[{"date_created":"2018-12-11T11:44:55Z","date_published":"2018-07-12T00:00:00Z","doi":"10.1007/978-3-319-95582-7_9","page":"147 - 164","day":"12","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer","title":"The compound interest in relaxing punctuality","article_processing_charge":"No","external_id":{"isi":["000489765800009"]},"author":[{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7765","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.","chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. https://doi.org/10.1007/978-3-319-95582-7_9.","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:10.1007/978-3-319-95582-7_9","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. https://doi.org/10.1007/978-3-319-95582-7_9","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.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","mla":"Ferrere, Thomas. The Compound Interest in Relaxing Punctuality. Vol. 10951, Springer, 2018, pp. 147–64, doi:10.1007/978-3-319-95582-7_9."},"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"volume":10951,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8637","checksum":"a045c213c42c445f1889326f8db82a0a","file_size":485576,"date_updated":"2020-10-09T06:22:41Z","creator":"dernst","file_name":"2018_LNCS_Ferrere.pdf","date_created":"2020-10-09T06:22:41Z"}],"publication_status":"published","intvolume":" 10951","month":"07","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Submitted Version","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."}],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-09T06:22:41Z","ddc":["000"],"date_updated":"2023-09-19T10:05:37Z","status":"public","conference":{"start_date":"2018-07-15","end_date":"2018-07-17","location":"Oxford, UK","name":"FM: International Symposium on Formal Methods"},"type":"conference","_id":"156"},{"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"104","department":[{"_id":"GradSch"}],"file_date_updated":"2018-12-18T09:46:00Z","date_updated":"2023-09-19T10:06:42Z","ddc":["580"],"scopus_import":"1","month":"10","intvolume":" 19","abstract":[{"lang":"eng","text":"The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host."}],"oa_version":"Published Version","issue":"10","volume":19,"license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","file":[{"creator":"dernst","file_size":682335,"date_updated":"2018-12-18T09:46:00Z","file_name":"2018_MolecPlantPath_Seitner.pdf","date_created":"2018-12-18T09:46:00Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"5740"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Seitner, Denise","last_name":"Seitner","first_name":"Denise"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"},{"last_name":"Djamei","full_name":"Djamei, Armin","first_name":"Armin"}],"publist_id":"7950","article_processing_charge":"No","external_id":{"isi":["000445624100006"]},"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","citation":{"chicago":"Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology. Wiley, 2018. https://doi.org/10.1111/mpp.12698.","ista":"Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287.","mla":"Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:10.1111/mpp.12698.","ieee":"D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” Molecular Plant Pathology, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018.","short":"D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287.","apa":"Seitner, D., Uhse, S., Gallei, M. C., & Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. Wiley. https://doi.org/10.1111/mpp.12698","ama":"Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 2018;19(10):2277-2287. doi:10.1111/mpp.12698"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Wiley","oa":1,"acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","page":"2277 - 2287","date_published":"2018-10-01T00:00:00Z","doi":"10.1111/mpp.12698","date_created":"2018-12-11T11:44:39Z","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Molecular Plant Pathology"},{"citation":{"mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"8014","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000454600500001"],"pmid":["30599087"]},"title":"The consequences of an introgression event","publisher":"Wiley","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"31","publication":"Molecular Ecology","page":"4973-4975","date_published":"2018-12-31T00:00:00Z","doi":"10.1111/mec.14950","date_created":"2018-12-11T11:44:18Z","_id":"40","type":"journal_article","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-19T10:06:08Z","ddc":["576"],"file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"NiBa"}],"abstract":[{"text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"12","intvolume":" 27","publication_identifier":{"issn":["1365294X"]},"publication_status":"published","file":[{"creator":"apreinsp","file_size":295452,"date_updated":"2020-07-14T12:46:22Z","file_name":"2018_MolecularEcology_BartonNick.pdf","date_created":"2019-07-19T06:54:46Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6652"}],"language":[{"iso":"eng"}],"issue":"24","volume":27,"related_material":{"record":[{"id":"9805","status":"public","relation":"research_data"}]}},{"citation":{"chicago":"Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.37888.","ista":"Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888.","mla":"Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” ELife, vol. 7, e37888, eLife Sciences Publications, 2018, doi:10.7554/eLife.37888.","apa":"Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.37888","ama":"Alanko JH, Sixt MK. The cell sets the tone. eLife. 2018;7. doi:10.7554/eLife.37888","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000434375000001"]},"author":[{"last_name":"Alanko","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"title":"The cell sets the tone","article_number":"e37888","year":"2018","has_accepted_license":"1","isi":1,"publication":"eLife","day":"06","date_created":"2019-01-20T22:59:19Z","doi":"10.7554/eLife.37888","date_published":"2018-06-06T00:00:00Z","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","date_updated":"2023-09-19T10:01:39Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:13Z","_id":"5861","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5973","checksum":"f1c7ec2a809408d763c4b529a98f9a3b","creator":"dernst","file_size":358141,"date_updated":"2020-07-14T12:47:13Z","file_name":"2018_eLife_Alanko.pdf","date_created":"2019-02-13T10:52:11Z"}],"volume":7,"abstract":[{"lang":"eng","text":"In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 7","month":"06"},{"citation":{"chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127.","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.","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.” The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:10.1105/tpc.18.00127.","ieee":"U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127","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. The Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula","last_name":"Kania"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"first_name":"Qing","full_name":"Lu, Qing","last_name":"Lu"},{"first_name":"Glenn R","last_name":"Hicks","full_name":"Hicks, Glenn R"},{"last_name":"Nerinckx","full_name":"Nerinckx, Wim","first_name":"Wim"},{"last_name":"Mishev","full_name":"Mishev, Kiril","first_name":"Kiril"},{"first_name":"Francois","last_name":"Peurois","full_name":"Peurois, Francois"},{"full_name":"Cherfils, Jacqueline","last_name":"Cherfils","first_name":"Jacqueline"},{"full_name":"De, Rycke Riet Maria","last_name":"De","first_name":"Rycke Riet Maria"},{"last_name":"Grones","full_name":"Grones, Peter","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"7776","external_id":{"isi":["000450000500023"],"pmid":["30018156"]},"article_processing_charge":"No","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}],"isi":1,"year":"2018","day":"12","publication":"The Plant Cell","page":"2553 - 2572","doi":"10.1105/tpc.18.00127","date_published":"2018-11-12T00:00:00Z","date_created":"2018-12-11T11:44:52Z","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.).","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"date_updated":"2023-09-19T10:09:12Z","department":[{"_id":"JiFr"}],"_id":"147","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"issn":["1040-4651"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":30,"issue":"10","ec_funded":1,"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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1105/tpc.18.00127","open_access":"1"}],"month":"11","intvolume":" 30"}]