[{"publication_status":"published","year":"2016","day":"01","publication":"Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling","language":[{"iso":"eng"}],"page":"88 - 96","date_published":"2016-01-01T00:00:00Z","volume":"2016-January","date_created":"2018-12-11T11:51:22Z","ec_funded":1,"abstract":[{"lang":"eng","text":"DEC-POMDPs extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. DEC-POMDPs have been studied with finite-horizon and infinite-horizon discounted-sum objectives, and there exist solvers both for exact and approximate solutions. In this work we consider Goal-DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the RTDP-Bel approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. Copyright "}],"oa_version":"None","scopus_import":1,"quality_controlled":"1","publisher":"AAAI Press","main_file_link":[{"url":"http://www.aaai.org/ocs/index.php/ICAPS/ICAPS16/paper/view/12999"}],"month":"01","citation":{"chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability in Goal-DEC-POMDPs.” In Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, 2016–January:88–96. AAAI Press, 2016.","ista":"Chatterjee K, Chmelik M. 2016. Indefinite-horizon reachability in Goal-DEC-POMDPs. Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 2016–January, 88–96.","mla":"Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability in Goal-DEC-POMDPs.” Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, vol. 2016–January, AAAI Press, 2016, pp. 88–96.","apa":"Chatterjee, K., & Chmelik, M. (2016). Indefinite-horizon reachability in Goal-DEC-POMDPs. In Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling (Vol. 2016–January, pp. 88–96). London, United Kingdom: AAAI Press.","ama":"Chatterjee K, Chmelik M. Indefinite-horizon reachability in Goal-DEC-POMDPs. In: Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling. Vol 2016-January. AAAI Press; 2016:88-96.","short":"K. Chatterjee, M. Chmelik, in:, Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, AAAI Press, 2016, pp. 88–96.","ieee":"K. Chatterjee and M. Chmelik, “Indefinite-horizon reachability in Goal-DEC-POMDPs,” in Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, London, United Kingdom, 2016, vol. 2016–January, pp. 88–96."},"date_updated":"2021-01-12T06:49:53Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"publist_id":"5946","department":[{"_id":"KrCh"}],"title":"Indefinite-horizon reachability in Goal-DEC-POMDPs","_id":"1324","type":"conference","conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","start_date":"2016-06-12","end_date":"2016-06-17","location":"London, United Kingdom"},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"status":"public"},{"page":"3120 - 3139","date_created":"2018-12-11T11:51:24Z","date_published":"2016-10-01T00:00:00Z","doi":"10.1093/gbe/evw221","year":"2016","has_accepted_license":"1","publication":"Genome Biology and Evolution","day":"01","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","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.","author":[{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"first_name":"Alberto","full_name":"López Ezquerra, Alberto","last_name":"López Ezquerra"},{"last_name":"Parsch","full_name":"Parsch, John","first_name":"John"},{"full_name":"Cordellier, Mathilde","last_name":"Cordellier","first_name":"Mathilde"}],"publist_id":"5940","title":"De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata","citation":{"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,” Genome Biology and Evolution, 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. Genome Biology and Evolution. 2016;8(10):3120-3139. doi:10.1093/gbe/evw221","apa":"Huylmans, A. K., 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. Oxford University Press. https://doi.org/10.1093/gbe/evw221","mla":"Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39, doi:10.1093/gbe/evw221.","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.","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.” Genome Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/gbe/evw221."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":8,"issue":"10","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:06Z","file_name":"IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf","date_updated":"2020-07-14T12:44:44Z","file_size":1406265,"creator":"system","file_id":"4924","checksum":"25c7adcb452d39d3b6343ff4b57a652d","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"scopus_import":1,"intvolume":" 8","month":"10","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","file_date_updated":"2020-07-14T12:44:44Z","department":[{"_id":"BeVi"}],"date_updated":"2021-01-12T06:49:55Z","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","pubrep_id":"663","status":"public","_id":"1329"},{"publication_status":"published","year":"2016","day":"01","publication":"Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems","language":[{"iso":"eng"}],"page":"1465 - 1466","date_published":"2016-01-01T00:00:00Z","date_created":"2018-12-11T11:51:23Z","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. "}],"oa_version":"Preprint","quality_controlled":"1","publisher":"ACM","scopus_import":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1602.07565","open_access":"1"}],"month":"01","date_updated":"2021-01-12T06:49:54Z","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Anchit Gupta, and Petr Novotný. “Stochastic Shortest Path with Energy Constraints in POMDPs.” In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, 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 & Multiagent Systems, 1465–1466.","mla":"Brázdil, Tomáš, et al. “Stochastic Shortest Path with Energy Constraints in POMDPs.” Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–66.","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 Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, 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: Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. ACM; 2016:1465-1466.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Gupta, A., & Novotný, P. (2016). Stochastic shortest path with energy constraints in POMDPs. In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems (pp. 1465–1466). Singapore: ACM."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5942","author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Chmelik","full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anchit","full_name":"Gupta, Anchit","last_name":"Gupta"},{"last_name":"Novotny","full_name":"Novotny, Petr","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"}],"title":"Stochastic shortest path with energy constraints in POMDPs","department":[{"_id":"KrCh"}],"_id":"1327","type":"conference","conference":{"start_date":"2016-05-09","end_date":"2016-05-13","location":"Singapore","name":"AAMAS: Autonomous Agents & Multiagent Systems"},"status":"public","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}]},{"language":[{"iso":"eng"}],"publication_status":"published","volume":9938,"ec_funded":1,"oa_version":"Preprint","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"}],"month":"09","intvolume":" 9938","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"https://arxiv.org/abs/1607.00678","open_access":"1"}],"date_updated":"2021-01-12T06:49:53Z","department":[{"_id":"KrCh"}],"_id":"1326","status":"public","type":"conference","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2016-10-17","location":"Chiba, Japan","end_date":"2016-10-20"},"day":"22","year":"2016","doi":"10.1007/978-3-319-46520-3_3","date_published":"2016-09-22T00:00:00Z","date_created":"2018-12-11T11:51:23Z","page":"32 - 49","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","quality_controlled":"1","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","chicago":"Brázdil, Tomáš, Antonín Kučera, and Petr Novotný. “Optimizing the Expected Mean Payoff in Energy Markov Decision Processes,” 9938:32–49. Springer, 2016. https://doi.org/10.1007/978-3-319-46520-3_3.","apa":"Brázdil, T., Kučera, A., & 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. https://doi.org/10.1007/978-3-319-46520-3_3","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:10.1007/978-3-319-46520-3_3","short":"T. Brázdil, A. Kučera, P. Novotný, in:, Springer, 2016, pp. 32–49.","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.","mla":"Brázdil, Tomáš, et al. Optimizing the Expected Mean Payoff in Energy Markov Decision Processes. Vol. 9938, Springer, 2016, pp. 32–49, doi:10.1007/978-3-319-46520-3_3."},"title":"Optimizing the expected mean payoff in Energy Markov Decision Processes","publist_id":"5943","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"},{"last_name":"Novotny","full_name":"Novotny, Petr","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}]},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":216,"issue":"2","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"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1506.06014"}],"scopus_import":1,"intvolume":" 216","month":"10","date_updated":"2021-01-12T06:49:56Z","department":[{"_id":"HeEd"}],"_id":"1330","type":"journal_article","status":"public","year":"2016","publication":"Israel Journal of Mathematics","day":"15","page":"833 - 845","date_created":"2018-12-11T11:51:24Z","date_published":"2016-10-15T00:00:00Z","doi":"10.1007/s11856-016-1429-z","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.","oa":1,"quality_controlled":"1","publisher":"Springer","citation":{"ista":"Akopyan A, Balitskiy A. 2016. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 216(2), 833–845.","chicago":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1429-z.","apa":"Akopyan, A., & Balitskiy, A. (2016). Billiards in convex bodies with acute angles. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1429-z","ama":"Akopyan A, Balitskiy A. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 2016;216(2):833-845. doi:10.1007/s11856-016-1429-z","short":"A. Akopyan, A. Balitskiy, Israel Journal of Mathematics 216 (2016) 833–845.","ieee":"A. Akopyan and A. Balitskiy, “Billiards in convex bodies with acute angles,” Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 833–845, 2016.","mla":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 833–45, doi:10.1007/s11856-016-1429-z."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5938","author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexey","full_name":"Balitskiy, Alexey","last_name":"Balitskiy"}],"title":"Billiards in convex bodies with acute angles","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}]},{"publication_status":"published","file":[{"file_id":"5196","checksum":"e43307754abe65b840a21939fe163618","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:10Z","file_name":"IST-2016-660-v1+1_ncomms11824.pdf","date_updated":"2020-07-14T12:44:44Z","file_size":1793846,"creator":"system"}],"language":[{"iso":"eng"}],"volume":7,"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"06","intvolume":" 7","date_updated":"2021-01-12T06:49:57Z","ddc":["570"],"department":[{"_id":"JoCs"}],"file_date_updated":"2020-07-14T12:44:44Z","_id":"1334","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"660","has_accepted_license":"1","year":"2016","day":"10","publication":"Nature Communications","date_published":"2016-06-10T00:00:00Z","doi":"10.1038/ncomms11824","date_created":"2018-12-11T11:51:26Z","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"citation":{"chicago":"Schönenberger, Philipp, Joseph O’Neill, and Jozsef L Csicsvari. “Activity Dependent Plasticity of Hippocampal Place Maps.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11824.","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.” Nature Communications, vol. 7, 11824, Nature Publishing Group, 2016, doi:10.1038/ncomms11824.","apa":"Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2016). Activity dependent plasticity of hippocampal place maps. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11824","ama":"Schönenberger P, O’Neill J, Csicsvari JL. Activity dependent plasticity of hippocampal place maps. Nature Communications. 2016;7. doi:10.1038/ncomms11824","ieee":"P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Activity dependent plasticity of hippocampal place maps,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","short":"P. Schönenberger, J. O’Neill, J.L. Csicsvari, Nature Communications 7 (2016)."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5934","author":[{"last_name":"Schönenberger","full_name":"Schönenberger, Philipp","first_name":"Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"O'Neill","full_name":"O'Neill, Joseph","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"}],"title":"Activity dependent plasticity of hippocampal place maps","article_number":"11824","project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511"},{"call_identifier":"FWF","_id":"257D4372-B435-11E9-9278-68D0E5697425","grant_number":"I2072-B27","name":"Interneuron plasticity during spatial learning"}]},{"citation":{"mla":"Zwack, Paul, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1249–58, doi:10.1104/pp.16.00415.","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. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00415","ama":"Zwack P, De Clercq I, Howton T, et al. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 2016;172(2):1249-1258. doi:10.1104/pp.16.00415","ieee":"P. Zwack et al., “Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1249–1258, 2016.","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.","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.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00415.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"5937","author":[{"last_name":"Zwack","full_name":"Zwack, Paul","first_name":"Paul"},{"first_name":"Inge","full_name":"De Clercq, Inge","last_name":"De Clercq"},{"first_name":"Timothy","last_name":"Howton","full_name":"Howton, Timothy"},{"first_name":"H Tucker","full_name":"Hallmark, H Tucker","last_name":"Hallmark"},{"id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Andrej","full_name":"Hurny, Andrej","last_name":"Hurny"},{"last_name":"Keshishian","full_name":"Keshishian, Erika","first_name":"Erika"},{"first_name":"Alyssa","last_name":"Parish","full_name":"Parish, Alyssa"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"first_name":"M Shahid","last_name":"Mukhtar","full_name":"Mukhtar, M Shahid"},{"first_name":"Frank","last_name":"Van Breusegem","full_name":"Van Breusegem, Frank"},{"first_name":"Aaron","last_name":"Rashotte","full_name":"Rashotte, Aaron"}],"title":"Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress","year":"2016","publication":"Plant Physiology","day":"02","page":"1249 - 1258","date_created":"2018-12-11T11:51:25Z","date_published":"2016-10-02T00:00:00Z","doi":"10.1104/pp.16.00415","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).","oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","date_updated":"2022-05-24T09:26:03Z","department":[{"_id":"EvBe"}],"_id":"1331","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"language":[{"iso":"eng"}],"issue":"2","volume":172,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.16.00415"}],"scopus_import":"1","intvolume":" 172","month":"10"},{"article_number":"10915","citation":{"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.","chicago":"Milinski, Manfred, Christian Hilbe, Dirk Semmann, Ralf Sommerfeld, and Jochem Marotzke. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10915.","ieee":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, and J. Marotzke, “Humans choose representatives who enforce cooperation in social dilemmas through extortion,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","short":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, J. Marotzke, Nature Communications 7 (2016).","apa":"Milinski, M., Hilbe, C., Semmann, D., Sommerfeld, R., & Marotzke, J. (2016). Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10915","ama":"Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 2016;7. doi:10.1038/ncomms10915","mla":"Milinski, Manfred, et al. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications, vol. 7, 10915, Nature Publishing Group, 2016, doi:10.1038/ncomms10915."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5935","author":[{"first_name":"Manfred","full_name":"Milinski, Manfred","last_name":"Milinski"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"first_name":"Dirk","last_name":"Semmann","full_name":"Semmann, Dirk"},{"last_name":"Sommerfeld","full_name":"Sommerfeld, Ralf","first_name":"Ralf"},{"first_name":"Jochem","last_name":"Marotzke","full_name":"Marotzke, Jochem"}],"title":"Humans choose representatives who enforce cooperation in social dilemmas through extortion","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.","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2016","day":"07","publication":"Nature Communications","date_published":"2016-03-07T00:00:00Z","doi":"10.1038/ncomms10915","date_created":"2018-12-11T11:51:25Z","_id":"1333","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"661","date_updated":"2021-01-12T06:49:57Z","ddc":["519","530","599"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:44:44Z","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 "representatives" 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"}],"oa_version":"Published Version","scopus_import":1,"month":"03","intvolume":" 7","publication_status":"published","file":[{"file_size":1432577,"date_updated":"2020-07-14T12:44:44Z","creator":"system","file_name":"IST-2016-661-v1+1_ncomms10915.pdf","date_created":"2018-12-12T10:10:44Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"9ea0d7ce59a555a1cb8353d5559407cb","file_id":"4834"}],"language":[{"iso":"eng"}],"volume":7},{"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:44:44Z","file_size":1844107,"creator":"system","date_created":"2018-12-12T10:13:52Z","file_name":"IST-2016-662-v1+1_ncomms10333.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ef147bcbb8bd37e9079cf3ce06f5815d","file_id":"5039"}],"publication_status":"published","volume":7,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 7","month":"01","scopus_import":1,"ddc":["570","579"],"date_updated":"2021-01-12T06:49:57Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:44:44Z","_id":"1332","pubrep_id":"662","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","publication":"Nature Communications","day":"20","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:51:25Z","doi":"10.1038/ncomms10333","date_published":"2016-01-20T00:00:00Z","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.","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10333.","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.” Nature Communications, vol. 7, 10333, Nature Publishing Group, 2016, doi:10.1038/ncomms10333.","ieee":"R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","short":"R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).","apa":"Chait, R. P., Palmer, A., Yelin, I., & Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10333","ama":"Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 2016;7. doi:10.1038/ncomms10333"},"title":"Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments","author":[{"first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait"},{"first_name":"Adam","full_name":"Palmer, Adam","last_name":"Palmer"},{"last_name":"Yelin","full_name":"Yelin, Idan","first_name":"Idan"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"publist_id":"5936","article_number":"10333"},{"status":"public","type":"conference","conference":{"location":"Edinburgh, United Kingdom","end_date":"2016-09-10","start_date":"2016-09-08","name":"SAS: Static Analysis Symposium"},"_id":"1335","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-01-12T06:49:58Z","month":"08","intvolume":" 9837","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"volume":9837,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"title":"Quantitative monitor automata","publist_id":"5932","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Monitor Automata,” 9837:23–38. Springer, 2016. https://doi.org/10.1007/978-3-662-53413-7_2.","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative monitor automata. SAS: Static Analysis Symposium, LNCS, vol. 9837, 23–38.","mla":"Chatterjee, Krishnendu, et al. Quantitative Monitor Automata. Vol. 9837, Springer, 2016, pp. 23–38, doi:10.1007/978-3-662-53413-7_2.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative monitor automata. In: Vol 9837. Springer; 2016:23-38. doi:10.1007/978-3-662-53413-7_2","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative monitor automata (Vol. 9837, pp. 23–38). Presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53413-7_2","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.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Springer, 2016, pp. 23–38."},"quality_controlled":"1","publisher":"Springer","oa":1,"doi":"10.1007/978-3-662-53413-7_2","date_published":"2016-08-31T00:00:00Z","date_created":"2018-12-11T11:51:26Z","page":"23 - 38","day":"31","year":"2016"},{"doi":"10.7554/eLife.19048","date_published":"2016-09-14T00:00:00Z","date_created":"2018-12-11T11:51:29Z","has_accepted_license":"1","year":"2016","day":"14","publication":"eLife","publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"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).","author":[{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"last_name":"Leung","full_name":"Leung, Jeffrey","first_name":"Jeffrey"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5908","title":"TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls","citation":{"chicago":"Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.19048.","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.” ELife, vol. 5, e19048, eLife Sciences Publications, 2016, doi:10.7554/eLife.19048.","ieee":"M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls,” eLife, vol. 5. eLife Sciences Publications, 2016.","short":"M. Fendrych, J. Leung, J. Friml, ELife 5 (2016).","ama":"Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 2016;5. doi:10.7554/eLife.19048","apa":"Fendrych, M., Leung, J., & Friml, J. (2016). TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.19048"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"article_number":"e19048","volume":5,"ec_funded":1,"publication_status":"published","file":[{"date_created":"2018-12-12T10:09:24Z","file_name":"IST-2016-693-v1+1_e19048-download.pdf","date_updated":"2020-07-14T12:44:45Z","file_size":5666343,"creator":"system","file_id":"4748","checksum":"9209541fbba00f24daad21a5d568540d","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"09","intvolume":" 5","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."}],"oa_version":"Published Version","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:45Z","date_updated":"2021-01-12T06:50:01Z","ddc":["581"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"654","_id":"1344"},{"scopus_import":1,"month":"09","intvolume":" 18","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","issue":"9","volume":18,"ec_funded":1,"publication_status":"published","file":[{"date_created":"2018-12-12T10:17:52Z","file_name":"IST-2016-655-v1+1_njp_18_9_093042.pdf","date_updated":"2020-07-14T12:44:45Z","file_size":1076029,"creator":"system","file_id":"5309","checksum":"2a43e235222755e31ffbd369882c61de","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"655","_id":"1343","department":[{"_id":"MiLe"}],"file_date_updated":"2020-07-14T12:44:45Z","date_updated":"2021-01-12T06:50:01Z","ddc":["530"],"quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1,"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).","doi":"10.1088/1367-2630/18/9/093042","date_published":"2016-09-22T00:00:00Z","date_created":"2018-12-11T11:51:29Z","has_accepted_license":"1","year":"2016","day":"22","publication":"New Journal of Physics","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"article_number":"093042","author":[{"id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kaczmarczyk","orcid":"0000-0002-1629-3675","full_name":"Kaczmarczyk, Jan"},{"full_name":"Weimer, Hendrik","last_name":"Weimer","first_name":"Hendrik"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5909","title":"Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model","citation":{"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.","chicago":"Kaczmarczyk, Jan, Hendrik Weimer, and Mikhail Lemeshko. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/9/093042.","ieee":"J. Kaczmarczyk, H. Weimer, and M. Lemeshko, “Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model,” New Journal of Physics, vol. 18, no. 9. IOP Publishing Ltd., 2016.","short":"J. Kaczmarczyk, H. Weimer, M. Lemeshko, New Journal of Physics 18 (2016).","ama":"Kaczmarczyk J, Weimer H, Lemeshko M. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 2016;18(9). doi:10.1088/1367-2630/18/9/093042","apa":"Kaczmarczyk, J., Weimer, H., & Lemeshko, M. (2016). Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/9/093042","mla":"Kaczmarczyk, Jan, et al. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics, vol. 18, no. 9, 093042, IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/9/093042."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"title":"The big match in small space","publist_id":"5927","author":[{"first_name":"Kristoffer","last_name":"Hansen","full_name":"Hansen, Kristoffer"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"last_name":"Koucký","full_name":"Koucký, Michal","first_name":"Michal"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","chicago":"Hansen, Kristoffer, Rasmus Ibsen-Jensen, and Michal Koucký. “The Big Match in Small Space,” 9928:64–76. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_6.","ama":"Hansen K, Ibsen-Jensen R, Koucký M. The big match in small space. In: Vol 9928. Springer; 2016:64-76. doi:10.1007/978-3-662-53354-3_6","apa":"Hansen, K., Ibsen-Jensen, R., & 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. https://doi.org/10.1007/978-3-662-53354-3_6","short":"K. Hansen, R. Ibsen-Jensen, M. Koucký, in:, Springer, 2016, pp. 64–76.","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.","mla":"Hansen, Kristoffer, et al. The Big Match in Small Space. Vol. 9928, Springer, 2016, pp. 64–76, doi:10.1007/978-3-662-53354-3_6."},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"date_published":"2016-09-01T00:00:00Z","doi":"10.1007/978-3-662-53354-3_6","date_created":"2018-12-11T11:51:28Z","page":"64 - 76","day":"01","year":"2016","publisher":"Springer","quality_controlled":"1","oa":1,"department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T06:50:00Z","status":"public","type":"conference","conference":{"name":"SAGT: Symposium on Algorithmic Game Theory","start_date":"2016-09-19","location":"Liverpool, United Kingdom","end_date":"2016-09-21"},"_id":"1340","volume":9928,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 9928","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1604.07634","open_access":"1"}],"oa_version":"Preprint","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]."}]},{"article_number":"16102","title":"Plasma membrane: Negative attraction","author":[{"last_name":"Molnar","full_name":"Molnar, Gergely","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"5907","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,” Nature Plants, vol. 2. Nature Publishing Group, 2016.","short":"G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016).","apa":"Molnar, G., Fendrych, M., & Friml, J. (2016). Plasma membrane: Negative attraction. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2016.102","ama":"Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. Nature Plants. 2016;2. doi:10.1038/nplants.2016.102","mla":"Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” Nature Plants, vol. 2, 16102, Nature Publishing Group, 2016, doi:10.1038/nplants.2016.102.","ista":"Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction. Nature Plants. 2, 16102.","chicago":"Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative Attraction.” Nature Plants. Nature Publishing Group, 2016. https://doi.org/10.1038/nplants.2016.102."},"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","date_created":"2018-12-11T11:51:30Z","doi":"10.1038/nplants.2016.102","date_published":"2016-07-01T00:00:00Z","publication":"Nature Plants","day":"01","year":"2016","has_accepted_license":"1","pubrep_id":"1007","status":"public","type":"journal_article","_id":"1345","file_date_updated":"2020-07-14T12:44:45Z","department":[{"_id":"JiFr"}],"ddc":["581"],"date_updated":"2021-01-12T06:50:02Z","intvolume":" 2","month":"07","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"volume":2,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:36Z","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","checksum":"9ba65f558563b287f875f48fa9f30fb2","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"date_created":"2018-12-12T10:12:37Z","file_name":"IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf","creator":"system","date_updated":"2020-07-14T12:44:45Z","file_size":430556,"file_id":"4955","checksum":"550d252be808d8ca2b43e83dddb4212f","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published"},{"status":"public","type":"journal_article","_id":"1342","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Spatiotemporal microbial evolution on antibiotic landscapes","publist_id":"5911","author":[{"first_name":"Michael","last_name":"Baym","full_name":"Baym, Michael"},{"last_name":"Lieberman","full_name":"Lieberman, Tami","first_name":"Tami"},{"first_name":"Eric","full_name":"Kelsic, Eric","last_name":"Kelsic"},{"first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187"},{"first_name":"Rotem","full_name":"Gross, Rotem","last_name":"Gross"},{"full_name":"Yelin, Idan","last_name":"Yelin","first_name":"Idan"},{"first_name":"Roy","full_name":"Kishony, Roy","last_name":"Kishony"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:50:01Z","citation":{"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.","chicago":"Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aag0822.","ama":"Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016;353(6304):1147-1151. doi:10.1126/science.aag0822","apa":"Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., & Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag0822","ieee":"M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016.","short":"M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151.","mla":"Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1147–51, doi:10.1126/science.aag0822."},"month":"09","intvolume":" 353","quality_controlled":"1","publisher":"American Association for the Advancement of Science","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/","open_access":"1"}],"oa":1,"oa_version":"Preprint","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."}],"volume":353,"issue":"6304","date_published":"2016-09-09T00:00:00Z","doi":"10.1126/science.aag0822","date_created":"2018-12-11T11:51:29Z","page":"1147 - 1151","day":"09","language":[{"iso":"eng"}],"publication":"Science","publication_status":"published","year":"2016"},{"status":"public","type":"journal_article","article_number":"143507","_id":"1339","title":"Tunable mechanical coupling between driven microelectromechanical resonators","department":[{"_id":"JoFi"}],"author":[{"first_name":"Gerard","full_name":"Verbiest, Gerard","last_name":"Verbiest"},{"first_name":"Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87","full_name":"Xu, Duo","last_name":"Xu"},{"first_name":"Matthias","last_name":"Goldsche","full_name":"Goldsche, Matthias"},{"first_name":"Timofiy","last_name":"Khodkov","full_name":"Khodkov, Timofiy"},{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"last_name":"Von Den Driesch","full_name":"Von Den Driesch, Nils","first_name":"Nils"},{"first_name":"Dan","full_name":"Buca, Dan","last_name":"Buca"},{"first_name":"Christoph","full_name":"Stampfer, Christoph","last_name":"Stampfer"}],"publist_id":"5928","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-21T10:35:06Z","citation":{"mla":"Verbiest, Gerard, et al. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter, vol. 109, 143507, American Institute of Physics, 2016, doi:10.1063/1.4964122.","ama":"Verbiest G, Xu D, Goldsche M, et al. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 2016;109. doi:10.1063/1.4964122","apa":"Verbiest, G., Xu, D., Goldsche, M., Khodkov, T., Barzanjeh, S., Von Den Driesch, N., … Stampfer, C. (2016). Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. American Institute of Physics. https://doi.org/10.1063/1.4964122","ieee":"G. Verbiest et al., “Tunable mechanical coupling between driven microelectromechanical resonators,” Applied Physics Letter, vol. 109. American Institute of Physics, 2016.","short":"G. Verbiest, D. Xu, M. Goldsche, T. Khodkov, S. Barzanjeh, N. Von Den Driesch, D. Buca, C. Stampfer, Applied Physics Letter 109 (2016).","chicago":"Verbiest, Gerard, Duo Xu, Matthias Goldsche, Timofiy Khodkov, Shabir Barzanjeh, Nils Von Den Driesch, Dan Buca, and Christoph Stampfer. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter. American Institute of Physics, 2016. https://doi.org/10.1063/1.4964122.","ista":"Verbiest G, Xu D, Goldsche M, Khodkov T, Barzanjeh S, Von Den Driesch N, Buca D, Stampfer C. 2016. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 109, 143507."},"month":"10","intvolume":" 109","publisher":"American Institute of Physics","scopus_import":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.04406"}],"oa":1,"oa_version":"Preprint","acknowledgement":"We acknowledge the support from the Helmholtz Nanoelectronic Facility (HNF) and funding from the ERC (GA-Nr. 280140).","abstract":[{"text":"We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive\r\nactuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By\r\nmeasuring the resonance frequencies of the system, we show that the comb-drive actuator and the\r\nsilicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate\r\n(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)\r\nplaced close to the silicon beam. In contrast, the effective spring constant of the system is insensitive\r\nto either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator\r\ncan be used to switch between different coupling rates with a frequency of at least 10 kHz.\r\n","lang":"eng"}],"date_published":"2016-10-04T00:00:00Z","doi":"10.1063/1.4964122","volume":109,"date_created":"2018-12-11T11:51:28Z","day":"04","language":[{"iso":"eng"}],"publication":"Applied Physics Letter","publication_status":"published","year":"2016"},{"oa":1,"quality_controlled":"1","publisher":"ACM","publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 ","day":"20","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:51:31Z","doi":"10.1145/2908812.2908909","date_published":"2016-07-20T00:00:00Z","page":"1163 - 1170","project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.","ama":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909","apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909","short":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170.","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170.","mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909."},"title":"When non-elitism outperforms elitism for crossing fitness valleys","publist_id":"5900","author":[{"first_name":"Pietro","full_name":"Oliveto, Pietro","last_name":"Oliveto"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"},{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"first_name":"Dirk","full_name":"Sudholt, Dirk","last_name":"Sudholt"},{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"}],"oa_version":"Published Version","abstract":[{"text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys.","lang":"eng"}],"month":"07","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:16:27Z","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","creator":"system","date_updated":"2020-07-14T12:44:45Z","file_size":979026,"checksum":"a1896e39e4113f2711e46b435d5f3e69","file_id":"5214","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","ec_funded":1,"_id":"1349","pubrep_id":"650","status":"public","conference":{"name":"GECCO: Genetic and evolutionary computation conference","end_date":"2016-07-24","location":"Denver, CO, USA","start_date":"2016-07-20"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","ddc":["576"],"date_updated":"2021-01-12T06:50:03Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:44:45Z"},{"file":[{"file_name":"IST-2017-823-v1+1_aaf1836_CombinedPDF_v2-1.pdf","date_created":"2018-12-12T10:12:27Z","file_size":19408143,"date_updated":"2020-07-14T12:44:46Z","creator":"system","file_id":"4945","checksum":"89caefa4e181424cbf0aecc835fcc5ec","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"6304","volume":353,"ec_funded":1,"oa_version":"Preprint","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3\r\nsynapses are thought to be the subcellular substrate of pattern completion. However, the\r\nsynaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.\r\nSimultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient\r\nmemory storage and retrieval in hippocampal networks."}],"month":"09","intvolume":" 353","scopus_import":1,"ddc":["570"],"date_updated":"2021-01-12T06:50:04Z","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:44:46Z","_id":"1350","status":"public","pubrep_id":"823","type":"journal_article","day":"09","publication":"Science","has_accepted_license":"1","year":"2016","doi":"10.1126/science.aaf1836","date_published":"2016-09-09T00:00:00Z","date_created":"2018-12-11T11:51:31Z","page":"1117 - 1123","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Guzmán, José, Alois Schlögl, Michael Frotscher, and Peter M Jonas. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf1836.","ista":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. 2016. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 353(6304), 1117–1123.","mla":"Guzmán, José, et al. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1117–23, doi:10.1126/science.aaf1836.","ieee":"J. Guzmán, A. Schlögl, M. Frotscher, and P. M. Jonas, “Synaptic mechanisms of pattern completion in the hippocampal CA3 network,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1117–1123, 2016.","short":"J. Guzmán, A. Schlögl, M. Frotscher, P.M. Jonas, Science 353 (2016) 1117–1123.","apa":"Guzmán, J., Schlögl, A., Frotscher, M., & Jonas, P. M. (2016). Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf1836","ama":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 2016;353(6304):1117-1123. doi:10.1126/science.aaf1836"},"title":"Synaptic mechanisms of pattern completion in the hippocampal CA3 network","publist_id":"5899","author":[{"full_name":"Guzmán, José","last_name":"Guzmán","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Frotscher, Michael","last_name":"Frotscher","first_name":"Michael"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24"}]},{"_id":"1347","status":"public","pubrep_id":"652","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_updated":"2021-01-12T06:50:03Z","file_date_updated":"2020-07-14T12:44:45Z","department":[{"_id":"MiLe"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"During the past 70 years, the quantum theory of angular momentum has been successfully applied to describing the properties of nuclei, atoms, and molecules, and their interactions with each other as well as with external fields. Because of the properties of quantum rotations, the angular-momentum algebra can be of tremendous complexity even for a few interacting particles, such as valence electrons of an atom, not to mention larger many-particle systems. In this work, we study an example of the latter: A rotating quantum impurity coupled to a many-body bosonic bath. In the regime of strong impurity-bath couplings, the problem involves the addition of an infinite number of angular momenta, which renders it intractable using currently available techniques. Here, we introduce a novel canonical transformation that allows us to eliminate the complex angular-momentum algebra from such a class of many-body problems. In addition, the transformation exposes the problem's constants of motion, and renders it solvable exactly in the limit of a slowly rotating impurity. We exemplify the technique by showing that there exists a critical rotational speed at which the impurity suddenly acquires one quantum of angular momentum from the many-particle bath. Such an instability is accompanied by the deformation of the phonon density in the frame rotating along with the impurity."}],"month":"01","intvolume":" 6","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:44:45Z","file_size":1165869,"creator":"system","date_created":"2018-12-12T10:15:59Z","file_name":"IST-2016-652-v1+1_PhysRevX.6.011012.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6757a164d3c38905e05b2b5a188cb8ff","file_id":"5183"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":6,"issue":"1","article_number":"011012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Schmidt, M. Lemeshko, Physical Review X 6 (2016).","ieee":"R. Schmidt and M. Lemeshko, “Deformation of a quantum many-particle system by a rotating impurity,” Physical Review X, vol. 6, no. 1. American Physical Society, 2016.","apa":"Schmidt, R., & Lemeshko, M. (2016). Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.6.011012","ama":"Schmidt R, Lemeshko M. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 2016;6(1). doi:10.1103/PhysRevX.6.011012","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X, vol. 6, no. 1, 011012, American Physical Society, 2016, doi:10.1103/PhysRevX.6.011012.","ista":"Schmidt R, Lemeshko M. 2016. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 6(1), 011012.","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X. American Physical Society, 2016. https://doi.org/10.1103/PhysRevX.6.011012."},"title":"Deformation of a quantum many-particle system by a rotating impurity","publist_id":"5902","author":[{"first_name":"Richard","full_name":"Schmidt, Richard","last_name":"Schmidt"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We are grateful to Eugene Demler, Jan Kaczmarczyk, Laleh Safari, and Hendrik Weimer for insightful discussions. The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory.","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"01","publication":"Physical Review X","has_accepted_license":"1","year":"2016","date_published":"2016-01-01T00:00:00Z","doi":"10.1103/PhysRevX.6.011012","date_created":"2018-12-11T11:51:30Z"},{"_id":"1348","status":"public","type":"conference","conference":{"end_date":"2018-08-19","location":"Helsinki, Finland","start_date":"2016-08-17","name":"IWOCA: International Workshop on Combinatorial Algorithms"},"date_updated":"2021-01-12T06:50:03Z","department":[{"_id":"UlWa"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function γ : V → ℕ is x-bounded if (i) x(u) < x(v) whenever γ(u) < γ(v) and (ii) γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where x(.) denotes the projection to the xaxis.We prove a characterization of isotopy classes of embeddings of connected graphs equipped with γ in the plane containing an x-bounded embedding.Then we present an efficient algorithm, which relies on our result, for testing the existence of an x-bounded embedding if the given graph is a forest.This partially answers a question raised recently by Angelini et al.and Chang et al., and proves that c-planarity testing of flat clustered graphs with three clusters is tractable when the underlying abstract graph is a forest."}],"month":"08","intvolume":" 9843","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.07144"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":9843,"ec_funded":1,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Fulek, in:, Springer, 2016, pp. 31–42.","ieee":"R. Fulek, “Bounded embeddings of graphs in the plane,” presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland, 2016, vol. 9843, pp. 31–42.","ama":"Fulek R. Bounded embeddings of graphs in the plane. In: Vol 9843. Springer; 2016:31-42. doi:10.1007/978-3-319-44543-4_3","apa":"Fulek, R. (2016). Bounded embeddings of graphs in the plane (Vol. 9843, pp. 31–42). Presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-319-44543-4_3","mla":"Fulek, Radoslav. Bounded Embeddings of Graphs in the Plane. Vol. 9843, Springer, 2016, pp. 31–42, doi:10.1007/978-3-319-44543-4_3.","ista":"Fulek R. 2016. Bounded embeddings of graphs in the plane. IWOCA: International Workshop on Combinatorial Algorithms, LNCS, vol. 9843, 31–42.","chicago":"Fulek, Radoslav. “Bounded Embeddings of Graphs in the Plane,” 9843:31–42. Springer, 2016. https://doi.org/10.1007/978-3-319-44543-4_3."},"title":"Bounded embeddings of graphs in the plane","publist_id":"5901","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek"}],"publisher":"Springer","quality_controlled":"1","oa":1,"day":"09","year":"2016","date_published":"2016-08-09T00:00:00Z","doi":"10.1007/978-3-319-44543-4_3","date_created":"2018-12-11T11:51:31Z","page":"31 - 42"}]