[{"page":"11031-11070","date_created":"2018-12-11T11:44:15Z","doi":"10.1002/ece3.4573","date_published":"2018-11-01T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Ecology and Evolution","day":"01","oa":1,"publisher":"Wiley","quality_controlled":"1","external_id":{"isi":["000451611000032"]},"article_processing_charge":"No","publist_id":"8026","author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"first_name":"Jaana","last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana"},{"first_name":"Ida","full_name":"Holmberg, Ida","last_name":"Holmberg"},{"full_name":"Pamminger, Tobias","last_name":"Pamminger","first_name":"Tobias"},{"first_name":"Silvio","last_name":"Erler","full_name":"Erler, Silvio"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"title":"Social environment affects the transcriptomic response to bacteria in ant queens","citation":{"mla":"Viljakainen, Lumi, et al. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution, vol. 8, no. 22, Wiley, 2018, pp. 11031–70, doi:10.1002/ece3.4573.","short":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer, Ecology and Evolution 8 (2018) 11031–11070.","ieee":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, and S. Cremer, “Social environment affects the transcriptomic response to bacteria in ant queens,” Ecology and Evolution, vol. 8, no. 22. Wiley, pp. 11031–11070, 2018.","apa":"Viljakainen, L., Jurvansuu, J., Holmberg, I., Pamminger, T., Erler, S., & Cremer, S. (2018). Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.4573","ama":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 2018;8(22):11031-11070. doi:10.1002/ece3.4573","chicago":"Viljakainen, Lumi, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio Erler, and Sylvia Cremer. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution. Wiley, 2018. https://doi.org/10.1002/ece3.4573.","ista":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. 2018. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 8(22), 11031–11070."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","license":"https://creativecommons.org/licenses/by/4.0/","volume":8,"issue":"22","publication_status":"published","publication_identifier":{"issn":["20457758"]},"language":[{"iso":"eng"}],"file":[{"checksum":"0d1355c78627ca7210aadd9a17a01915","file_id":"5682","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Viljakainen_et_al-2018-Ecology_and_Evolution.pdf","date_created":"2018-12-17T08:27:04Z","creator":"dernst","file_size":1272096,"date_updated":"2020-07-14T12:45:52Z"}],"scopus_import":"1","intvolume":" 8","month":"11","abstract":[{"text":"Social insects have evolved enormous capacities to collectively build nests and defend their colonies against both predators and pathogens. The latter is achieved by a combination of individual immune responses and sophisticated collective behavioral and organizational disease defenses, that is, social immunity. We investigated how the presence or absence of these social defense lines affects individual-level immunity in ant queens after bacterial infection. To this end, we injected queens of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control solution, reared them either with workers or alone and analyzed their gene expression patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us to test for the effect of bacterial infection, social context, as well as the interaction between the two over the course of infection and raising of an immune response. We found that social isolation per se affected queen gene expression for metabolism genes, but not for immune genes. When infected, queens reared with and without workers up-regulated similar numbers of innate immune genes revealing activation of Toll and Imd signaling pathways and melanization. Interestingly, however, they mostly regulated different genes along the pathways and showed a different pattern of overall gene up-regulation or down-regulation. Hence, we can conclude that the absence of workers does not compromise the onset of an individual immune response by the queens, but that the social environment impacts the route of the individual innate immune responses.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:45:52Z","date_updated":"2023-09-19T09:29:12Z","ddc":["576","591"],"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","status":"public","_id":"29"},{"_id":"806","status":"public","type":"journal_article","date_updated":"2023-09-19T09:29:45Z","department":[{"_id":"SyCr"}],"oa_version":"None","abstract":[{"text":"Social insect colonies have evolved many collectively performed adaptations that reduce the impact of infectious disease and that are expected to maximize their fitness. This colony-level protection is termed social immunity, and it enhances the health and survival of the colony. In this review, we address how social immunity emerges from its mechanistic components to produce colony-level disease avoidance, resistance, and tolerance. To understand the evolutionary causes and consequences of social immunity, we highlight the need for studies that evaluate the effects of social immunity on colony fitness. We discuss the role that host life history and ecology have on predicted eco-evolutionary dynamics, which differ among the social insect lineages. Throughout the review, we highlight current gaps in our knowledge and promising avenues for future research, which we hope will bring us closer to an integrated understanding of socio-eco-evo-immunology.","lang":"eng"}],"intvolume":" 63","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1545-4487"]},"volume":63,"related_material":{"record":[{"status":"public","id":"819","relation":"dissertation_contains"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology, vol. 63, Annual Reviews, 2018, pp. 105–23, doi:10.1146/annurev-ento-020117-043110.","ieee":"S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution of colony-level disease protection,” Annual Review of Entomology, vol. 63. Annual Reviews, pp. 105–123, 2018.","short":"S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.","ama":"Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 2018;63:105-123. doi:10.1146/annurev-ento-020117-043110","apa":"Cremer, S., Pull, C., & Fürst, M. (2018). Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. Annual Reviews. https://doi.org/10.1146/annurev-ento-020117-043110","chicago":"Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology. Annual Reviews, 2018. https://doi.org/10.1146/annurev-ento-020117-043110.","ista":"Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 63, 105–123."},"title":"Social immunity: Emergence and evolution of colony-level disease protection","external_id":{"isi":["000424633700008"]},"article_processing_charge":"No","publist_id":"6844","author":[{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","last_name":"Pull"},{"first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias"}],"publisher":"Annual Reviews","quality_controlled":"1","publication":"Annual Review of Entomology","day":"07","year":"2018","isi":1,"date_created":"2018-12-11T11:48:36Z","doi":"10.1146/annurev-ento-020117-043110","date_published":"2018-01-07T00:00:00Z","page":"105 - 123"},{"related_material":{"record":[{"id":"6894","status":"public","relation":"dissertation_contains"}]},"volume":10981,"publication_status":"published","publication_identifier":{"issn":["03029743"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6dca832f575d6b3f0ea9dff56f579142","file_id":"5310","date_updated":"2020-07-14T12:44:50Z","file_size":563710,"creator":"system","date_created":"2018-12-12T10:17:53Z","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf"}],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 10981","month":"07","abstract":[{"text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:44:50Z","date_updated":"2023-09-19T09:30:43Z","ddc":["005"],"conference":{"start_date":"2018-07-14","location":"Oxford, United Kingdom","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"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":"conference","pubrep_id":"1010","status":"public","_id":"140","page":"468 - 486","date_created":"2018-12-11T11:44:50Z","doi":"10.1007/978-3-319-96145-3_25","date_published":"2018-07-18T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"day":"18","oa":1,"quality_controlled":"1","publisher":"Springer","article_processing_charge":"No","external_id":{"isi":["000491481600025"]},"author":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"last_name":"Giacobbe","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"publist_id":"7783","title":"Space-time interpolants","citation":{"ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486.","chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_25.","ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:10.1007/978-3-319-96145-3_25","apa":"Frehse, G., Giacobbe, M., & Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_25","short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.","mla":"Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer, 2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"citation":{"mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry, vol. 21, no. 3, 19, Springer, 2018, doi:10.1007/s11040-018-9275-3.","ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” Mathematical Physics Analysis and Geometry, vol. 21, no. 3. Springer, 2018.","short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 2018;21(3). doi:10.1007/s11040-018-9275-3","apa":"Moser, T., & Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-018-9275-3","chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry. Springer, 2018. https://doi.org/10.1007/s11040-018-9275-3.","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Moser, Thomas","last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"publist_id":"7767","external_id":{"isi":["000439639700001"]},"article_processing_charge":"No","title":"Stability of the 2+2 fermionic system with point interactions","article_number":"19","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Mathematical Physics Analysis and Geometry","doi":"10.1007/s11040-018-9275-3","date_published":"2018-09-01T00:00:00Z","date_created":"2018-12-11T11:44:55Z","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2023-09-19T09:31:15Z","ddc":["530"],"department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:45:01Z","_id":"154","article_type":"original","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","publication_identifier":{"eissn":["15729656"],"issn":["13850172"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5729","checksum":"411c4db5700d7297c9cd8ebc5dd29091","creator":"dernst","file_size":496973,"date_updated":"2020-07-14T12:45:01Z","file_name":"2018_MathPhysics_Moser.pdf","date_created":"2018-12-17T16:49:02Z"}],"language":[{"iso":"eng"}],"issue":"3","volume":21,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"52"}]},"ec_funded":1,"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"}],"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 21"},{"status":"public","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","_id":"5787","file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-09-19T09:32:49Z","intvolume":" 60","month":"12","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Branching morphogenesis remains a subject of abiding interest. Although much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions and cell lineage tracing, it has been argued that morphogenesis follows \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, set of local rules, \r\nwithout recourse to a rigid and deterministic sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications.","lang":"eng"}],"volume":60,"issue":"9","language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-06T10:40:46Z","file_name":"2018_DevGrowh_Hannezo.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:11Z","file_size":1313606,"checksum":"a6d30b0785db902c734a84fecb2eadd9","file_id":"5933","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_identifier":{"issn":["00121592"]},"title":"Statistical theory of branching morphogenesis","article_processing_charge":"No","external_id":{"isi":["000453555100002"]},"author":[{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin D.","full_name":"Simons, Benjamin D.","last_name":"Simons"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.","apa":"Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570","ieee":"E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521, 2018.","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570."},"oa":1,"quality_controlled":"1","publisher":"Wiley","date_created":"2018-12-30T22:59:14Z","date_published":"2018-12-09T00:00:00Z","doi":"10.1111/dgd.12570","page":"512-521","publication":"Development Growth and Differentiation","day":"09","year":"2018","has_accepted_license":"1","isi":1},{"_id":"297","type":"conference","conference":{"start_date":"2018-04-14","end_date":"2018-04-20","location":"Thessaloniki, Greece","name":"TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems"},"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":"2023-09-19T09:57:08Z","ddc":["000"],"file_date_updated":"2020-07-14T12:45:57Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"text":"Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LNCS"],"month":"04","intvolume":" 10805","publication_status":"published","file":[{"creator":"dernst","file_size":1829940,"date_updated":"2020-07-14T12:45:57Z","file_name":"2018_LNCS_Brazdil.pdf","date_created":"2018-12-17T16:29:08Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5723","checksum":"b13874ffb114932ad9cc2586b7469db4"}],"language":[{"iso":"eng"}],"volume":10805,"ec_funded":1,"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"citation":{"apa":"Brázdil, T., Chatterjee, K., Kretinsky, J., & Toman, V. (2018). Strategy representation by decision trees in reactive synthesis (Vol. 10805, pp. 385–407). Presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89960-2_21","ama":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. Strategy representation by decision trees in reactive synthesis. In: Vol 10805. Springer; 2018:385-407. doi:10.1007/978-3-319-89960-2_21","ieee":"T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10805, pp. 385–407.","short":"T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp. 385–407.","mla":"Brázdil, Tomáš, et al. Strategy Representation by Decision Trees in Reactive Synthesis. Vol. 10805, Springer, 2018, pp. 385–407, doi:10.1007/978-3-319-89960-2_21.","ista":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. 2018. Strategy representation by decision trees in reactive synthesis. TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10805, 385–407.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Jan Kretinsky, and Viktor Toman. “Strategy Representation by Decision Trees in Reactive Synthesis,” 10805:385–407. Springer, 2018. https://doi.org/10.1007/978-3-319-89960-2_21."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Toman","full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7584","article_processing_charge":"No","external_id":{"isi":["000546326300021"]},"title":"Strategy representation by decision trees in reactive synthesis","publisher":"Springer","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"12","page":"385 - 407","doi":"10.1007/978-3-319-89960-2_21","date_published":"2018-04-12T00:00:00Z","date_created":"2018-12-11T11:45:41Z"},{"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"10199","status":"public"}]},"volume":10982,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","file_id":"5737","creator":"dernst","file_size":675606,"date_updated":"2020-07-14T12:44:53Z","file_name":"2018_LNCS_Chatterjee.pdf","date_created":"2018-12-18T08:52:38Z"}],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 10982","month":"07","abstract":[{"lang":"eng","text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"KrCh"}],"date_updated":"2023-09-19T09:59:55Z","ddc":["000"],"conference":{"location":"Oxford, United Kingdom","end_date":"2018-07-17","start_date":"2018-07-14","name":"CAV: Computer Aided Verification"},"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":"conference","status":"public","_id":"141","page":"178-197","date_created":"2018-12-11T11:44:51Z","date_published":"2018-07-18T00:00:00Z","doi":"10.1007/978-3-319-96142-2_13","year":"2018","has_accepted_license":"1","isi":1,"day":"18","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","article_processing_charge":"No","external_id":{"isi":["000491469700013"]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"},{"last_name":"Oraee","full_name":"Oraee, Simin","first_name":"Simin"},{"last_name":"Toman","full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7782","title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","citation":{"chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13.","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.","mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp. 178–97, doi:10.1007/978-3-319-96142-2_13.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13","apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., & Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}]},{"citation":{"chicago":"Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Sustained Space Complexity,” 10821:99–130. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_4.","ista":"Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt 2018: Advances in Cryptology, LNCS, vol. 10821, 99–130.","mla":"Alwen, Joel F., et al. Sustained Space Complexity. Vol. 10821, Springer, 2018, pp. 99–130, doi:10.1007/978-3-319-78375-8_4.","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, Springer, 2018, pp. 99–130.","ieee":"J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Sustained space complexity,” presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 99–130.","apa":"Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2018). Sustained space complexity (Vol. 10821, pp. 99–130). Presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_4","ama":"Alwen JF, Blocki J, Pietrzak KZ. Sustained space complexity. In: Vol 10821. Springer; 2018:99-130. doi:10.1007/978-3-319-78375-8_4"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jeremiah","full_name":"Blocki, Jeremiah","last_name":"Blocki"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7583","external_id":{"isi":["000517098700004"],"arxiv":["1705.05313"]},"article_processing_charge":"No","title":"Sustained space complexity","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"isi":1,"year":"2018","day":"31","page":"99 - 130","doi":"10.1007/978-3-319-78375-8_4","date_published":"2018-03-31T00:00:00Z","date_created":"2018-12-11T11:45:41Z","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2023-09-19T09:59:30Z","department":[{"_id":"KrPi"}],"_id":"298","type":"conference","conference":{"name":"Eurocrypt 2018: Advances in Cryptology","start_date":"2018-04-29","location":"Tel Aviv, Israel","end_date":"2018-05-03"},"status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":10821,"ec_funded":1,"abstract":[{"text":"Memory-hard functions (MHF) are functions whose evaluation cost is dominated by memory cost. MHFs are egalitarian, in the sense that evaluating them on dedicated hardware (like FPGAs or ASICs) is not much cheaper than on off-the-shelf hardware (like x86 CPUs). MHFs have interesting cryptographic applications, most notably to password hashing and securing blockchains.\r\n\r\nAlwen and Serbinenko [STOC’15] define the cumulative memory complexity (cmc) of a function as the sum (over all time-steps) of the amount of memory required to compute the function. They advocate that a good MHF must have high cmc. Unlike previous notions, cmc takes into account that dedicated hardware might exploit amortization and parallelism. Still, cmc has been critizised as insufficient, as it fails to capture possible time-memory trade-offs; as memory cost doesn’t scale linearly, functions with the same cmc could still have very different actual hardware cost.\r\n\r\nIn this work we address this problem, and introduce the notion of sustained-memory complexity, which requires that any algorithm evaluating the function must use a large amount of memory for many steps. We construct functions (in the parallel random oracle model) whose sustained-memory complexity is almost optimal: our function can be evaluated using n steps and O(n/log(n)) memory, in each step making one query to the (fixed-input length) random oracle, while any algorithm that can make arbitrary many parallel queries to the random oracle, still needs Ω(n/log(n)) memory for Ω(n) steps.\r\n\r\nAs has been done for various notions (including cmc) before, we reduce the task of constructing an MHFs with high sustained-memory complexity to proving pebbling lower bounds on DAGs. Our main technical contribution is the construction is a family of DAGs on n nodes with constant indegree with high “sustained-space complexity”, meaning that any parallel black-pebbling strategy requires Ω(n/log(n)) pebbles for at least Ω(n) steps.\r\n\r\nAlong the way we construct a family of maximally “depth-robust” DAGs with maximum indegree O(logn) , improving upon the construction of Mahmoody et al. [ITCS’13] which had maximum indegree O(log2n⋅","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/1705.05313","open_access":"1"}],"month":"03","intvolume":" 10821"},{"publication_status":"published","file":[{"file_size":3359316,"date_updated":"2020-07-14T12:46:13Z","creator":"dernst","file_name":"2018_JournalExperimBotany_Vu.pdf","date_created":"2018-12-18T09:47:51Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5741","checksum":"34cb0a1611588b75bd6f4913fb4e30f1"}],"language":[{"iso":"eng"}],"issue":"19","volume":69,"abstract":[{"text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 69","date_updated":"2023-09-19T10:00:46Z","ddc":["581"],"file_date_updated":"2020-07-14T12:46:13Z","department":[{"_id":"JiFr"}],"_id":"36","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","has_accepted_license":"1","isi":1,"year":"2018","day":"31","publication":"Journal of Experimental Botany","page":"4609 - 4624","date_published":"2018-08-31T00:00:00Z","doi":"10.1093/jxb/ery204","date_created":"2018-12-11T11:44:17Z","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"citation":{"ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Lam","full_name":"Vu, Lam","last_name":"Vu"},{"last_name":"Zhu","full_name":"Zhu, Tingting","first_name":"Tingting"},{"first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328"},{"first_name":"Brigitte","full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte"},{"first_name":"Kris","full_name":"Gevaert, Kris","last_name":"Gevaert"},{"first_name":"Ive","full_name":"De Smet, Ive","last_name":"De Smet"}],"publist_id":"8019","external_id":{"isi":["000443568700010"]},"article_processing_charge":"No","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","status":"public","_id":"326","file_date_updated":"2020-07-14T12:46:06Z","department":[{"_id":"RySh"}],"date_updated":"2023-09-19T09:58:40Z","ddc":["570"],"scopus_import":"1","intvolume":" 47","month":"03","abstract":[{"lang":"eng","text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites."}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":47,"issue":"9","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":4850261,"date_updated":"2020-07-14T12:46:06Z","creator":"dernst","file_name":"2018_EJN_Sawada.pdf","date_created":"2018-12-17T16:16:50Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5721","checksum":"98e901d8229e44aa8f3b51d248dedd09"}],"external_id":{"isi":["000431496400001"]},"article_processing_charge":"No","publist_id":"7539","author":[{"first_name":"Kazuaki","full_name":"Sawada, Kazuaki","last_name":"Sawada"},{"last_name":"Kawakami","full_name":"Kawakami, Ryosuke","first_name":"Ryosuke"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nemoto","full_name":"Nemoto, Tomomi","first_name":"Tomomi"}],"title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","citation":{"ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 2018;47(9):1033-1042. doi:10.1111/ejn.13901","apa":"Sawada, K., Kawakami, R., Shigemoto, R., & Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. Wiley. https://doi.org/10.1111/ejn.13901","ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” European Journal of Neuroscience, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018.","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:10.1111/ejn.13901.","ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience. Wiley, 2018. https://doi.org/10.1111/ejn.13901."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Wiley","page":"1033 - 1042","date_created":"2018-12-11T11:45:50Z","date_published":"2018-03-07T00:00:00Z","doi":"10.1111/ejn.13901","year":"2018","has_accepted_license":"1","isi":1,"publication":"European Journal of Neuroscience","day":"07"},{"author":[{"first_name":"Kun","last_name":"Qu","full_name":"Qu, Kun"},{"first_name":"Bärbel","full_name":"Glass, Bärbel","last_name":"Glass"},{"last_name":"Doležal","full_name":"Doležal, Michal","first_name":"Michal"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Schur","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078"},{"last_name":"Murciano","full_name":"Murciano, Brice","first_name":"Brice"},{"first_name":"Alan","full_name":"Rein, Alan","last_name":"Rein"},{"first_name":"Michaela","full_name":"Rumlová, Michaela","last_name":"Rumlová"},{"last_name":"Ruml","full_name":"Ruml, Tomáš","first_name":"Tomáš"},{"first_name":"Hans-Georg","full_name":"Kräusslich, Hans-Georg","last_name":"Kräusslich"},{"full_name":"Briggs, John A. G.","last_name":"Briggs","first_name":"John A. G."}],"external_id":{"isi":["000452866000022"],"pmid":["30478053"]},"article_processing_charge":"No","title":"Structure and architecture of immature and mature murine leukemia virus capsids","citation":{"ieee":"K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018.","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115.","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760.","chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"E11751-E11760","doi":"10.1073/pnas.1811580115","date_published":"2018-12-11T00:00:00Z","date_created":"2018-12-20T21:09:37Z","isi":1,"year":"2018","day":"11","publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","oa":1,"department":[{"_id":"FlSc"}],"date_updated":"2023-09-19T09:57:45Z","type":"journal_article","status":"public","_id":"5770","volume":115,"issue":"50","publication_identifier":{"issn":["00278424"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053"}],"month":"12","intvolume":" 115","abstract":[{"lang":"eng","text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry."}],"pmid":1,"oa_version":"Submitted Version"},{"citation":{"chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001.","ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001.","apa":"Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001","ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7197","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"external_id":{"isi":["000424959200003"]},"article_processing_charge":"No","title":"Synthesis from component libraries with costs","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"isi":1,"year":"2018","day":"15","publication":"Theoretical Computer Science","page":"50 - 72","date_published":"2018-02-15T00:00:00Z","doi":"10.1016/j.tcs.2017.11.001","date_created":"2018-12-11T11:47:28Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"date_updated":"2023-09-19T10:00:21Z","department":[{"_id":"ToHe"}],"_id":"608","article_type":"original","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":712,"ec_funded":1,"abstract":[{"text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529"}],"month":"02","intvolume":" 712"},{"department":[{"_id":"RySh"}],"date_updated":"2023-09-19T09:58:11Z","type":"journal_article","status":"public","_id":"705","issue":"6","volume":55,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 55","abstract":[{"lang":"eng","text":"Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins."}],"oa_version":"None","publist_id":"6991","author":[{"last_name":"Miklosi","full_name":"Miklosi, Andras","first_name":"Andras"},{"first_name":"Giorgia","full_name":"Del Favero, Giorgia","last_name":"Del Favero"},{"last_name":"Bulat","full_name":"Bulat, Tanja","first_name":"Tanja"},{"last_name":"Höger","full_name":"Höger, Harald","first_name":"Harald"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"first_name":"Doris","full_name":"Marko, Doris","last_name":"Marko"},{"last_name":"Lubec","full_name":"Lubec, Gert","first_name":"Gert"}],"article_processing_charge":"No","external_id":{"isi":["000431991500025"]},"title":"Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes","citation":{"apa":"Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D., & Lubec, G. (2018). Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. Springer. https://doi.org/10.1007/s12035-017-0688-y","ama":"Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 2018;55(6):4857 – 4869. doi:10.1007/s12035-017-0688-y","ieee":"A. Miklosi et al., “Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” Molecular Neurobiology, vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.","short":"A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.","mla":"Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology, vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:10.1007/s12035-017-0688-y.","ista":"Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G. 2018. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869.","chicago":"Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology. Springer, 2018. https://doi.org/10.1007/s12035-017-0688-y."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"4857 – 4869","date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s12035-017-0688-y","date_created":"2018-12-11T11:48:02Z","isi":1,"year":"2018","day":"01","publication":"Molecular Neurobiology","quality_controlled":"1","publisher":"Springer"},{"acknowledgement":"In-Data-Review","oa":1,"quality_controlled":"1","publisher":"Cell Press","publication":"Cell","day":"12","year":"2018","isi":1,"date_created":"2018-12-11T11:44:53Z","date_published":"2018-07-12T00:00:00Z","doi":"10.1016/j.cell.2018.06.033","page":"448 - 464.e24","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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.","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.” Cell. Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24. doi:10.1016/j.cell.2018.06.033","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. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033","ieee":"T. Nishiyama et al., “The Chara genome: Secondary complexity and implications for plant terrestrialization,” Cell, 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.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033."},"title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","external_id":{"pmid":["30007417"],"isi":["000438482800019"]},"article_processing_charge":"No","author":[{"last_name":"Nishiyama","full_name":"Nishiyama, Tomoaki","first_name":"Tomoaki"},{"first_name":"Hidetoshi","full_name":"Sakayama, Hidetoshi","last_name":"Sakayama"},{"last_name":"De Vries","full_name":"De Vries, Jan","first_name":"Jan"},{"full_name":"Buschmann, Henrik","last_name":"Buschmann","first_name":"Henrik"},{"last_name":"Saint Marcoux","full_name":"Saint Marcoux, Denis","first_name":"Denis"},{"first_name":"Kristian","full_name":"Ullrich, Kristian","last_name":"Ullrich"},{"first_name":"Fabian","last_name":"Haas","full_name":"Haas, Fabian"},{"first_name":"Lisa","last_name":"Vanderstraeten","full_name":"Vanderstraeten, Lisa"},{"first_name":"Dirk","full_name":"Becker, Dirk","last_name":"Becker"},{"first_name":"Daniel","full_name":"Lang, Daniel","last_name":"Lang"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"first_name":"Stephane","full_name":"Rombauts, Stephane","last_name":"Rombauts"},{"last_name":"Wilhelmsson","full_name":"Wilhelmsson, Per","first_name":"Per"},{"first_name":"Philipp","last_name":"Janitza","full_name":"Janitza, Philipp"},{"full_name":"Kern, Ramona","last_name":"Kern","first_name":"Ramona"},{"first_name":"Alexander","full_name":"Heyl, Alexander","last_name":"Heyl"},{"first_name":"Florian","last_name":"Rümpler","full_name":"Rümpler, Florian"},{"first_name":"Luz","last_name":"Calderón Villalobos","full_name":"Calderón Villalobos, Luz"},{"first_name":"John","full_name":"Clay, John","last_name":"Clay"},{"full_name":"Skokan, Roman","last_name":"Skokan","first_name":"Roman"},{"last_name":"Toyoda","full_name":"Toyoda, Atsushi","first_name":"Atsushi"},{"full_name":"Suzuki, Yutaka","last_name":"Suzuki","first_name":"Yutaka"},{"first_name":"Hiroshi","last_name":"Kagoshima","full_name":"Kagoshima, Hiroshi"},{"first_name":"Elio","full_name":"Schijlen, Elio","last_name":"Schijlen"},{"first_name":"Navindra","last_name":"Tajeshwar","full_name":"Tajeshwar, Navindra"},{"first_name":"Bruno","last_name":"Catarino","full_name":"Catarino, Bruno"},{"first_name":"Alexander","full_name":"Hetherington, Alexander","last_name":"Hetherington"},{"first_name":"Assia","last_name":"Saltykova","full_name":"Saltykova, Assia"},{"first_name":"Clemence","last_name":"Bonnot","full_name":"Bonnot, Clemence"},{"last_name":"Breuninger","full_name":"Breuninger, Holger","first_name":"Holger"},{"last_name":"Symeonidi","full_name":"Symeonidi, Aikaterini","first_name":"Aikaterini"},{"first_name":"Guru","full_name":"Radhakrishnan, Guru","last_name":"Radhakrishnan"},{"first_name":"Filip","last_name":"Van Nieuwerburgh","full_name":"Van Nieuwerburgh, Filip"},{"full_name":"Deforce, Dieter","last_name":"Deforce","first_name":"Dieter"},{"last_name":"Chang","full_name":"Chang, Caren","first_name":"Caren"},{"full_name":"Karol, Kenneth","last_name":"Karol","first_name":"Kenneth"},{"full_name":"Hedrich, Rainer","last_name":"Hedrich","first_name":"Rainer"},{"last_name":"Ulvskov","full_name":"Ulvskov, Peter","first_name":"Peter"},{"first_name":"Gernot","last_name":"Glöckner","full_name":"Glöckner, Gernot"},{"first_name":"Charles","last_name":"Delwiche","full_name":"Delwiche, Charles"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"first_name":"Yves","last_name":"Van De Peer","full_name":"Van De Peer, Yves"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"last_name":"Beilby","full_name":"Beilby, Mary","first_name":"Mary"},{"first_name":"Liam","full_name":"Dolan, Liam","last_name":"Dolan"},{"first_name":"Yuji","last_name":"Kohara","full_name":"Kohara, Yuji"},{"full_name":"Sugano, Sumio","last_name":"Sugano","first_name":"Sumio"},{"full_name":"Fujiyama, Asao","last_name":"Fujiyama","first_name":"Asao"},{"last_name":"Delaux","full_name":"Delaux, Pierre Marc","first_name":"Pierre Marc"},{"last_name":"Quint","full_name":"Quint, Marcel","first_name":"Marcel"},{"first_name":"Gunter","last_name":"Theissen","full_name":"Theissen, Gunter"},{"last_name":"Hagemann","full_name":"Hagemann, Martin","first_name":"Martin"},{"first_name":"Jesper","last_name":"Harholt","full_name":"Harholt, Jesper"},{"full_name":"Dunand, Christophe","last_name":"Dunand","first_name":"Christophe"},{"first_name":"Sabine","full_name":"Zachgo, Sabine","last_name":"Zachgo"},{"full_name":"Langdale, Jane","last_name":"Langdale","first_name":"Jane"},{"full_name":"Maumus, Florian","last_name":"Maumus","first_name":"Florian"},{"full_name":"Van Der Straeten, Dominique","last_name":"Van Der Straeten","first_name":"Dominique"},{"first_name":"Sven B","last_name":"Gould","full_name":"Gould, Sven B"},{"first_name":"Stefan","last_name":"Rensing","full_name":"Rensing, Stefan"}],"publist_id":"7774","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"intvolume":" 174","month":"07","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":174,"issue":"2","_id":"148","status":"public","type":"journal_article","date_updated":"2023-09-19T10:02:47Z","department":[{"_id":"JiFr"}]},{"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d9d3ad3215ac0e581731443fca312266","file_id":"5934","creator":"dernst","date_updated":"2020-07-14T12:46:22Z","file_size":1543354,"date_created":"2019-02-06T11:40:54Z","file_name":"2018_PlantJourn_Cavallari.pdf"}],"language":[{"iso":"eng"}],"volume":94,"issue":"6","abstract":[{"text":"The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 94","date_updated":"2023-09-19T10:07:08Z","ddc":["580"],"file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"EvBe"}],"_id":"403","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","has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"The Plant Journal","page":"1010 - 1022","date_published":"2018-06-01T00:00:00Z","doi":"10.1111/tpj.13914","date_created":"2018-12-11T11:46:17Z","acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","publisher":"Wiley","quality_controlled":"1","oa":1,"citation":{"chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914.","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.","mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914.","ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914","apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7426","author":[{"first_name":"Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola","last_name":"Cavallari"},{"full_name":"Nibau, Candida","last_name":"Nibau","first_name":"Candida"},{"last_name":"Fuchs","full_name":"Fuchs, Armin","first_name":"Armin"},{"last_name":"Dadarou","full_name":"Dadarou, Despoina","first_name":"Despoina"},{"first_name":"Andrea","full_name":"Barta, Andrea","last_name":"Barta"},{"first_name":"John","last_name":"Doonan","full_name":"Doonan, John"}],"external_id":{"isi":["000434365500008"]},"article_processing_charge":"No","title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A"},{"oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:44:55Z","doi":"10.1007/978-3-319-95582-7_9","date_published":"2018-07-12T00:00:00Z","page":"147 - 164","day":"12","year":"2018","has_accepted_license":"1","isi":1,"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"title":"The compound interest in relaxing punctuality","article_processing_charge":"No","external_id":{"isi":["000489765800009"]},"author":[{"last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","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.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","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. 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","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."},"intvolume":" 10951","month":"07","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"volume":10951,"language":[{"iso":"eng"}],"file":[{"date_created":"2020-10-09T06:22:41Z","file_name":"2018_LNCS_Ferrere.pdf","creator":"dernst","date_updated":"2020-10-09T06:22:41Z","file_size":485576,"file_id":"8637","checksum":"a045c213c42c445f1889326f8db82a0a","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","status":"public","conference":{"name":"FM: International Symposium on Formal Methods","start_date":"2018-07-15","location":"Oxford, UK","end_date":"2018-07-17"},"type":"conference","_id":"156","file_date_updated":"2020-10-09T06:22:41Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-09-19T10:05:37Z"},{"acknowledgement":"the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"01","publication":"Molecular Plant Pathology","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1111/mpp.12698","date_published":"2018-10-01T00:00:00Z","date_created":"2018-12-11T11:44:39Z","page":"2277 - 2287","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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.","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.","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.","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."},"title":"The core effector Cce1 is required for early infection of maize by Ustilago maydis","author":[{"first_name":"Denise","last_name":"Seitner","full_name":"Seitner, Denise"},{"first_name":"Simon","last_name":"Uhse","full_name":"Uhse, Simon"},{"full_name":"Gallei, Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Armin","full_name":"Djamei, Armin","last_name":"Djamei"}],"publist_id":"7950","article_processing_charge":"No","external_id":{"isi":["000445624100006"]},"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"10","intvolume":" 19","scopus_import":"1","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"}],"publication_status":"published","volume":19,"issue":"10","_id":"104","status":"public","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)"},"ddc":["580"],"date_updated":"2023-09-19T10:06:42Z","file_date_updated":"2018-12-18T09:46:00Z","department":[{"_id":"GradSch"}]},{"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","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."}],"month":"12","intvolume":" 27","scopus_import":"1","file":[{"creator":"apreinsp","date_updated":"2020-07-14T12:46:22Z","file_size":295452,"date_created":"2019-07-19T06:54:46Z","file_name":"2018_MolecularEcology_BartonNick.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6652"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1365294X"]},"publication_status":"published","volume":27,"issue":"24","related_material":{"record":[{"status":"public","id":"9805","relation":"research_data"}]},"_id":"40","status":"public","article_type":"letter_note","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)"},"ddc":["576"],"date_updated":"2023-09-19T10:06:08Z","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:22Z","publisher":"Wiley","quality_controlled":"1","oa":1,"day":"31","publication":"Molecular Ecology","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-12-31T00:00:00Z","doi":"10.1111/mec.14950","date_created":"2018-12-11T11:44:18Z","page":"4973-4975","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. 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.","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","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."},"title":"The consequences of an introgression event","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8014","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["30599087"],"isi":["000454600500001"]}},{"scopus_import":"1","month":"06","intvolume":" 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","volume":7,"publication_identifier":{"issn":["2050084X"]},"publication_status":"published","file":[{"checksum":"f1c7ec2a809408d763c4b529a98f9a3b","file_id":"5973","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_eLife_Alanko.pdf","date_created":"2019-02-13T10:52:11Z","creator":"dernst","file_size":358141,"date_updated":"2020-07-14T12:47:13Z"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","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":"5861","file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"MiSi"}],"date_updated":"2023-09-19T10:01:39Z","ddc":["570"],"publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"date_published":"2018-06-06T00:00:00Z","doi":"10.7554/eLife.37888","date_created":"2019-01-20T22:59:19Z","has_accepted_license":"1","isi":1,"year":"2018","day":"06","publication":"eLife","article_number":"e37888","author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","last_name":"Alanko","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"external_id":{"isi":["000434375000001"]},"article_processing_charge":"No","title":"The cell sets the tone","citation":{"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.","ieee":"J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"J.H. Alanko, M.K. Sixt, ELife 7 (2018).","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"doi":"10.1105/tpc.18.00127","date_published":"2018-11-12T00:00:00Z","date_created":"2018-12-11T11:44:52Z","page":"2553 - 2572","day":"12","publication":"The Plant Cell","isi":1,"year":"2018","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"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.).","title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","author":[{"id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula","last_name":"Kania","full_name":"Kania, Urszula"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"last_name":"Lu","full_name":"Lu, Qing","first_name":"Qing"},{"last_name":"Hicks","full_name":"Hicks, Glenn R","first_name":"Glenn R"},{"full_name":"Nerinckx, Wim","last_name":"Nerinckx","first_name":"Wim"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"last_name":"Peurois","full_name":"Peurois, Francois","first_name":"Francois"},{"full_name":"Cherfils, Jacqueline","last_name":"Cherfils","first_name":"Jacqueline"},{"first_name":"Rycke Riet Maria","last_name":"De","full_name":"De, Rycke Riet Maria"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7776","article_processing_charge":"No","external_id":{"pmid":["30018156"],"isi":["000450000500023"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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.","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."},"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"issue":"10","volume":30,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1040-4651"]},"publication_status":"published","month":"11","intvolume":" 30","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1105/tpc.18.00127","open_access":"1"}],"oa_version":"Published Version","pmid":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."}],"department":[{"_id":"JiFr"}],"date_updated":"2023-09-19T10:09:12Z","status":"public","article_type":"original","type":"journal_article","_id":"147"}]