi":["000438970200010"]},"doi":"10.1038/s41589-018-0090-8","oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:03Z","language":[{"iso":"eng"}],"publication":"Nature Chemical Biology","article_processing_charge":"No","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-16T00:00:00Z","article_type":"original","status":"public","ddc":["570"],"page":"764 - 767","citation":{"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.","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.","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>","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.","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>.","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>","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>."},"volume":14,"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"}],"date_updated":"2023-09-13T09:36:35Z","publist_id":"7762","has_accepted_license":"1","quality_controlled":"1","department":[{"_id":"JoDa"}],"publisher":"Nature Publishing Group","related_material":{"link":[{"url":"https://doi.org/10.1038/s41589-021-00744-3","relation":"erratum"}]},"type":"journal_article","year":"2018","_id":"159","month":"07","isi":1,"publication_status":"published","author":[{"last_name":"Fehrentz","first_name":"Timm","full_name":"Fehrentz, Timm"},{"last_name":"Huber","first_name":"Florian","full_name":"Huber, Florian"},{"first_name":"Nina","last_name":"Hartrampf","full_name":"Hartrampf, Nina"},{"last_name":"Bruegmann","first_name":"Tobias","full_name":"Bruegmann, Tobias"},{"full_name":"Frank, James","last_name":"Frank","first_name":"James"},{"full_name":"Fine, Nicholas","last_name":"Fine","first_name":"Nicholas"},{"last_name":"Malan","first_name":"Daniela","full_name":"Malan, Daniela"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G"},{"full_name":"Tikhonov, Denis","first_name":"Denis","last_name":"Tikhonov"},{"full_name":"Sumser, Maritn","first_name":"Maritn","last_name":"Sumser"},{"full_name":"Sasse, Philipp","first_name":"Philipp","last_name":"Sasse"},{"last_name":"Hodson","first_name":"David","full_name":"Hodson, David"},{"full_name":"Zhorov, Boris","last_name":"Zhorov","first_name":"Boris"},{"last_name":"Klocker","first_name":"Nikolaj","full_name":"Klocker, Nikolaj"},{"last_name":"Trauner","first_name":"Dirk","full_name":"Trauner, Dirk"}],"intvolume":"        14","date_created":"2018-12-11T11:44:56Z"},{"department":[{"_id":"BjHo"}],"publisher":"American Physical Society","pubrep_id":"1062","volume":3,"citation":{"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>","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>.","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.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","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>","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>.","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303."},"quality_controlled":"1","has_accepted_license":"1","publist_id":"8039","abstract":[{"lang":"eng","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."}],"date_updated":"2023-09-13T08:57:05Z","author":[{"last_name":"Varshney","first_name":"Atul","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"}],"ec_funded":1,"month":"10","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"publication_status":"published","date_created":"2018-12-11T11:44:10Z","intvolume":"         3","_id":"16","year":"2018","article_number":"103303","type":"journal_article","scopus_import":"1","issue":"10","external_id":{"isi":["000447469200001"]},"file":[{"file_size":1838431,"date_created":"2018-12-12T10:13:56Z","creator":"system","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","file_id":"5043","access_level":"open_access","date_updated":"2020-07-14T12:45:04Z","relation":"main_file","content_type":"application/pdf","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf"}],"doi":"10.1103/PhysRevFluids.3.103303","oa_version":"Submitted Version","day":"16","oa":1,"article_type":"original","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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_published":"2018-10-16T00:00:00Z","ddc":["532"],"status":"public","file_date_updated":"2020-07-14T12:45:04Z","article_processing_charge":"No","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","language":[{"iso":"eng"}],"publication":"Physical Review Fluids"},{"ddc":["000"],"status":"public","alternative_title":["LNCS"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-18T00:00:00Z","title":"Layered Concurrent Programs","article_processing_charge":"No","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:04Z","doi":"10.1007/978-3-319-96145-3_5","oa_version":"Published Version","scopus_import":"1","external_id":{"isi":["000491481600005"]},"file":[{"creator":"dernst","date_created":"2018-12-17T12:52:12Z","file_size":1603844,"file_name":"2018_LNCS_Kragl.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:04Z","access_level":"open_access","file_id":"5705","checksum":"c64fff560fe5a7532ec10626ad1c215e"}],"day":"18","oa":1,"date_created":"2018-12-11T11:44:57Z","intvolume":"     10981","author":[{"orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","last_name":"Kragl","full_name":"Kragl, Bernhard"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"}],"month":"07","isi":1,"project":[{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"publication_status":"published","_id":"160","year":"2018","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8332"}]},"type":"conference","publisher":"Springer","conference":{"name":"CAV: Computer Aided Verification","start_date":"2018-07-14","location":"Oxford, UK","end_date":"2018-07-17"},"department":[{"_id":"ToHe"}],"has_accepted_license":"1","publist_id":"7761","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-09-13T08:45:09Z","citation":{"ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","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>","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>.","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>","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102."},"page":"79 - 102","volume":10981},{"day":"30","oa":1,"issue":"1","scopus_import":"1","external_id":{"isi":["000440149300021"]},"file":[{"file_size":1043205,"date_created":"2018-12-17T16:44:28Z","creator":"dernst","date_updated":"2020-07-14T12:45:06Z","access_level":"open_access","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18","file_id":"5728","relation":"main_file","content_type":"application/pdf","file_name":"2018_NatureComm_DeMartino.pdf"}],"doi":"10.1038/s41467-018-05417-9","oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:06Z","title":"Statistical mechanics for metabolic networks during steady state growth","article_processing_charge":"No","language":[{"iso":"eng"}],"publication":"Nature Communications","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-30T00:00:00Z","ddc":["570"],"status":"public","citation":{"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>.","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>","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.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","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."},"volume":9,"publist_id":"7760","quality_controlled":"1","has_accepted_license":"1","abstract":[{"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.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2024-02-21T13:45:39Z","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"publisher":"Springer Nature","_id":"161","year":"2018","article_number":"2988","related_material":{"record":[{"relation":"popular_science","status":"public","id":"5587"}]},"type":"journal_article","author":[{"orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","last_name":"De Martino","first_name":"Daniele"},{"first_name":"Andersson Anna","last_name":"Mc","full_name":"Mc, Andersson Anna"},{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"month":"07","isi":1,"publication_status":"published","project":[{"grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"date_created":"2018-12-11T11:44:57Z","intvolume":"         9"}]