[{"volume":9938,"acknowledgement":"The research was funded by the Czech Science Foundation Grant No. P202/12/G061 and by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].","publisher":"Springer","page":"32 - 49","arxiv":1,"language":[{"iso":"eng"}],"oa":1,"author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr","first_name":"Petr","last_name":"Novotny"}],"citation":{"chicago":"Brázdil, Tomáš, Antonín Kučera, and Petr Novotný. “Optimizing the Expected Mean Payoff in Energy Markov Decision Processes,” 9938:32–49. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-46520-3_3\">https://doi.org/10.1007/978-3-319-46520-3_3</a>.","apa":"Brázdil, T., Kučera, A., &#38; Novotný, P. (2016). Optimizing the expected mean payoff in Energy Markov Decision Processes (Vol. 9938, pp. 32–49). Presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan: Springer. <a href=\"https://doi.org/10.1007/978-3-319-46520-3_3\">https://doi.org/10.1007/978-3-319-46520-3_3</a>","mla":"Brázdil, Tomáš, et al. <i>Optimizing the Expected Mean Payoff in Energy Markov Decision Processes</i>. Vol. 9938, Springer, 2016, pp. 32–49, doi:<a href=\"https://doi.org/10.1007/978-3-319-46520-3_3\">10.1007/978-3-319-46520-3_3</a>.","ista":"Brázdil T, Kučera A, Novotný P. 2016. Optimizing the expected mean payoff in Energy Markov Decision Processes. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 9938, 32–49.","short":"T. Brázdil, A. Kučera, P. Novotný, in:, Springer, 2016, pp. 32–49.","ama":"Brázdil T, Kučera A, Novotný P. Optimizing the expected mean payoff in Energy Markov Decision Processes. In: Vol 9938. Springer; 2016:32-49. doi:<a href=\"https://doi.org/10.1007/978-3-319-46520-3_3\">10.1007/978-3-319-46520-3_3</a>","ieee":"T. Brázdil, A. Kučera, and P. Novotný, “Optimizing the expected mean payoff in Energy Markov Decision Processes,” presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan, 2016, vol. 9938, pp. 32–49."},"conference":{"end_date":"2016-10-20","name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2016-10-17","location":"Chiba, Japan"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00678"}],"type":"conference","article_processing_charge":"No","scopus_import":"1","fulldoi":"https://doi.org/10.1007/978-3-319-46520-3_3","doi":"10.1007/978-3-319-46520-3_3","publication_status":"published","date_created":"2018-12-11T11:51:23Z","year":"2016","date_updated":"2025-09-22T08:25:26Z","quality_controlled":"1","publist_id":"5943","intvolume":"      9938","date_published":"2016-09-22T00:00:00Z","_id":"1326","ec_funded":1,"abstract":[{"text":"Energy Markov Decision Processes (EMDPs) are finite-state Markov decision processes where each transition is assigned an integer counter update and a rational payoff. An EMDP configuration is a pair s(n), where s is a control state and n is the current counter value. The configurations are changed by performing transitions in the standard way. We consider the problem of computing a safe strategy (i.e., a strategy that keeps the counter non-negative) which maximizes the expected mean payoff. ","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"KrCh"}],"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"alternative_title":["LNCS"],"external_id":{"isi":["000389808100003"],"arxiv":["1607.00678"]},"title":"Optimizing the expected mean payoff in Energy Markov Decision Processes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","day":"22","month":"09","status":"public","isi":1},{"publist_id":"5942","date_updated":"2025-06-04T10:26:23Z","quality_controlled":"1","publication":"Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems","date_published":"2016-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","year":"2016","publication_status":"published","date_created":"2018-12-11T11:51:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Stochastic shortest path with energy constraints in POMDPs","status":"public","day":"01","month":"01","department":[{"_id":"KrCh"}],"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","_id":"1327","ec_funded":1,"abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize the expected total cost until the target set is reached. We extend the traditional framework of POMDPs to model energy consumption, which represents a hard constraint. The energy levels may increase and decrease with transitions, and the hard constraint requires that the energy level must remain positive in all steps till the target is reached. First, we present a novel algorithm for solving POMDPs with energy levels, developing on existing POMDP solvers and using RTDP as its main method. Our second contribution is related to policy representation. For larger POMDP instances the policies computed by existing solvers are too large to be understandable. We present an automated procedure based on machine learning techniques that automatically extracts important decisions of the policy allowing us to compute succinct human readable policies. Finally, we show experimentally that our algorithm performs well and computes succinct policies on a number of POMDP instances from the literature that were naturally enhanced with energy levels. "}],"external_id":{"arxiv":["1602.07565"]},"publisher":"ACM","language":[{"iso":"eng"}],"oa":1,"arxiv":1,"page":"1465 - 1466","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1602.07565","open_access":"1"}],"conference":{"end_date":"2016-05-13","name":"AAMAS: Autonomous Agents & Multiagent Systems","start_date":"2016-05-09","location":"Singapore"},"citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Anchit Gupta, and Petr Novotný. “Stochastic Shortest Path with Energy Constraints in POMDPs.” In <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i>, 1465–66. ACM, 2016.","ista":"Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. 2016. Stochastic shortest path with energy constraints in POMDPs. Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. AAMAS: Autonomous Agents &#38; Multiagent Systems, 1465–1466.","mla":"Brázdil, Tomáš, et al. “Stochastic Shortest Path with Energy Constraints in POMDPs.” <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i>, ACM, 2016, pp. 1465–66.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Gupta, A., &#38; Novotný, P. (2016). Stochastic shortest path with energy constraints in POMDPs. In <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i> (pp. 1465–1466). Singapore: ACM.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, P. Novotný, in:, Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–1466.","ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, and P. Novotný, “Stochastic shortest path with energy constraints in POMDPs,” in <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i>, Singapore, 2016, pp. 1465–1466.","ama":"Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. Stochastic shortest path with energy constraints in POMDPs. In: <i>Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems</i>. ACM; 2016:1465-1466."},"author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"full_name":"Gupta, Anchit","first_name":"Anchit","last_name":"Gupta"},{"full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny"}]},{"has_accepted_license":"1","title":"Heavy-hole states in germanium hut wires","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","relation":"dissertation_contains","id":"7996"}]},"month":"09","day":"22","isi":1,"status":"public","abstract":[{"lang":"eng","text":"Hole spins have gained considerable interest in the past few years due to their potential for fast electrically controlled qubits. Here, we study holes confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature magnetotransport measurements reveal a large anisotropy between the in-plane and out-of-plane g-factors of up to 18. Numerical simulations verify that this large anisotropy originates from a confined wave function of heavy-hole character. A light-hole admixture of less than 1% is estimated for the states of lowest energy, leading to a surprisingly large reduction of the out-of-plane g-factors compared with those for pure heavy holes. Given this tiny light-hole contribution, the spin lifetimes are expected to be very long, even in isotopically nonpurified samples."}],"_id":"1328","ec_funded":1,"oa_version":"Published Version","department":[{"_id":"GeKa"}],"project":[{"grant_number":"335497","_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires"}],"external_id":{"isi":["000387625000025"]},"date_updated":"2026-04-08T07:27:13Z","quality_controlled":"1","publist_id":"5941","intvolume":"        16","date_published":"2016-09-22T00:00:00Z","publication":"Nano Letters","scopus_import":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.1021/acs.nanolett.6b02715","doi":"10.1021/acs.nanolett.6b02715","date_created":"2018-12-11T11:51:24Z","publication_status":"published","year":"2016","type":"journal_article","issue":"11","author":[{"last_name":"Watzinger","first_name":"Hannes","full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kloeffel, Christoph","first_name":"Christoph","last_name":"Kloeffel"},{"orcid":"0000-0003-2424-8636","full_name":"Vukusic, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","last_name":"Vukusic"},{"last_name":"Rossell","first_name":"Marta","full_name":"Rossell, Marta"},{"first_name":"Violetta","full_name":"Sessi, Violetta","last_name":"Sessi"},{"last_name":"Kukucka","first_name":"Josip","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kirchschlager","first_name":"Raimund","full_name":"Kirchschlager, Raimund"},{"first_name":"Elisabeth","id":"33662F76-F248-11E8-B48F-1D18A9856A87","full_name":"Lausecker, Elisabeth","last_name":"Lausecker"},{"first_name":"Alisha","id":"49CBC780-F248-11E8-B48F-1D18A9856A87","full_name":"Truhlar, Alisha","last_name":"Truhlar"},{"last_name":"Glaser","first_name":"Martin","full_name":"Glaser, Martin"},{"first_name":"Armando","full_name":"Rastelli, Armando","last_name":"Rastelli"},{"last_name":"Fuhrer","full_name":"Fuhrer, Andreas","first_name":"Andreas"},{"full_name":"Loss, Daniel","first_name":"Daniel","last_name":"Loss"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"file_date_updated":"2020-07-14T12:44:44Z","citation":{"chicago":"Watzinger, Hannes, Christoph Kloeffel, Lada Vukušić, Marta Rossell, Violetta Sessi, Josip Kukucka, Raimund Kirchschlager, et al. “Heavy-Hole States in Germanium Hut Wires.” <i>Nano Letters</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">https://doi.org/10.1021/acs.nanolett.6b02715</a>.","apa":"Watzinger, H., Kloeffel, C., Vukušić, L., Rossell, M., Sessi, V., Kukucka, J., … Katsaros, G. (2016). Heavy-hole states in germanium hut wires. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">https://doi.org/10.1021/acs.nanolett.6b02715</a>","ista":"Watzinger H, Kloeffel C, Vukušić L, Rossell M, Sessi V, Kukucka J, Kirchschlager R, Lausecker E, Truhlar A, Glaser M, Rastelli A, Fuhrer A, Loss D, Katsaros G. 2016. Heavy-hole states in germanium hut wires. Nano Letters. 16(11), 6879–6885.","mla":"Watzinger, Hannes, et al. “Heavy-Hole States in Germanium Hut Wires.” <i>Nano Letters</i>, vol. 16, no. 11, American Chemical Society, 2016, pp. 6879–85, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">10.1021/acs.nanolett.6b02715</a>.","short":"H. Watzinger, C. Kloeffel, L. Vukušić, M. Rossell, V. Sessi, J. Kukucka, R. Kirchschlager, E. Lausecker, A. Truhlar, M. Glaser, A. Rastelli, A. Fuhrer, D. Loss, G. Katsaros, Nano Letters 16 (2016) 6879–6885.","ama":"Watzinger H, Kloeffel C, Vukušić L, et al. Heavy-hole states in germanium hut wires. <i>Nano Letters</i>. 2016;16(11):6879-6885. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">10.1021/acs.nanolett.6b02715</a>","ieee":"H. Watzinger <i>et al.</i>, “Heavy-hole states in germanium hut wires,” <i>Nano Letters</i>, vol. 16, no. 11. American Chemical Society, pp. 6879–6885, 2016."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ddc":["539"],"pubrep_id":"664","publisher":"American Chemical Society","page":"6879 - 6885","language":[{"iso":"eng"}],"oa":1,"volume":16,"file":[{"checksum":"b63feece90d7b620ece49ca632e34ff3","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:14:04Z","file_size":535121,"date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-664-v1+1_acs.nanolett.6b02715.pdf","file_id":"5053","creator":"system"}],"acknowledgement":"The work was supported by the EC FP7 ICT project SiSPIN no. 323841, the EC FP7 ICT project PAMS no. 610446, the ERC Starting Grant no. 335497, the FWF-I-1190-N20 project, and the Swiss NSF. We acknowledge F. Schäffler for fruitful discussions related to the hut wire growth and for giving us access to the molecular beam epitaxy system, M. Schatzl for her support in electron beam lithography, and V. Jadris ̌ko for helping us with the COMSOL simulations. Finally, we thank G. Bauer for his continuous support. "},{"_id":"1329","abstract":[{"text":"Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"BeVi"}],"external_id":{"isi":["000386121300005"]},"has_accepted_license":"1","title":"De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","month":"10","isi":1,"status":"public","scopus_import":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.1093/gbe/evw221","doi":"10.1093/gbe/evw221","date_created":"2018-12-11T11:51:24Z","publication_status":"published","year":"2016","quality_controlled":"1","date_updated":"2025-09-22T08:24:02Z","publist_id":"5940","intvolume":"         8","date_published":"2016-10-01T00:00:00Z","publication":"Genome Biology and Evolution","author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","first_name":"Ann K","last_name":"Huylmans"},{"last_name":"López Ezquerra","first_name":"Alberto","full_name":"López Ezquerra, Alberto"},{"full_name":"Parsch, John","first_name":"John","last_name":"Parsch"},{"first_name":"Mathilde","full_name":"Cordellier, Mathilde","last_name":"Cordellier"}],"file_date_updated":"2020-07-14T12:44:44Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"citation":{"chicago":"Huylmans, Ann K, Alberto López Ezquerra, John Parsch, and Mathilde Cordellier. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/gbe/evw221\">https://doi.org/10.1093/gbe/evw221</a>.","ista":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. 2016. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 8(10), 3120–3139.","mla":"Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” <i>Genome Biology and Evolution</i>, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39, doi:<a href=\"https://doi.org/10.1093/gbe/evw221\">10.1093/gbe/evw221</a>.","apa":"Huylmans, A. K., López Ezquerra, A., Parsch, J., &#38; Cordellier, M. (2016). De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evw221\">https://doi.org/10.1093/gbe/evw221</a>","short":"A.K. Huylmans, A. López Ezquerra, J. Parsch, M. Cordellier, Genome Biology and Evolution 8 (2016) 3120–3139.","ieee":"A. K. Huylmans, A. López Ezquerra, J. Parsch, and M. Cordellier, “De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata,” <i>Genome Biology and Evolution</i>, vol. 8, no. 10. Oxford University Press, pp. 3120–3139, 2016.","ama":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. <i>Genome Biology and Evolution</i>. 2016;8(10):3120-3139. doi:<a href=\"https://doi.org/10.1093/gbe/evw221\">10.1093/gbe/evw221</a>"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","type":"journal_article","issue":"10","volume":8,"file":[{"date_created":"2018-12-12T10:12:06Z","access_level":"open_access","content_type":"application/pdf","checksum":"25c7adcb452d39d3b6343ff4b57a652d","relation":"main_file","file_id":"4924","creator":"system","file_size":1406265,"file_name":"IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf","date_updated":"2020-07-14T12:44:44Z"}],"acknowledgement":"This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). The authors would like to thank I. Schrank, L. Theodosiou, M. Kredler, C. Laforsch, J. Wolinska, J. Griebel, R. Jaenichen, and K. Otte for providing the necessary resources and help for maintaining Daphnia cultures in the laboratory. H. Lainer supported us for the molecular laboratory work. D. Gilbert and J. K. Colbourne contributed ideas for the bioinformatics analysis, and L. Hardulak did the orthology mapping including more insect species. This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). This work benefits from and contributes to the Daphnia Genomics Consortium.","ddc":["576"],"pubrep_id":"663","publisher":"Oxford University Press","page":"3120 - 3139","oa":1,"language":[{"iso":"eng"}]},{"publisher":"Springer","oa":1,"language":[{"iso":"eng"}],"arxiv":1,"page":"833 - 845","volume":216,"acknowledgement":"Supported by People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n°[291734]. Supported by the Russian Foundation for Basic Research grant 15-31-20403 (mol a ved), by the Russian Foundation for Basic Research grant 15-01-99563 A, in part by the Moebius Contest Foundation for Young Scientists, and in part by the Simons Foundation.","type":"journal_article","issue":"2","main_file_link":[{"url":"https://arxiv.org/abs/1506.06014","open_access":"1"}],"citation":{"chicago":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” <i>Israel Journal of Mathematics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11856-016-1429-z\">https://doi.org/10.1007/s11856-016-1429-z</a>.","ista":"Akopyan A, Balitskiy A. 2016. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 216(2), 833–845.","mla":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2, Springer, 2016, pp. 833–45, doi:<a href=\"https://doi.org/10.1007/s11856-016-1429-z\">10.1007/s11856-016-1429-z</a>.","apa":"Akopyan, A., &#38; Balitskiy, A. (2016). Billiards in convex bodies with acute angles. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-016-1429-z\">https://doi.org/10.1007/s11856-016-1429-z</a>","short":"A. Akopyan, A. Balitskiy, Israel Journal of Mathematics 216 (2016) 833–845.","ama":"Akopyan A, Balitskiy A. Billiards in convex bodies with acute angles. <i>Israel Journal of Mathematics</i>. 2016;216(2):833-845. doi:<a href=\"https://doi.org/10.1007/s11856-016-1429-z\">10.1007/s11856-016-1429-z</a>","ieee":"A. Akopyan and A. Balitskiy, “Billiards in convex bodies with acute angles,” <i>Israel Journal of Mathematics</i>, vol. 216, no. 2. Springer, pp. 833–845, 2016."},"author":[{"last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","first_name":"Arseniy"},{"first_name":"Alexey","full_name":"Balitskiy, Alexey","last_name":"Balitskiy"}],"intvolume":"       216","publist_id":"5938","date_updated":"2025-09-22T08:23:27Z","quality_controlled":"1","publication":"Israel Journal of Mathematics","date_published":"2016-10-15T00:00:00Z","doi":"10.1007/s11856-016-1429-z","fulldoi":"https://doi.org/10.1007/s11856-016-1429-z","scopus_import":"1","article_processing_charge":"No","year":"2016","publication_status":"published","date_created":"2018-12-11T11:51:24Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Billiards in convex bodies with acute angles","isi":1,"status":"public","month":"10","day":"15","corr_author":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"department":[{"_id":"HeEd"}],"oa_version":"Preprint","abstract":[{"text":"In this paper we investigate the existence of closed billiard trajectories in not necessarily smooth convex bodies. In particular, we show that if a body K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K is acute (in a certain sense), then there is a closed billiard trajectory in K.","lang":"eng"}],"_id":"1330","ec_funded":1,"external_id":{"arxiv":["1506.06014"],"isi":["000386356400012"]}},{"language":[{"iso":"eng"}],"oa":1,"page":"1249 - 1258","publisher":"American Society of Plant Biologists","ddc":["580"],"acknowledgement":"This work was financially supported by the following: The Alabama Agricultural Experiment Station HATCH grants 370222-310010-2055 and 370225-310006-2055 for funding to P.J.Z., E.A.K, A.M.P., and A.M.R. P.J.Z. and E.A.K were supported by an Auburn University Cellular and Molecular Biosciences Research Fellowship. I.D.C. is a postdoctoral fellow of the Research Foundation Flanders (FWO) (FWO/PDO14/043) and is also supported by FWO travel\r\ngrant 12N2415N. F.V.B. was supported by grants from the Interuniversity Attraction Poles Programme (IUAP P7/29 MARS) initiated by the Belgian Science Policy Office and Ghent University (Multidisciplinary Research Partnership Biotechnology for a Sustainable Economy, grant 01MRB510W).","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"volume":172,"issue":"2","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1104/pp.16.00415","open_access":"1"}],"citation":{"chicago":"Zwack, Paul, Inge De Clercq, Timothy Howton, H Tucker Hallmark, Andrej Hurny, Erika Keshishian, Alyssa Parish, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2016. <a href=\"https://doi.org/10.1104/pp.16.00415\">https://doi.org/10.1104/pp.16.00415</a>.","apa":"Zwack, P., De Clercq, I., Howton, T., Hallmark, H. T., Hurny, A., Keshishian, E., … Rashotte, A. (2016). Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.16.00415\">https://doi.org/10.1104/pp.16.00415</a>","ista":"Zwack P, De Clercq I, Howton T, Hallmark HT, Hurny A, Keshishian E, Parish A, Benková E, Mukhtar MS, Van Breusegem F, Rashotte A. 2016. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 172(2), 1249–1258.","mla":"Zwack, Paul, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” <i>Plant Physiology</i>, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1249–58, doi:<a href=\"https://doi.org/10.1104/pp.16.00415\">10.1104/pp.16.00415</a>.","short":"P. Zwack, I. De Clercq, T. Howton, H.T. Hallmark, A. Hurny, E. Keshishian, A. Parish, E. Benková, M.S. Mukhtar, F. Van Breusegem, A. Rashotte, Plant Physiology 172 (2016) 1249–1258.","ieee":"P. Zwack <i>et al.</i>, “Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress,” <i>Plant Physiology</i>, vol. 172, no. 2. American Society of Plant Biologists, pp. 1249–1258, 2016.","ama":"Zwack P, De Clercq I, Howton T, et al. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. <i>Plant Physiology</i>. 2016;172(2):1249-1258. doi:<a href=\"https://doi.org/10.1104/pp.16.00415\">10.1104/pp.16.00415</a>"},"author":[{"first_name":"Paul","full_name":"Zwack, Paul","last_name":"Zwack"},{"full_name":"De Clercq, Inge","first_name":"Inge","last_name":"De Clercq"},{"last_name":"Howton","full_name":"Howton, Timothy","first_name":"Timothy"},{"first_name":"H Tucker","full_name":"Hallmark, H Tucker","last_name":"Hallmark"},{"id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426","first_name":"Andrej","last_name":"Hurny"},{"last_name":"Keshishian","full_name":"Keshishian, Erika","first_name":"Erika"},{"last_name":"Parish","full_name":"Parish, Alyssa","first_name":"Alyssa"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková"},{"first_name":"M Shahid","full_name":"Mukhtar, M Shahid","last_name":"Mukhtar"},{"full_name":"Van Breusegem, Frank","first_name":"Frank","last_name":"Van Breusegem"},{"full_name":"Rashotte, Aaron","first_name":"Aaron","last_name":"Rashotte"}],"publication":"Plant Physiology","date_published":"2016-10-02T00:00:00Z","publist_id":"5937","intvolume":"       172","quality_controlled":"1","date_updated":"2026-06-18T17:30:26Z","year":"2016","publication_status":"published","date_created":"2018-12-11T11:51:25Z","article_type":"original","fulldoi":"https://doi.org/10.1104/pp.16.00415","doi":"10.1104/pp.16.00415","scopus_import":"1","article_processing_charge":"No","day":"02","month":"10","isi":1,"status":"public","title":"Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000391147700047"]},"department":[{"_id":"EvBe"}],"abstract":[{"lang":"eng","text":"Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6- dependent genes and establishes a novel connection between cytokinin and oxidative stress response."}],"_id":"1331","oa_version":"Published Version"},{"month":"01","day":"20","status":"public","isi":1,"title":"Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","external_id":{"isi":["000369021700002"]},"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"1332","abstract":[{"lang":"eng","text":"Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance."}],"oa_version":"Published Version","publication":"Nature Communications","date_published":"2016-01-20T00:00:00Z","publist_id":"5936","intvolume":"         7","quality_controlled":"1","date_updated":"2025-09-22T08:22:19Z","year":"2016","date_created":"2018-12-11T11:51:25Z","publication_status":"published","fulldoi":"https://doi.org/10.1038/ncomms10333","doi":"10.1038/ncomms10333","scopus_import":"1","article_processing_charge":"No","type":"journal_article","article_number":"10333","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"short":"R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).","ieee":"R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ama":"Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms10333\">10.1038/ncomms10333</a>","chicago":"Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms10333\">https://doi.org/10.1038/ncomms10333</a>.","apa":"Chait, R. P., Palmer, A., Yelin, I., &#38; Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms10333\">https://doi.org/10.1038/ncomms10333</a>","ista":"Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333.","mla":"Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” <i>Nature Communications</i>, vol. 7, 10333, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms10333\">10.1038/ncomms10333</a>."},"author":[{"last_name":"Chait","first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P"},{"first_name":"Adam","full_name":"Palmer, Adam","last_name":"Palmer"},{"last_name":"Yelin","first_name":"Idan","full_name":"Yelin, Idan"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"file_date_updated":"2020-07-14T12:44:44Z","oa":1,"language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","pubrep_id":"662","ddc":["570","579"],"acknowledgement":"This work was partially supported by US National Institutes of Health grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant No. 152/11, and the European Research Council FP7 ERC Grant 281891.","file":[{"file_id":"5039","creator":"system","file_name":"IST-2016-662-v1+1_ncomms10333.pdf","date_updated":"2020-07-14T12:44:44Z","file_size":1844107,"date_created":"2018-12-12T10:13:52Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"ef147bcbb8bd37e9079cf3ce06f5815d"}],"volume":7},{"oa":1,"language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","pubrep_id":"661","ddc":["519","530","599"],"acknowledgement":"We thank the students for participation; H.-J. Krambeck for writing the software for the game; H. Arndt, T. Bakker, L. Becks, H. Brendelberger, S. Dobler and T. Reusch for support; and the Max Planck Society for the Advancement of Science for funding.","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:10:44Z","checksum":"9ea0d7ce59a555a1cb8353d5559407cb","relation":"main_file","creator":"system","file_id":"4834","file_size":1432577,"date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-661-v1+1_ncomms10915.pdf"}],"volume":7,"type":"journal_article","article_number":"10915","citation":{"apa":"Milinski, M., Hilbe, C., Semmann, D., Sommerfeld, R., &#38; Marotzke, J. (2016). Humans choose representatives who enforce cooperation in social dilemmas through extortion. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms10915\">https://doi.org/10.1038/ncomms10915</a>","ista":"Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. 2016. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 7, 10915.","mla":"Milinski, Manfred, et al. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” <i>Nature Communications</i>, vol. 7, 10915, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms10915\">10.1038/ncomms10915</a>.","chicago":"Milinski, Manfred, Christian Hilbe, Dirk Semmann, Ralf Sommerfeld, and Jochem Marotzke. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms10915\">https://doi.org/10.1038/ncomms10915</a>.","ieee":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, and J. Marotzke, “Humans choose representatives who enforce cooperation in social dilemmas through extortion,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ama":"Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. Humans choose representatives who enforce cooperation in social dilemmas through extortion. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms10915\">10.1038/ncomms10915</a>","short":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, J. Marotzke, Nature Communications 7 (2016)."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:44:44Z","author":[{"first_name":"Manfred","full_name":"Milinski, Manfred","last_name":"Milinski"},{"first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe"},{"full_name":"Semmann, Dirk","first_name":"Dirk","last_name":"Semmann"},{"full_name":"Sommerfeld, Ralf","first_name":"Ralf","last_name":"Sommerfeld"},{"full_name":"Marotzke, Jochem","first_name":"Jochem","last_name":"Marotzke"}],"publication":"Nature Communications","date_published":"2016-03-07T00:00:00Z","intvolume":"         7","publist_id":"5935","quality_controlled":"1","date_updated":"2025-09-22T08:21:34Z","year":"2016","publication_status":"published","date_created":"2018-12-11T11:51:25Z","doi":"10.1038/ncomms10915","fulldoi":"https://doi.org/10.1038/ncomms10915","scopus_import":"1","article_processing_charge":"No","isi":1,"status":"public","day":"07","month":"03","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Humans choose representatives who enforce cooperation in social dilemmas through extortion","has_accepted_license":"1","external_id":{"isi":["000371720200001"]},"department":[{"_id":"KrCh"}],"oa_version":"Published Version","_id":"1333","abstract":[{"text":"Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the &quot;representatives&quot; treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most.","lang":"eng"}]},{"article_number":"11824","type":"journal_article","author":[{"last_name":"Schönenberger","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp","first_name":"Philipp"},{"first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","full_name":"O'Neill, Joseph","last_name":"O'Neill"},{"last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:44:44Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"ista":"Schönenberger P, O’Neill J, Csicsvari JL. 2016. Activity dependent plasticity of hippocampal place maps. Nature Communications. 7, 11824.","mla":"Schönenberger, Philipp, et al. “Activity Dependent Plasticity of Hippocampal Place Maps.” <i>Nature Communications</i>, vol. 7, 11824, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11824\">10.1038/ncomms11824</a>.","apa":"Schönenberger, P., O’Neill, J., &#38; Csicsvari, J. L. (2016). Activity dependent plasticity of hippocampal place maps. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11824\">https://doi.org/10.1038/ncomms11824</a>","chicago":"Schönenberger, Philipp, Joseph O’Neill, and Jozsef L Csicsvari. “Activity Dependent Plasticity of Hippocampal Place Maps.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11824\">https://doi.org/10.1038/ncomms11824</a>.","ieee":"P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Activity dependent plasticity of hippocampal place maps,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ama":"Schönenberger P, O’Neill J, Csicsvari JL. Activity dependent plasticity of hippocampal place maps. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11824\">10.1038/ncomms11824</a>","short":"P. Schönenberger, J. O’Neill, J.L. Csicsvari, Nature Communications 7 (2016)."},"ddc":["570"],"pubrep_id":"660","publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"oa":1,"volume":7,"file":[{"checksum":"e43307754abe65b840a21939fe163618","relation":"main_file","date_created":"2018-12-12T10:16:10Z","access_level":"open_access","content_type":"application/pdf","file_size":1793846,"file_name":"IST-2016-660-v1+1_ncomms11824.pdf","date_updated":"2020-07-14T12:44:44Z","creator":"system","file_id":"5196"}],"has_accepted_license":"1","title":"Activity dependent plasticity of hippocampal place maps","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","day":"10","month":"06","status":"public","isi":1,"_id":"1334","ec_funded":1,"abstract":[{"lang":"eng","text":"Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping."}],"oa_version":"Published Version","department":[{"_id":"JoCs"}],"project":[{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"name":"Interneuron plasticity during spatial learning","call_identifier":"FWF","_id":"257D4372-B435-11E9-9278-68D0E5697425","grant_number":"I2072-B27"}],"external_id":{"isi":["000378007300001"]},"quality_controlled":"1","date_updated":"2025-09-22T08:20:24Z","publist_id":"5934","intvolume":"         7","date_published":"2016-06-10T00:00:00Z","publication":"Nature Communications","scopus_import":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.1038/ncomms11824","doi":"10.1038/ncomms11824","date_created":"2018-12-11T11:51:26Z","publication_status":"published","year":"2016"},{"scopus_import":"1","article_processing_charge":"No","doi":"10.1007/978-3-662-53413-7_2","fulldoi":"https://doi.org/10.1007/978-3-662-53413-7_2","date_created":"2018-12-11T11:51:26Z","publication_status":"published","year":"2016","date_updated":"2025-09-22T08:19:49Z","quality_controlled":"1","intvolume":"      9837","publist_id":"5932","date_published":"2016-08-31T00:00:00Z","oa_version":"Preprint","abstract":[{"text":"In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties.","lang":"eng"}],"_id":"1335","ec_funded":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"alternative_title":["LNCS"],"external_id":{"isi":["000388924600002"],"arxiv":["1604.06764"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Quantitative monitor automata","corr_author":"1","isi":1,"status":"public","day":"31","month":"08","volume":9837,"publisher":"Springer","page":"23 - 38","oa":1,"language":[{"iso":"eng"}],"arxiv":1,"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop"}],"conference":{"location":"Edinburgh, United Kingdom","name":"SAS: Static Analysis Symposium","start_date":"2016-09-08","end_date":"2016-09-10"},"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Monitor Automata,” 9837:23–38. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53413-7_2\">https://doi.org/10.1007/978-3-662-53413-7_2</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Monitor Automata</i>. Vol. 9837, Springer, 2016, pp. 23–38, doi:<a href=\"https://doi.org/10.1007/978-3-662-53413-7_2\">10.1007/978-3-662-53413-7_2</a>.","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative monitor automata. SAS: Static Analysis Symposium, LNCS, vol. 9837, 23–38.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Quantitative monitor automata (Vol. 9837, pp. 23–38). Presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53413-7_2\">https://doi.org/10.1007/978-3-662-53413-7_2</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Springer, 2016, pp. 23–38.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative monitor automata. In: Vol 9837. Springer; 2016:23-38. doi:<a href=\"https://doi.org/10.1007/978-3-662-53413-7_2\">10.1007/978-3-662-53413-7_2</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative monitor automata,” presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom, 2016, vol. 9837, pp. 23–38."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"type":"conference"},{"status":"public","day":"08","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography","has_accepted_license":"1","extern":"1","OA_type":"gold","OA_place":"publisher","oa_version":"Published Version","abstract":[{"lang":"eng","text":"It has previously been shown that the use of racemic mixtures of naturally chiral macromolecules such as protein and DNA can significantly aid the crystallogenesis process, thereby addressing one of the major bottlenecks to structure determination by X-ray crystallographic methods—that of crystal growth. Although previous studies have provided convincing evidence of the applicability of the racemic crystallization technique to DNA through the study of well-characterized DNA structures, we sought to apply this method to a historically challenging DNA sequence. For this purpose we chose a non-self-complementary DNA duplex containing the biologically-relevant Pribnow box consensus sequence ‘TATAAT’. Four racemic crystal structures of this previously un-crystallizable DNA target are reported (with resolutions in the range of 1.65–2.3 Å), with further crystallographic studies and structural analysis providing insight into the racemic crystallization process as well as structural details of this highly pertinent DNA sequence."}],"_id":"21101","publication":"Nucleic Acids Research","date_published":"2016-07-08T00:00:00Z","intvolume":"        44","date_updated":"2026-02-23T09:16:14Z","quality_controlled":"1","year":"2016","article_type":"original","publication_status":"published","date_created":"2026-01-29T21:46:40Z","doi":"10.1093/nar/gkw367","fulldoi":"https://doi.org/10.1093/nar/gkw367","article_processing_charge":"No","type":"journal_article","issue":"12","main_file_link":[{"url":"https://doi.org/10.1093/nar/gkw367","open_access":"1"}],"DOAJ_listed":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"citation":{"short":"P.K. Mandal, G.W. Collie, S.C. Srivastava, B. Kauffmann, I. Huc, Nucleic Acids Research 44 (2016) 5936–5943.","ieee":"P. K. Mandal, G. W. Collie, S. C. Srivastava, B. Kauffmann, and I. Huc, “Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography,” <i>Nucleic Acids Research</i>, vol. 44, no. 12. Oxford University Press, pp. 5936–5943, 2016.","ama":"Mandal PK, Collie GW, Srivastava SC, Kauffmann B, Huc I. Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. <i>Nucleic Acids Research</i>. 2016;44(12):5936-5943. doi:<a href=\"https://doi.org/10.1093/nar/gkw367\">10.1093/nar/gkw367</a>","chicago":"Mandal, Pradeep K, Gavin W. Collie, Suresh C. Srivastava, Brice Kauffmann, and Ivan Huc. “Structure Elucidation of the Pribnow Box Consensus Promoter Sequence by Racemic DNA Crystallography.” <i>Nucleic Acids Research</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/nar/gkw367\">https://doi.org/10.1093/nar/gkw367</a>.","ista":"Mandal PK, Collie GW, Srivastava SC, Kauffmann B, Huc I. 2016. Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. Nucleic Acids Research. 44(12), 5936–5943.","mla":"Mandal, Pradeep K., et al. “Structure Elucidation of the Pribnow Box Consensus Promoter Sequence by Racemic DNA Crystallography.” <i>Nucleic Acids Research</i>, vol. 44, no. 12, Oxford University Press, 2016, pp. 5936–43, doi:<a href=\"https://doi.org/10.1093/nar/gkw367\">10.1093/nar/gkw367</a>.","apa":"Mandal, P. K., Collie, G. W., Srivastava, S. C., Kauffmann, B., &#38; Huc, I. (2016). Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkw367\">https://doi.org/10.1093/nar/gkw367</a>"},"author":[{"last_name":"Mandal","id":"6a3def15-d4b4-11ef-9fa9-a24c1f545ec3","orcid":"0000-0001-5996-956X","full_name":"Mandal, Pradeep K","first_name":"Pradeep K"},{"first_name":"Gavin W.","full_name":"Collie, Gavin W.","last_name":"Collie"},{"full_name":"Srivastava, Suresh C.","first_name":"Suresh C.","last_name":"Srivastava"},{"full_name":"Kauffmann, Brice","first_name":"Brice","last_name":"Kauffmann"},{"last_name":"Huc","full_name":"Huc, Ivan","first_name":"Ivan"}],"oa":1,"language":[{"iso":"eng"}],"page":"5936-5943","publisher":"Oxford University Press","ddc":["570"],"publication_identifier":{"issn":["0305-1048"],"eissn":["1362-4962"]},"volume":44},{"volume":8,"publication_identifier":{"eissn":["2040-3372"],"issn":["2040-3364"]},"publisher":"Royal Society of Chemistry","page":"19280-19286","oa":1,"language":[{"iso":"eng"}],"author":[{"last_name":"Kundu","first_name":"Pintu K.","full_name":"Kundu, Pintu K."},{"last_name":"Das","full_name":"Das, Sanjib","first_name":"Sanjib"},{"first_name":"Johannes","full_name":"Ahrens, Johannes","last_name":"Ahrens"},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"citation":{"short":"P.K. Kundu, S. Das, J. Ahrens, R. Klajn, Nanoscale 8 (2016) 19280–19286.","ama":"Kundu PK, Das S, Ahrens J, Klajn R. Controlling the lifetimes of dynamic nanoparticle aggregates by spiropyran functionalization. <i>Nanoscale</i>. 2016;8(46):19280-19286. doi:<a href=\"https://doi.org/10.1039/c6nr05959g\">10.1039/c6nr05959g</a>","ieee":"P. K. Kundu, S. Das, J. Ahrens, and R. Klajn, “Controlling the lifetimes of dynamic nanoparticle aggregates by spiropyran functionalization,” <i>Nanoscale</i>, vol. 8, no. 46. Royal Society of Chemistry, pp. 19280–19286, 2016.","chicago":"Kundu, Pintu K., Sanjib Das, Johannes Ahrens, and Rafal Klajn. “Controlling the Lifetimes of Dynamic Nanoparticle Aggregates by Spiropyran Functionalization.” <i>Nanoscale</i>. Royal Society of Chemistry, 2016. <a href=\"https://doi.org/10.1039/c6nr05959g\">https://doi.org/10.1039/c6nr05959g</a>.","apa":"Kundu, P. K., Das, S., Ahrens, J., &#38; Klajn, R. (2016). Controlling the lifetimes of dynamic nanoparticle aggregates by spiropyran functionalization. <i>Nanoscale</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c6nr05959g\">https://doi.org/10.1039/c6nr05959g</a>","ista":"Kundu PK, Das S, Ahrens J, Klajn R. 2016. Controlling the lifetimes of dynamic nanoparticle aggregates by spiropyran functionalization. Nanoscale. 8(46), 19280–19286.","mla":"Kundu, Pintu K., et al. “Controlling the Lifetimes of Dynamic Nanoparticle Aggregates by Spiropyran Functionalization.” <i>Nanoscale</i>, vol. 8, no. 46, Royal Society of Chemistry, 2016, pp. 19280–86, doi:<a href=\"https://doi.org/10.1039/c6nr05959g\">10.1039/c6nr05959g</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1039/C6NR05959G"}],"type":"journal_article","issue":"46","scopus_import":"1","article_processing_charge":"No","fulldoi":"https://doi.org/10.1039/c6nr05959g","doi":"10.1039/c6nr05959g","date_created":"2023-08-01T09:42:22Z","article_type":"original","publication_status":"published","year":"2016","date_updated":"2024-10-14T12:16:21Z","quality_controlled":"1","intvolume":"         8","date_published":"2016-10-19T00:00:00Z","publication":"Nanoscale","pmid":1,"abstract":[{"lang":"eng","text":"Novel light-responsive nanoparticles were synthesized by decorating the surfaces of gold and silver nanoparticles with a nitrospiropyran molecular photoswitch. Upon exposure to UV light in nonpolar solvents, these nanoparticles self-assembled to afford spherical aggregates, which disassembled rapidly when the UV stimulus was turned off. The sizes of these aggregates depended on the nanoparticle concentration, and their lifetimes could be controlled by adjusting the surface concentration of nitrospiropyran on the nanoparticles. The conformational flexibility of nitrospiropyran, which was altered by modifying the structure of the background ligand, had a profound impact on the self-assembly process. By coating the nanoparticles with a spiropyran lacking the nitro group, a conceptually different self-assembly system, relying on a reversible proton transfer, was realized. The resulting particles spontaneously (in the dark) assembled into aggregates that could be readily disassembled upon exposure to blue light."}],"_id":"13385","oa_version":"Published Version","external_id":{"pmid":["27830865"]},"extern":"1","title":"Controlling the lifetimes of dynamic nanoparticle aggregates by spiropyran functionalization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Materials Science"],"day":"19","month":"10","status":"public"},{"volume":17,"publication_identifier":{"eissn":["1439-7641"],"issn":["1439-4235"]},"publisher":"Wiley","page":"1711-1711","language":[{"iso":"eng"}],"oa":1,"author":[{"first_name":"T.","full_name":"Udayabhaskararao, T.","last_name":"Udayabhaskararao"},{"last_name":"Kundu","full_name":"Kundu, Pintu K.","first_name":"Pintu K."},{"first_name":"Johannes","full_name":"Ahrens, Johannes","last_name":"Ahrens"},{"full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn"}],"citation":{"apa":"Udayabhaskararao, T., Kundu, P. K., Ahrens, J., &#38; Klajn, R. (2016). <i>Inside cover: Reversible photoisomerization of spiropyran on the surfaces of Au25 nanoclusters (ChemPhysChem 12/2016)</i>. <i>ChemPhysChem</i> (Vol. 17, pp. 1711–1711). Wiley. <a href=\"https://doi.org/10.1002/cphc.201600480\">https://doi.org/10.1002/cphc.201600480</a>","mla":"Udayabhaskararao, T., et al. “Inside Cover: Reversible Photoisomerization of Spiropyran on the Surfaces of Au25 Nanoclusters (ChemPhysChem 12/2016).” <i>ChemPhysChem</i>, vol. 17, no. 12, Wiley, 2016, pp. 1711–1711, doi:<a href=\"https://doi.org/10.1002/cphc.201600480\">10.1002/cphc.201600480</a>.","ista":"Udayabhaskararao T, Kundu PK, Ahrens J, Klajn R. 2016. Inside cover: Reversible photoisomerization of spiropyran on the surfaces of Au25 nanoclusters (ChemPhysChem 12/2016), Wiley,p.","chicago":"Udayabhaskararao, T., Pintu K. Kundu, Johannes Ahrens, and Rafal Klajn. <i>Inside Cover: Reversible Photoisomerization of Spiropyran on the Surfaces of Au25 Nanoclusters (ChemPhysChem 12/2016)</i>. <i>ChemPhysChem</i>. Vol. 17. Wiley, 2016. <a href=\"https://doi.org/10.1002/cphc.201600480\">https://doi.org/10.1002/cphc.201600480</a>.","ama":"Udayabhaskararao T, Kundu PK, Ahrens J, Klajn R. <i>Inside Cover: Reversible Photoisomerization of Spiropyran on the Surfaces of Au25 Nanoclusters (ChemPhysChem 12/2016)</i>. Vol 17. Wiley; 2016:1711-1711. doi:<a href=\"https://doi.org/10.1002/cphc.201600480\">10.1002/cphc.201600480</a>","ieee":"T. Udayabhaskararao, P. K. Kundu, J. Ahrens, and R. Klajn, <i>Inside cover: Reversible photoisomerization of spiropyran on the surfaces of Au25 nanoclusters (ChemPhysChem 12/2016)</i>, vol. 17, no. 12. Wiley, 2016, pp. 1711–1711.","short":"T. Udayabhaskararao, P.K. Kundu, J. Ahrens, R. Klajn, Inside Cover: Reversible Photoisomerization of Spiropyran on the Surfaces of Au25 Nanoclusters (ChemPhysChem 12/2016), Wiley, 2016."},"main_file_link":[{"url":"https://doi.org/10.1002/cphc.201600480","open_access":"1"}],"issue":"12","type":"other_academic_publication","article_processing_charge":"No","doi":"10.1002/cphc.201600480","fulldoi":"https://doi.org/10.1002/cphc.201600480","publication_status":"published","date_created":"2023-08-01T09:43:07Z","year":"2016","date_updated":"2024-10-14T12:16:44Z","quality_controlled":"1","intvolume":"        17","date_published":"2016-06-17T00:00:00Z","publication":"ChemPhysChem","oa_version":"Published Version","abstract":[{"text":"The Inside Cover picture illustrates the fluorescent properties of a gold nanocluster functionalized with several copies of a red-emitting merocyanine (image by Ella Marushchenko). The red fluorescence can be turned on and off reversibly by using an external stimulus.","lang":"eng"}],"_id":"13388","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Inside cover: Reversible photoisomerization of spiropyran on the surfaces of Au25 nanoclusters (ChemPhysChem 12/2016)","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"status":"public","day":"17","month":"06"},{"date_created":"2018-12-11T11:51:28Z","publication_status":"published","year":"2016","article_processing_charge":"No","scopus_import":"1","doi":"10.1007/978-3-662-53354-3_6","fulldoi":"https://doi.org/10.1007/978-3-662-53354-3_6","date_published":"2016-09-01T00:00:00Z","quality_controlled":"1","date_updated":"2025-09-22T08:18:27Z","intvolume":"      9928","publist_id":"5927","alternative_title":["LNCS"],"external_id":{"isi":["000389020400006"],"arxiv":["1604.07634"]},"oa_version":"Preprint","ec_funded":1,"_id":"1340","abstract":[{"lang":"eng","text":"We study repeated games with absorbing states, a type of two-player, zero-sum concurrent mean-payoff games with the prototypical example being the Big Match of Gillete (1957). These games may not allow optimal strategies but they always have ε-optimal strategies. In this paper we design ε-optimal strategies for Player 1 in these games that use only O(log log T) space. Furthermore, we construct strategies for Player 1 that use space s(T), for an arbitrary small unbounded non-decreasing function s, and which guarantee an ε-optimal value for Player 1 in the limit superior sense. The previously known strategies use space Ω(log T) and it was known that no strategy can use constant space if it is ε-optimal even in the limit superior sense. We also give a complementary lower bound. Furthermore, we also show that no Markov strategy, even extended with finite memory, can ensure value greater than 0 in the Big Match, answering a question posed by Neyman [11]."}],"department":[{"_id":"KrCh"}],"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"status":"public","isi":1,"day":"01","month":"09","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"The big match in small space","volume":9928,"page":"64 - 76","language":[{"iso":"eng"}],"oa":1,"arxiv":1,"publisher":"Springer","author":[{"first_name":"Kristoffer","full_name":"Hansen, Kristoffer","last_name":"Hansen"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Koucký, Michal","first_name":"Michal","last_name":"Koucký"}],"citation":{"ieee":"K. Hansen, R. Ibsen-Jensen, and M. Koucký, “The big match in small space,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 64–76.","ama":"Hansen K, Ibsen-Jensen R, Koucký M. The big match in small space. In: Vol 9928. Springer; 2016:64-76. doi:<a href=\"https://doi.org/10.1007/978-3-662-53354-3_6\">10.1007/978-3-662-53354-3_6</a>","short":"K. Hansen, R. Ibsen-Jensen, M. Koucký, in:, Springer, 2016, pp. 64–76.","apa":"Hansen, K., Ibsen-Jensen, R., &#38; Koucký, M. (2016). The big match in small space (Vol. 9928, pp. 64–76). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53354-3_6\">https://doi.org/10.1007/978-3-662-53354-3_6</a>","ista":"Hansen K, Ibsen-Jensen R, Koucký M. 2016. The big match in small space. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 64–76.","mla":"Hansen, Kristoffer, et al. <i>The Big Match in Small Space</i>. Vol. 9928, Springer, 2016, pp. 64–76, doi:<a href=\"https://doi.org/10.1007/978-3-662-53354-3_6\">10.1007/978-3-662-53354-3_6</a>.","chicago":"Hansen, Kristoffer, Rasmus Ibsen-Jensen, and Michal Koucký. “The Big Match in Small Space,” 9928:64–76. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53354-3_6\">https://doi.org/10.1007/978-3-662-53354-3_6</a>."},"conference":{"location":"Liverpool, United Kingdom","name":"SAGT: Symposium on Algorithmic Game Theory","start_date":"2016-09-19","end_date":"2016-09-21"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.07634"}],"type":"conference"},{"type":"conference","author":[{"last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","first_name":"Guy"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"file_date_updated":"2020-07-14T12:44:45Z","conference":{"end_date":"2016-09-21","location":"Liverpool, United Kingdom","start_date":"2016-09-19","name":"SAGT: Symposium on Algorithmic Game Theory"},"citation":{"short":"G. Avni, T.A. Henzinger, O. Kupferman, in:, Springer, 2016, pp. 153–166.","ieee":"G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 153–166.","ama":"Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. In: Vol 9928. Springer; 2016:153-166. doi:<a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">10.1007/978-3-662-53354-3_13</a>","chicago":"Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation Games,” 9928:153–66. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">https://doi.org/10.1007/978-3-662-53354-3_13</a>.","apa":"Avni, G., Henzinger, T. A., &#38; Kupferman, O. (2016). Dynamic resource allocation games (Vol. 9928, pp. 153–166). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">https://doi.org/10.1007/978-3-662-53354-3_13</a>","mla":"Avni, Guy, et al. <i>Dynamic Resource Allocation Games</i>. Vol. 9928, Springer, 2016, pp. 153–66, doi:<a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">10.1007/978-3-662-53354-3_13</a>.","ista":"Avni G, Henzinger TA, Kupferman O. 2016. Dynamic resource allocation games. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 153–166."},"ddc":["000"],"pubrep_id":"645","publisher":"Springer","page":"153 - 166","language":[{"iso":"eng"}],"oa":1,"volume":9928,"file":[{"creator":"system","file_id":"5073","date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-645-v1+1_sagt-cr.pdf","file_size":243458,"date_created":"2018-12-12T10:14:22Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0825eefd4e22774f6f62cb7d7389b05a"}],"acknowledgement":"This research was supported in part by the European Research Council (ERC) under grants 267989 (QUAREM) and 278410 (QUALITY), and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).","has_accepted_license":"1","title":"Dynamic resource allocation games","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","day":"01","related_material":{"record":[{"status":"public","id":"6761","relation":"later_version"}]},"month":"09","status":"public","isi":1,"_id":"1341","abstract":[{"lang":"eng","text":"In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability."}],"ec_funded":1,"oa_version":"Preprint","department":[{"_id":"ToHe"}],"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"alternative_title":["LNCS"],"external_id":{"isi":["000389020400013"]},"quality_controlled":"1","date_updated":"2026-04-16T09:35:14Z","publist_id":"5926","intvolume":"      9928","date_published":"2016-09-01T00:00:00Z","article_processing_charge":"No","scopus_import":"1","fulldoi":"https://doi.org/10.1007/978-3-662-53354-3_13","doi":"10.1007/978-3-662-53354-3_13","date_created":"2018-12-11T11:51:28Z","publication_status":"published","year":"2016"},{"day":"09","month":"09","status":"public","isi":1,"title":"Spatiotemporal microbial evolution on antibiotic landscapes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000382626800052"]},"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"1342","abstract":[{"lang":"eng","text":"A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics."}],"oa_version":"Preprint","publication":"Science","date_published":"2016-09-09T00:00:00Z","publist_id":"5911","intvolume":"       353","date_updated":"2025-09-22T08:17:11Z","quality_controlled":"1","year":"2016","date_created":"2018-12-11T11:51:29Z","publication_status":"published","fulldoi":"https://doi.org/10.1126/science.aag0822","doi":"10.1126/science.aag0822","article_processing_charge":"No","scopus_import":"1","type":"journal_article","issue":"6304","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/","open_access":"1"}],"citation":{"chicago":"Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” <i>Science</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aag0822\">https://doi.org/10.1126/science.aag0822</a>.","ista":"Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151.","mla":"Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” <i>Science</i>, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1147–51, doi:<a href=\"https://doi.org/10.1126/science.aag0822\">10.1126/science.aag0822</a>.","apa":"Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., &#38; Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aag0822\">https://doi.org/10.1126/science.aag0822</a>","short":"M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151.","ama":"Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on antibiotic landscapes. <i>Science</i>. 2016;353(6304):1147-1151. doi:<a href=\"https://doi.org/10.1126/science.aag0822\">10.1126/science.aag0822</a>","ieee":"M. Baym <i>et al.</i>, “Spatiotemporal microbial evolution on antibiotic landscapes,” <i>Science</i>, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016."},"author":[{"last_name":"Baym","full_name":"Baym, Michael","first_name":"Michael"},{"first_name":"Tami","full_name":"Lieberman, Tami","last_name":"Lieberman"},{"full_name":"Kelsic, Eric","first_name":"Eric","last_name":"Kelsic"},{"first_name":"Remy P","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait"},{"last_name":"Gross","first_name":"Rotem","full_name":"Gross, Rotem"},{"last_name":"Yelin","full_name":"Yelin, Idan","first_name":"Idan"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}],"language":[{"iso":"eng"}],"oa":1,"page":"1147 - 1151","publisher":"American Association for the Advancement of Science","volume":353},{"volume":18,"file":[{"date_created":"2018-12-12T10:17:52Z","content_type":"application/pdf","access_level":"open_access","checksum":"2a43e235222755e31ffbd369882c61de","relation":"main_file","file_id":"5309","creator":"system","file_size":1076029,"file_name":"IST-2016-655-v1+1_njp_18_9_093042.pdf","date_updated":"2020-07-14T12:44:45Z"}],"acknowledgement":"We acknowledge stimulating discussions with Ken Brown, Tommaso Calarco, Andrew Daley, Suzanne\r\nMcEndoo, Tobias Osborne, Cindy Regal, Luis Santos, Micha\r\nł\r\nTomza, and Martin Zwierlein. The work was supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734], by the Volkswagen Foundation, and by DFG within SFB 1227 (DQ-mat).","ddc":["530"],"pubrep_id":"655","publisher":"IOP Publishing","language":[{"iso":"eng"}],"oa":1,"file_date_updated":"2020-07-14T12:44:45Z","author":[{"last_name":"Kaczmarczyk","full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Weimer, Hendrik","first_name":"Hendrik","last_name":"Weimer"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"chicago":"Kaczmarczyk, Jan, Hendrik Weimer, and Mikhail Lemeshko. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” <i>New Journal of Physics</i>. IOP Publishing, 2016. <a href=\"https://doi.org/10.1088/1367-2630/18/9/093042\">https://doi.org/10.1088/1367-2630/18/9/093042</a>.","mla":"Kaczmarczyk, Jan, et al. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” <i>New Journal of Physics</i>, vol. 18, no. 9, 093042, IOP Publishing, 2016, doi:<a href=\"https://doi.org/10.1088/1367-2630/18/9/093042\">10.1088/1367-2630/18/9/093042</a>.","ista":"Kaczmarczyk J, Weimer H, Lemeshko M. 2016. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 18(9), 093042.","apa":"Kaczmarczyk, J., Weimer, H., &#38; Lemeshko, M. (2016). Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/18/9/093042\">https://doi.org/10.1088/1367-2630/18/9/093042</a>","short":"J. Kaczmarczyk, H. Weimer, M. Lemeshko, New Journal of Physics 18 (2016).","ieee":"J. Kaczmarczyk, H. Weimer, and M. Lemeshko, “Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model,” <i>New Journal of Physics</i>, vol. 18, no. 9. IOP Publishing, 2016.","ama":"Kaczmarczyk J, Weimer H, Lemeshko M. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. <i>New Journal of Physics</i>. 2016;18(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/18/9/093042\">10.1088/1367-2630/18/9/093042</a>"},"article_number":"093042","type":"journal_article","issue":"9","article_processing_charge":"No","scopus_import":"1","doi":"10.1088/1367-2630/18/9/093042","fulldoi":"https://doi.org/10.1088/1367-2630/18/9/093042","date_created":"2018-12-11T11:51:29Z","publication_status":"published","year":"2016","date_updated":"2025-09-22T08:16:37Z","quality_controlled":"1","intvolume":"        18","publist_id":"5909","date_published":"2016-09-22T00:00:00Z","publication":"New Journal of Physics","oa_version":"Published Version","ec_funded":1,"_id":"1343","abstract":[{"text":"The Fermi-Hubbard model is one of the key models of condensed matter physics, which holds a\r\n\r\npotential for explaining the mystery of high-temperature superconductivity. Recent progress in\r\n\r\nultracold atoms in optical lattices has paved the way to studying the model’s phase diagram using\r\n\r\nthe tools of quantum simulation, which emerged as a promising alternative to the numerical\r\n\r\ncalculations plagued by the infamous sign problem. However, the temperatures achieved using\r\n\r\nelaborate laser cooling protocols so far have been too high to show the appearance of\r\n\r\nantiferromagnetic (AF) and superconducting quantum phases directly. In this work, we demonstrate\r\n\r\nthat using the machinery of dissipative quantum state engineering, one can observe the emergence of\r\n\r\nthe AF order in the Fermi-Hubbard model with fermions in optical lattices. The core of the approach\r\n\r\nis to add incoherent laser scattering in such a way that the AF state emerges as the dark state of\r\n\r\nthe driven-dissipative dynamics. The proposed controlled dissipation channels described in this work\r\n\r\nare straightforward to add to already existing experimental setups.","lang":"eng"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"MiLe"}],"external_id":{"isi":["000385516800002"]},"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model","corr_author":"1","isi":1,"status":"public","day":"22","month":"09"},{"author":[{"id":"43905548-F248-11E8-B48F-1D18A9856A87","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych"},{"full_name":"Leung, Jeffrey","first_name":"Jeffrey","last_name":"Leung"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"file_date_updated":"2020-07-14T12:44:45Z","citation":{"short":"M. Fendrych, J. Leung, J. Friml, ELife 5 (2016).","ieee":"M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls,” <i>eLife</i>, vol. 5. eLife Sciences Publications, 2016.","ama":"Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. <i>eLife</i>. 2016;5. doi:<a href=\"https://doi.org/10.7554/eLife.19048\">10.7554/eLife.19048</a>","chicago":"Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” <i>ELife</i>. eLife Sciences Publications, 2016. <a href=\"https://doi.org/10.7554/eLife.19048\">https://doi.org/10.7554/eLife.19048</a>.","ista":"Fendrych M, Leung J, Friml J. 2016. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 5, e19048.","mla":"Fendrych, Matyas, et al. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” <i>ELife</i>, vol. 5, e19048, eLife Sciences Publications, 2016, doi:<a href=\"https://doi.org/10.7554/eLife.19048\">10.7554/eLife.19048</a>.","apa":"Fendrych, M., Leung, J., &#38; Friml, J. (2016). TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.19048\">https://doi.org/10.7554/eLife.19048</a>"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_number":"e19048","type":"journal_article","file":[{"checksum":"9209541fbba00f24daad21a5d568540d","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:09:24Z","file_size":5666343,"file_name":"IST-2016-693-v1+1_e19048-download.pdf","date_updated":"2020-07-14T12:44:45Z","creator":"system","file_id":"4748"}],"acknowledgement":"The authors express their gratitude to Veronika Bierbaum, Robert Hauschild for help with MATLAB,\r\nDaniel von Wangenheim for the gravitropism assay. We are thankful to Bill Gray, Mark Estelle,\r\nMichael Prigge, Ottoline Leyser, Claudia Oecking for sharing the seeds with us. We thank Katelyn\r\nSageman-Furnas and the members of the Friml lab for critical reading of the manuscript. The\r\nresearch leading to these results has received funding from the People Programme (Marie Curie\r\nActions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant\r\nagreement n° 291734. This work was also supported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP).","volume":5,"language":[{"iso":"eng"}],"oa":1,"ddc":["581"],"pubrep_id":"654","publisher":"eLife Sciences Publications","external_id":{"isi":["000385559100001"]},"abstract":[{"lang":"eng","text":"Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms."}],"_id":"1344","ec_funded":1,"oa_version":"Published Version","department":[{"_id":"JiFr"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"corr_author":"1","day":"14","month":"09","isi":1,"status":"public","has_accepted_license":"1","title":"TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","date_created":"2018-12-11T11:51:29Z","year":"2016","article_processing_charge":"No","scopus_import":"1","fulldoi":"https://doi.org/10.7554/eLife.19048","doi":"10.7554/eLife.19048","date_published":"2016-09-14T00:00:00Z","publication":"eLife","quality_controlled":"1","date_updated":"2025-09-22T08:16:03Z","publist_id":"5908","intvolume":"         5"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Plasma membrane: Negative attraction","has_accepted_license":"1","isi":1,"status":"public","month":"07","day":"01","corr_author":"1","department":[{"_id":"JiFr"}],"oa_version":"Published Version","_id":"1345","abstract":[{"text":"The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components.","lang":"eng"}],"external_id":{"isi":["000380346500013"]},"intvolume":"         2","publist_id":"5907","date_updated":"2025-09-22T08:15:28Z","quality_controlled":"1","publication":"Nature Plants","date_published":"2016-07-01T00:00:00Z","doi":"10.1038/nplants.2016.102","fulldoi":"https://doi.org/10.1038/nplants.2016.102","article_processing_charge":"No","scopus_import":"1","year":"2016","publication_status":"published","date_created":"2018-12-11T11:51:30Z","type":"journal_article","article_number":"16102","citation":{"short":"G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016).","ieee":"G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,” <i>Nature Plants</i>, vol. 2. Nature Publishing Group, 2016.","ama":"Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. <i>Nature Plants</i>. 2016;2. doi:<a href=\"https://doi.org/10.1038/nplants.2016.102\">10.1038/nplants.2016.102</a>","chicago":"Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative Attraction.” <i>Nature Plants</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nplants.2016.102\">https://doi.org/10.1038/nplants.2016.102</a>.","ista":"Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction. Nature Plants. 2, 16102.","mla":"Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” <i>Nature Plants</i>, vol. 2, 16102, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/nplants.2016.102\">10.1038/nplants.2016.102</a>.","apa":"Molnar, G., Fendrych, M., &#38; Friml, J. (2016). Plasma membrane: Negative attraction. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nplants.2016.102\">https://doi.org/10.1038/nplants.2016.102</a>"},"file_date_updated":"2020-07-14T12:44:45Z","author":[{"last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Molnar, Gergely","first_name":"Gergely"},{"last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"publisher":"Nature Publishing Group","pubrep_id":"1007","ddc":["581"],"language":[{"iso":"eng"}],"oa":1,"volume":2,"file":[{"file_name":"IST-2018-1007-v1+1_Molnar_NatPlants_2016.pdf","date_updated":"2020-07-14T12:44:45Z","file_size":127781,"creator":"system","file_id":"4954","relation":"main_file","checksum":"9ba65f558563b287f875f48fa9f30fb2","content_type":"application/pdf","date_created":"2018-12-12T10:12:36Z","access_level":"open_access"},{"relation":"main_file","checksum":"550d252be808d8ca2b43e83dddb4212f","date_created":"2018-12-12T10:12:37Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf","file_size":430556,"file_id":"4955","creator":"system"}]},{"external_id":{"isi":["000377899800001"]},"abstract":[{"text":"ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane.","lang":"eng"}],"_id":"1346","ec_funded":1,"oa_version":"Published Version","department":[{"_id":"JiFr"}],"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"day":"08","month":"06","related_material":{"record":[{"status":"public","id":"7172","relation":"dissertation_contains"}]},"status":"public","isi":1,"has_accepted_license":"1","title":"Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:51:30Z","publication_status":"published","year":"2016","article_processing_charge":"No","scopus_import":"1","fulldoi":"https://doi.org/10.1038/ncomms11710","doi":"10.1038/ncomms11710","date_published":"2016-06-08T00:00:00Z","publication":"Nature Communications","quality_controlled":"1","date_updated":"2026-04-08T13:54:44Z","publist_id":"5906","intvolume":"         7","author":[{"first_name":"Wim","full_name":"Dejonghe, Wim","last_name":"Dejonghe"},{"last_name":"Kuenen","full_name":"Kuenen, Sabine","first_name":"Sabine"},{"last_name":"Mylle","full_name":"Mylle, Evelien","first_name":"Evelien"},{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","full_name":"Vasileva, Mina K","first_name":"Mina K","last_name":"Vasileva"},{"last_name":"Keech","full_name":"Keech, Olivier","first_name":"Olivier"},{"last_name":"Viotti","full_name":"Viotti, Corrado","first_name":"Corrado"},{"last_name":"Swerts","first_name":"Jef","full_name":"Swerts, Jef"},{"last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fausto","full_name":"Ortiz Morea, Fausto","last_name":"Ortiz Morea"},{"full_name":"Mishev, Kiril","first_name":"Kiril","last_name":"Mishev"},{"full_name":"Delang, Simon","first_name":"Simon","last_name":"Delang"},{"last_name":"Scholl","full_name":"Scholl, Stefan","first_name":"Stefan"},{"first_name":"Xavier","full_name":"Zarza, Xavier","last_name":"Zarza"},{"last_name":"Heilmann","full_name":"Heilmann, Mareike","first_name":"Mareike"},{"last_name":"Kourelis","full_name":"Kourelis, Jiorgos","first_name":"Jiorgos"},{"last_name":"Kasprowicz","full_name":"Kasprowicz, Jaroslaw","first_name":"Jaroslaw"},{"last_name":"Nguyen","first_name":"Le","full_name":"Nguyen, Le"},{"last_name":"Drozdzecki","first_name":"Andrzej","full_name":"Drozdzecki, Andrzej"},{"last_name":"Van Houtte","first_name":"Isabelle","full_name":"Van Houtte, Isabelle"},{"full_name":"Szatmári, Anna","first_name":"Anna","last_name":"Szatmári"},{"last_name":"Majda","first_name":"Mateusz","full_name":"Majda, Mateusz"},{"last_name":"Baisa","full_name":"Baisa, Gary","first_name":"Gary"},{"full_name":"Bednarek, Sebastian","first_name":"Sebastian","last_name":"Bednarek"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"last_name":"Audenaert","first_name":"Dominique","full_name":"Audenaert, Dominique"},{"last_name":"Testerink","full_name":"Testerink, Christa","first_name":"Christa"},{"last_name":"Munnik","first_name":"Teun","full_name":"Munnik, Teun"},{"first_name":"Daniël","full_name":"Van Damme, Daniël","last_name":"Van Damme"},{"last_name":"Heilmann","full_name":"Heilmann, Ingo","first_name":"Ingo"},{"first_name":"Karin","full_name":"Schumacher, Karin","last_name":"Schumacher"},{"last_name":"Winne","full_name":"Winne, Johan","first_name":"Johan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"full_name":"Verstreken, Patrik","first_name":"Patrik","last_name":"Verstreken"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"}],"file_date_updated":"2020-07-14T12:44:45Z","citation":{"ama":"Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11710\">10.1038/ncomms11710</a>","ieee":"W. Dejonghe <i>et al.</i>, “Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","short":"W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J. Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza, M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte, A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink, T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken, E. Russinova, Nature Communications 7 (2016).","apa":"Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C., … Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11710\">https://doi.org/10.1038/ncomms11710</a>","ista":"Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 7, 11710.","mla":"Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” <i>Nature Communications</i>, vol. 7, 11710, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11710\">10.1038/ncomms11710</a>.","chicago":"Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech, Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11710\">https://doi.org/10.1038/ncomms11710</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_number":"11710","type":"journal_article","file":[{"creator":"system","file_id":"5369","file_size":3532505,"date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-653-v1+1_ncomms11710_1_.pdf","access_level":"open_access","date_created":"2018-12-12T10:18:47Z","content_type":"application/pdf","checksum":"e8dc81b3e44db5a7718d7f1501ce1aa7","relation":"main_file"}],"acknowledgement":"We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys for literature searches, VIB Bio Imaging Core for help with imaging conditions and Martine De Cock for help in preparing the article. This work was supported by the Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.); the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.); a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.), the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R.","volume":7,"oa":1,"language":[{"iso":"eng"}],"ddc":["570"],"publisher":"Nature Publishing Group","pubrep_id":"653"}]