[{"_id":"5405","pubrep_id":"128","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2013-07-08T00:00:00Z","page":"22","abstract":[{"lang":"eng","text":"The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2-1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2-1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic) with only parity objectives, or with only mean-payoff objectives. We present an algorithm running\r\nin time O(d · n^{2d}·MeanGame) to compute the set of almost-sure winning states from which the objective\r\ncan be ensured with probability 1, where n is the number of states of the game, d the number of priorities\r\nof the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states\r\nin 2-1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems\r\nwith both functional requirement (given as a qualitative objective) and performance requirement (given\r\nas a quantitative objective)."}],"ddc":["000","005","510"],"citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Perfect-Information Stochastic Mean-Payoff Parity Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-128-v1-1\">10.15479/AT:IST-2013-128-v1-1</a>.","short":"K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, Perfect-Information Stochastic Mean-Payoff Parity Games, IST Austria, 2013.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj. <i>Perfect-Information Stochastic Mean-Payoff Parity Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-128-v1-1\">https://doi.org/10.15479/AT:IST-2013-128-v1-1</a>.","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, <i>Perfect-information stochastic mean-payoff parity games</i>. IST Austria, 2013.","ista":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2013. Perfect-information stochastic mean-payoff parity games, IST Austria, 22p.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., &#38; Oualhadj, Y. (2013). <i>Perfect-information stochastic mean-payoff parity games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-128-v1-1\">https://doi.org/10.15479/AT:IST-2013-128-v1-1</a>","ama":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. <i>Perfect-Information Stochastic Mean-Payoff Parity Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-128-v1-1\">10.15479/AT:IST-2013-128-v1-1</a>"},"date_created":"2018-12-12T11:39:09Z","alternative_title":["IST Austria Technical Report"],"file":[{"access_level":"open_access","date_created":"2018-12-12T11:53:54Z","date_updated":"2020-07-14T12:46:45Z","file_size":387467,"file_id":"5516","file_name":"IST-2013-128-v1+1_full_stoch_mpp.pdf","relation":"main_file","checksum":"ede787a10e74e4f7db302fab8f12f3ca","creator":"system","content_type":"application/pdf"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"full_name":"Gimbert, Hugo","last_name":"Gimbert","first_name":"Hugo"},{"full_name":"Oualhadj, Youssouf","last_name":"Oualhadj","first_name":"Youssouf"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:45Z","month":"07","oa":1,"type":"technical_report","year":"2013","has_accepted_license":"1","related_material":{"record":[{"id":"2212","relation":"later_version","status":"public"}]},"date_updated":"2023-02-23T10:33:08Z","publisher":"IST Austria","day":"08","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","doi":"10.15479/AT:IST-2013-128-v1-1","title":"Perfect-information stochastic mean-payoff parity games","department":[{"_id":"KrCh"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5406","language":[{"iso":"eng"}],"pubrep_id":"130","page":"11","abstract":[{"text":"We consider the distributed synthesis problem fortemporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTLand our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3)Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.","lang":"eng"}],"status":"public","date_published":"2013-07-08T00:00:00Z","alternative_title":["IST Austria Technical Report"],"ddc":["005"],"citation":{"apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Pavlogiannis, A. (2013). <i>Distributed synthesis for LTL Fragments</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-130-v1-1\">https://doi.org/10.15479/AT:IST-2013-130-v1-1</a>","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL Fragments, IST Austria, 11p.","ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. <i>Distributed Synthesis for LTL Fragments</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-130-v1-1\">10.15479/AT:IST-2013-130-v1-1</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, Distributed Synthesis for LTL Fragments, IST Austria, 2013.","mla":"Chatterjee, Krishnendu, et al. <i>Distributed Synthesis for LTL Fragments</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-130-v1-1\">10.15479/AT:IST-2013-130-v1-1</a>.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, <i>Distributed synthesis for LTL Fragments</i>. IST Austria, 2013.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. <i>Distributed Synthesis for LTL Fragments</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-130-v1-1\">https://doi.org/10.15479/AT:IST-2013-130-v1-1</a>."},"date_created":"2018-12-12T11:39:09Z","oa_version":"Published Version","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"file":[{"date_created":"2018-12-12T11:54:18Z","date_updated":"2020-07-14T12:46:45Z","access_level":"open_access","file_id":"5540","file_size":467895,"checksum":"855513ebaf6f72228800c5fdb522f93c","creator":"system","relation":"main_file","file_name":"IST-2013-130-v1+1_Distributed_Synthesis.pdf","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:46:45Z","month":"07","type":"technical_report","oa":1,"has_accepted_license":"1","related_material":{"record":[{"id":"1376","relation":"later_version","status":"public"}]},"year":"2013","day":"08","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"date_updated":"2023-02-21T17:01:26Z","publisher":"IST Austria","doi":"10.15479/AT:IST-2013-130-v1-1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"Distributed synthesis for LTL Fragments"},{"year":"2013","has_accepted_license":"1","oa":1,"type":"report","title":"Technical requirements and features","department":[{"_id":"E-Lib"}],"publisher":"IST Austria","date_updated":"2020-07-14T23:07:51Z","publication_status":"published","day":"13","date_published":"2013-07-13T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the mandatory features, which need to be fulfilled to provide an institutional repository as a platform and also a service to the scientists at the institute. It also includes optional features, which would be of strong benefit for the scientists and would increase the usage of the repository, and hence the visibility of research at IST Austria."}],"_id":"5407","language":[{"iso":"eng"}],"pubrep_id":"135","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","file_date_updated":"2020-07-14T12:46:46Z","author":[{"full_name":"Porsche, Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","last_name":"Porsche","first_name":"Jana"}],"oa_version":"Published Version","file":[{"file_name":"IST-2013-135-v1+1_Features.pdf","relation":"main_file","creator":"system","checksum":"9e4f9abf79a56f651f0012a34909880f","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T11:53:02Z","date_updated":"2020-07-14T12:46:46Z","file_size":90311,"file_id":"5463"}],"date_created":"2018-12-12T11:39:09Z","citation":{"chicago":"Porsche, Jana. <i>Technical Requirements and Features</i>. IST Austria, 2013.","ieee":"J. Porsche, <i>Technical requirements and features</i>. IST Austria, 2013.","short":"J. Porsche, Technical Requirements and Features, IST Austria, 2013.","mla":"Porsche, Jana. <i>Technical Requirements and Features</i>. IST Austria, 2013.","ama":"Porsche J. <i>Technical Requirements and Features</i>. IST Austria; 2013.","ista":"Porsche J. 2013. Technical requirements and features, IST Austria,p.","apa":"Porsche, J. (2013). <i>Technical requirements and features</i>. IST Austria."},"ddc":["020"]},{"pubrep_id":"141","_id":"5408","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-09-12T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"We consider two-player partial-observation stochastic games where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are omega-regular conditions specified as parity objectives. The qualitative analysis problem given a partial-observation stochastic game and a parity objective asks whether  there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, they were shown to be decidable in 2EXPTIME under finite-memory  strategies. We improve the complexity and show that the qualitative analysis problems for partial-observation stochastic parity games under finite-memory strategies are \r\nEXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis. "}],"page":"17","date_created":"2018-12-12T11:39:10Z","citation":{"short":"K. Chatterjee, L. Doyen, S. Nain, M. Vardi, The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies, IST Austria, 2013.","mla":"Chatterjee, Krishnendu, et al. <i>The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-141-v1-1\">10.15479/AT:IST-2013-141-v1-1</a>.","ieee":"K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, <i>The complexity of partial-observation stochastic parity games with finite-memory strategies</i>. IST Austria, 2013.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. <i>The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-141-v1-1\">https://doi.org/10.15479/AT:IST-2013-141-v1-1</a>.","apa":"Chatterjee, K., Doyen, L., Nain, S., &#38; Vardi, M. (2013). <i>The complexity of partial-observation stochastic parity games with finite-memory strategies</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-141-v1-1\">https://doi.org/10.15479/AT:IST-2013-141-v1-1</a>","ista":"Chatterjee K, Doyen L, Nain S, Vardi M. 2013. The complexity of partial-observation stochastic parity games with finite-memory strategies, IST Austria, 17p.","ama":"Chatterjee K, Doyen L, Nain S, Vardi M. <i>The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-141-v1-1\">10.15479/AT:IST-2013-141-v1-1</a>"},"ddc":["000","005"],"alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:46Z","month":"09","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"last_name":"Nain","first_name":"Sumit","full_name":"Nain, Sumit"},{"full_name":"Vardi, Moshe","first_name":"Moshe","last_name":"Vardi"}],"oa_version":"Published Version","file":[{"file_size":300481,"file_id":"5477","access_level":"open_access","date_created":"2018-12-12T11:53:16Z","date_updated":"2020-07-14T12:46:46Z","content_type":"application/pdf","relation":"main_file","file_name":"IST-2013-141-v1+1_main-tech-rpt.pdf","creator":"system","checksum":"226bc791124f8d3138379778ce834e86"}],"oa":1,"type":"technical_report","year":"2013","related_material":{"record":[{"relation":"later_version","id":"2213","status":"public"}]},"has_accepted_license":"1","publisher":"IST Austria","date_updated":"2023-02-23T10:33:11Z","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","day":"12","title":"The complexity of partial-observation stochastic parity games with finite-memory strategies","department":[{"_id":"KrCh"}],"doi":"10.15479/AT:IST-2013-141-v1-1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5409","pubrep_id":"144","language":[{"iso":"eng"}],"page":"12","abstract":[{"lang":"eng","text":"The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. \r\nIn this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in timestamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than delta away from the parameter, for delta>0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and we show analogous decidability results for rectangular automata."}],"status":"public","date_published":"2013-10-30T00:00:00Z","alternative_title":["IST Austria Technical Report"],"ddc":["000"],"citation":{"apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Majumdar, R. (2013). <i>Edit distance for timed automata</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-144-v1-1\">https://doi.org/10.15479/AT:IST-2013-144-v1-1</a>","ista":"Chatterjee K, Ibsen-Jensen R, Majumdar R. 2013. Edit distance for timed automata, IST Austria, 12p.","ama":"Chatterjee K, Ibsen-Jensen R, Majumdar R. <i>Edit Distance for Timed Automata</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-144-v1-1\">10.15479/AT:IST-2013-144-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Edit Distance for Timed Automata</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-144-v1-1\">10.15479/AT:IST-2013-144-v1-1</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, Edit Distance for Timed Automata, IST Austria, 2013.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, <i>Edit distance for timed automata</i>. IST Austria, 2013.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Rupak Majumdar. <i>Edit Distance for Timed Automata</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-144-v1-1\">https://doi.org/10.15479/AT:IST-2013-144-v1-1</a>."},"date_created":"2018-12-12T11:39:10Z","file":[{"access_level":"open_access","date_created":"2018-12-12T11:53:08Z","date_updated":"2020-07-14T12:46:46Z","file_size":336377,"file_id":"5469","relation":"main_file","file_name":"IST-2013-144-v1+1_main.pdf","creator":"system","checksum":"0f7633081ba8299c543322f0ad08571f","content_type":"application/pdf"}],"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:46:46Z","month":"10","type":"technical_report","oa":1,"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"2216","relation":"later_version"}]},"year":"2013","day":"30","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"date_updated":"2023-02-23T10:33:18Z","publisher":"IST Austria","doi":"10.15479/AT:IST-2013-144-v1-1","title":"Edit distance for timed automata","department":[{"_id":"KrCh"}]},{"type":"technical_report","oa":1,"related_material":{"record":[{"id":"1481","relation":"later_version","status":"public"}]},"has_accepted_license":"1","year":"2013","day":"03","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"date_updated":"2023-02-23T10:00:50Z","publisher":"IST Austria","doi":"10.15479/AT:IST-2013-146-v1-1","department":[{"_id":"KrCh"}],"title":"Automatic generation of alternative starting positions for traditional board games","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"5410","pubrep_id":"146","page":"13","abstract":[{"lang":"eng","text":"Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in development of mathematical and logical skills, but also in emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. \r\nOur approach generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. Also, the presence of such states for standard game variants like Tic-Tac-Toe on board size 4x4 opens up new games to be played that have not been played for ages since the default start state is heavily biased. "}],"date_published":"2013-12-03T00:00:00Z","status":"public","alternative_title":["IST Austria Technical Report"],"ddc":["000","005"],"citation":{"ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, <i>Automatic generation of alternative starting positions for traditional board games</i>. IST Austria, 2013.","chicago":"Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. <i>Automatic Generation of Alternative Starting Positions for Traditional Board Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">https://doi.org/10.15479/AT:IST-2013-146-v1-1</a>.","mla":"Ahmed, Umair, et al. <i>Automatic Generation of Alternative Starting Positions for Traditional Board Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">10.15479/AT:IST-2013-146-v1-1</a>.","short":"U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative Starting Positions for Traditional Board Games, IST Austria, 2013.","ama":"Ahmed U, Chatterjee K, Gulwani S. <i>Automatic Generation of Alternative Starting Positions for Traditional Board Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">10.15479/AT:IST-2013-146-v1-1</a>","apa":"Ahmed, U., Chatterjee, K., &#38; Gulwani, S. (2013). <i>Automatic generation of alternative starting positions for traditional board games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-146-v1-1\">https://doi.org/10.15479/AT:IST-2013-146-v1-1</a>","ista":"Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative starting positions for traditional board games, IST Austria, 13p."},"date_created":"2018-12-12T11:39:10Z","oa_version":"Published Version","author":[{"full_name":"Ahmed, Umair","last_name":"Ahmed","first_name":"Umair"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gulwani, Sumit","last_name":"Gulwani","first_name":"Sumit"}],"file":[{"content_type":"application/pdf","checksum":"409f3aaaf1184e4057b89cbb449dac80","creator":"system","relation":"main_file","file_name":"IST-2013-146-v1+1_main.pdf","file_id":"5528","file_size":818189,"date_created":"2018-12-12T11:54:06Z","date_updated":"2020-07-14T12:46:46Z","access_level":"open_access"}],"month":"12","file_date_updated":"2020-07-14T12:46:46Z"},{"pubrep_id":"195","_id":"5747","language":[{"iso":"eng"}],"page":"174-190","place":"Berlin, Heidelberg","ddc":["005"],"citation":{"apa":"Dragoi, C., Gupta, A., &#38; Henzinger, T. A. (2013). Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In <i>Computer Aided Verification</i> (Vol. 8044, pp. 174–190). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">https://doi.org/10.1007/978-3-642-39799-8_11</a>","ista":"Dragoi C, Gupta A, Henzinger TA. 2013.Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In: Computer Aided Verification. vol. 8044, 174–190.","ama":"Dragoi C, Gupta A, Henzinger TA. Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates. In: <i>Computer Aided Verification</i>. Vol 8044. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013:174-190. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">10.1007/978-3-642-39799-8_11</a>","short":"C. Dragoi, A. Gupta, T.A. Henzinger, in:, Computer Aided Verification, Springer Berlin Heidelberg, Berlin, Heidelberg, 2013, pp. 174–190.","mla":"Dragoi, Cezara, et al. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” <i>Computer Aided Verification</i>, vol. 8044, Springer Berlin Heidelberg, 2013, pp. 174–90, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">10.1007/978-3-642-39799-8_11</a>.","ieee":"C. Dragoi, A. Gupta, and T. A. Henzinger, “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates,” in <i>Computer Aided Verification</i>, vol. 8044, Berlin, Heidelberg: Springer Berlin Heidelberg, 2013, pp. 174–190.","chicago":"Dragoi, Cezara, Ashutosh Gupta, and Thomas A Henzinger. “Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates.” In <i>Computer Aided Verification</i>, 8044:174–90. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_11\">https://doi.org/10.1007/978-3-642-39799-8_11</a>."},"file":[{"creator":"dernst","checksum":"a901cc6b71db08b61c0d4c0cbacc6287","file_name":"2013_CAV_Dragoi.pdf","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-18T13:13:33Z","access_level":"open_access","file_id":"5748","file_size":236480}],"author":[{"full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","last_name":"Dragoi"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:10Z","oa":1,"article_processing_charge":"No","ec_funded":1,"year":"2013","conference":{"end_date":"2013-07-19","start_date":"2013-07-13","name":"CAV 2013","location":"Saint Petersburg, Russia"},"has_accepted_license":"1","series_title":"CAV","date_updated":"2023-09-05T14:16:07Z","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642397981","9783642397998"],"issn":["0302-9743"]},"doi":"10.1007/978-3-642-39799-8_11","title":"Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates","intvolume":"      8044","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Computer Aided Verification","date_published":"2013-01-01T00:00:00Z","status":"public","date_created":"2018-12-18T13:10:21Z","scopus_import":"1","oa_version":"None","type":"book_chapter","volume":8044,"publisher":"Springer Berlin Heidelberg","publication_status":"published","quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"department":[{"_id":"ToHe"}]},{"alternative_title":["IST Austria Technical Report"],"date_created":"2019-05-13T14:13:27Z","citation":{"apa":"Henzinger, T. A., Payer, H., &#38; Sezgin, A. (2013). <i>Replacing competition with cooperation to achieve scalable lock-free FIFO queues </i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">https://doi.org/10.15479/AT:IST-2013-124-v1-1</a>","ista":"Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation to achieve scalable lock-free FIFO queues , IST Austria, 23p.","ama":"Henzinger TA, Payer H, Sezgin A. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">10.15479/AT:IST-2013-124-v1-1</a>","short":"T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013.","mla":"Henzinger, Thomas A., et al. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">10.15479/AT:IST-2013-124-v1-1</a>.","ieee":"T. A. Henzinger, H. Payer, and A. Sezgin, <i>Replacing competition with cooperation to achieve scalable lock-free FIFO queues </i>. IST Austria, 2013.","chicago":"Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. <i>Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues </i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-124-v1-1\">https://doi.org/10.15479/AT:IST-2013-124-v1-1</a>."},"ddc":["000","005"],"month":"06","file_date_updated":"2020-07-14T12:47:30Z","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Hannes","last_name":"Payer","full_name":"Payer, Hannes"},{"first_name":"Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali"}],"file":[{"date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-13T14:11:39Z","access_level":"open_access","file_id":"6441","file_size":549684,"checksum":"a219ba4eada6cd62befed52262ee15d4","creator":"dernst","file_name":"2013_TechRep_Henzinger.pdf","relation":"main_file","content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"6440","pubrep_id":"124","abstract":[{"text":"In order to guarantee that each method of a data structure updates the logical state exactly once, al-most all non-blocking implementations employ Compare-And-Swap (CAS) based synchronization. For FIFO  queue  implementations  this  translates  into  concurrent  enqueue  or  dequeue  methods competing among themselves to update the same variable, the tail or the head, respectively, leading to high contention and poor scalability. Recent non-blocking queue implementations try to alleviate high contentionby increasing the number of contention points, all the while using CAS-based synchronization. Furthermore, obtaining a wait-free implementation with competition is achieved by additional synchronization which leads to further degradation of performance.In this paper we formalize the notion of competitiveness of a synchronizing statement which can beused as a measure for the scalability of concurrent implementations.  We present a new queue implementation, the Speculative Pairing (SP) queue, which, as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead of CAS. We prove that the SP queue is linearizable and lock-free.We also show that replacing CAS with FAI leads to wait-freedom for dequeue methods without an adverse effect on performance.  In fact, our experiments suggest that the SP queue can perform and scale better than the state-of-the-art queue implementations.","lang":"eng"}],"page":"23","date_published":"2013-06-13T00:00:00Z","status":"public","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"day":"13","publisher":"IST Austria","date_updated":"2020-07-14T23:06:19Z","department":[{"_id":"ToHe"}],"title":"Replacing competition with cooperation to achieve scalable lock-free FIFO queues ","doi":"10.15479/AT:IST-2013-124-v1-1","type":"technical_report","oa":1,"has_accepted_license":"1","year":"2013"},{"department":[{"_id":"PeJo"}],"quality_controlled":"1","pmid":1,"publication_status":"published","publisher":"De Gruyter","type":"journal_article","volume":58,"oa_version":"Submitted Version","date_created":"2021-12-01T14:35:35Z","abstract":[{"text":"Stimfit is a free cross-platform software package for viewing and analyzing electrophysiological data. It supports most standard file types for cellular neurophysiology and other biomedical formats. Its analysis algorithms have been used and validated in several experimental laboratories. Its embedded Python scripting interface makes Stimfit highly extensible and customizable.","lang":"eng"}],"publication":"Biomedical Engineering / Biomedizinische Technik","date_published":"2013-08-01T00:00:00Z","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"        58","doi":"10.1515/bmt-2013-4181","title":"Stimfit: A fast visualization and analysis environment for cellular neurophysiology","external_id":{"pmid":["24042795"]},"day":"01","publication_identifier":{"issn":["0013-5585"],"eissn":["1862-278X"]},"date_updated":"2021-12-02T12:51:12Z","conference":{"location":"Graz, Austria","name":"BMT: Biomedizinische Technik ","start_date":"2013-09-19","end_date":"2013-09-21"},"has_accepted_license":"1","year":"2013","oa":1,"article_processing_charge":"No","file":[{"date_updated":"2021-12-01T14:38:08Z","date_created":"2021-12-01T14:38:08Z","access_level":"open_access","success":1,"file_id":"10397","file_size":149825,"checksum":"cdfc5339b530a25d6079f7223f0b1f16","creator":"schloegl","relation":"main_file","file_name":"Schloegl_Abstract-BMT2013.pdf","content_type":"application/pdf"}],"author":[{"last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"full_name":"Schmidt-Hieber, C.","first_name":"C.","last_name":"Schmidt-Hieber"},{"first_name":"S. J.","last_name":"Guzman","full_name":"Guzman, S. J."}],"article_number":"000010151520134181","file_date_updated":"2021-12-01T14:38:08Z","month":"08","article_type":"original","ddc":["005","610"],"keyword":["biomedical engineering","data analysis","free software"],"citation":{"ieee":"A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A fast visualization and analysis environment for cellular neurophysiology,” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G. De Gruyter, 2013.","chicago":"Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>. De Gruyter, 2013. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>.","short":"A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering / Biomedizinische Technik 58 (2013).","mla":"Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” <i>Biomedical Engineering / Biomedizinische Technik</i>, vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>.","ama":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. 2013;58(SI-1-Track-G). doi:<a href=\"https://doi.org/10.1515/bmt-2013-4181\">10.1515/bmt-2013-4181</a>","apa":"Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., &#38; Guzman, S. J. (2013). Stimfit: A fast visualization and analysis environment for cellular neurophysiology. <i>Biomedical Engineering / Biomedizinische Technik</i>. Graz, Austria: De Gruyter. <a href=\"https://doi.org/10.1515/bmt-2013-4181\">https://doi.org/10.1515/bmt-2013-4181</a>","ista":"Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization and analysis environment for cellular neurophysiology. Biomedical Engineering / Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181."},"issue":"SI-1-Track-G","language":[{"iso":"eng"}],"_id":"10396"},{"type":"journal_article","volume":153,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2013.02.033"}],"publisher":"Elsevier","publication_status":"published","quality_controlled":"1","pmid":1,"department":[{"_id":"DaZi"}],"intvolume":"       153","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"Cell","status":"public","date_published":"2013-03-28T00:00:00Z","abstract":[{"text":"Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway.","lang":"eng"}],"date_created":"2021-06-04T12:23:28Z","extern":"1","scopus_import":"1","oa_version":"Published Version","oa":1,"article_processing_charge":"No","year":"2013","date_updated":"2021-12-14T08:25:35Z","day":"28","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"external_id":{"pmid":["23540698"]},"doi":"10.1016/j.cell.2013.02.033","title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","_id":"9459","language":[{"iso":"eng"}],"issue":"1","page":"193-205","citation":{"ama":"Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. 2013;153(1):193-205. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>","apa":"Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>","ista":"Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 153(1), 193–205.","ieee":"A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>, vol. 153, no. 1. Elsevier, pp. 193–205, 2013.","chicago":"Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">https://doi.org/10.1016/j.cell.2013.02.033</a>.","mla":"Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>, vol. 153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.02.033\">10.1016/j.cell.2013.02.033</a>.","short":"A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K. Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205."},"article_type":"original","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"last_name":"Hsieh","first_name":"Ping-Hung","full_name":"Hsieh, Ping-Hung"},{"last_name":"Coleman-Derr","first_name":"Devin","full_name":"Coleman-Derr, Devin"},{"full_name":"Eshed-Williams, Leor","first_name":"Leor","last_name":"Eshed-Williams"},{"full_name":"Thao, Ka","first_name":"Ka","last_name":"Thao"},{"first_name":"Stacey L.","last_name":"Harmer","full_name":"Harmer, Stacey L."},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"}],"month":"03"},{"year":"2013","oa":1,"article_processing_charge":"No","external_id":{"pmid":["23613580"]},"doi":"10.1073/pnas.1306164110","title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","date_updated":"2021-12-14T08:26:44Z","day":"07","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"issue":"19","page":"7934-7939","_id":"9481","language":[{"iso":"eng"}],"author":[{"last_name":"Rodrigues","first_name":"Jessica A.","full_name":"Rodrigues, Jessica A."},{"full_name":"Ruan, Randy","last_name":"Ruan","first_name":"Randy"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"last_name":"Sharma","first_name":"Manoj K.","full_name":"Sharma, Manoj K."},{"first_name":"Rita","last_name":"Sharma","full_name":"Sharma, Rita"},{"full_name":"Ronald, Pamela C","last_name":"Ronald","first_name":"Pamela C"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"month":"05","keyword":["Multidisciplinary"],"citation":{"apa":"Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald, P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>","ista":"Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. Proceedings of the National Academy of Sciences. 110(19), 7934–7939.","ama":"Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2013;110(19):7934-7939. doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>","short":"J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110 (2013) 7934–7939.","mla":"Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7934–39, doi:<a href=\"https://doi.org/10.1073/pnas.1306164110\">10.1073/pnas.1306164110</a>.","ieee":"J. A. Rodrigues <i>et al.</i>, “Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 110, no. 19. National Academy of Sciences, pp. 7934–7939, 2013.","chicago":"Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted Expression of Genes and Small RNA Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1306164110\">https://doi.org/10.1073/pnas.1306164110</a>."},"article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1306164110"}],"type":"journal_article","volume":110,"quality_controlled":"1","pmid":1,"department":[{"_id":"DaZi"}],"publisher":"National Academy of Sciences","publication_status":"published","publication":"Proceedings of the National Academy of Sciences","date_published":"2013-05-07T00:00:00Z","status":"public","abstract":[{"text":"Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo, exhibits extensive localized DNA demethylation on maternally inherited chromosomes. Demethylation mediates parent-of-origin–specific (imprinted) gene expression but is apparently unnecessary for the extensive accumulation of maternally biased small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation is generally parent-of-origin specific is unknown. Imprinted expression of sRNA also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing of the Kitaake rice cultivar that enabled us to show that localized hypomethylation in rice endosperm occurs solely on the maternal genome, preferring regions of high DNA accessibility. Maternally expressed imprinted genes are enriched for hypomethylation at putative promoter regions and transcriptional termini and paternally expressed genes at promoters and gene bodies, mirroring our recent results in A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are expressed from both parental genomes and correlate with hypomethylation. Overlaps between imprinted sRNA loci and imprinted genes expressed from opposite alleles suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling tissues primarily originate from small class II (cut-and-paste) transposable elements, those in endosperm are more uniformly derived, including sequences from other transposon classes, as well as genic and intergenic regions. Our data indicate that the endosperm exhibits a unique pattern of sRNA expression and suggest that localized hypomethylation of maternal endosperm DNA is conserved in flowering plants.","lang":"eng"}],"intvolume":"       110","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","date_created":"2021-06-07T07:31:02Z","scopus_import":"1","extern":"1"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2013.01.014"}],"type":"journal_article","volume":24,"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"quality_controlled":"1","pmid":1,"publication_status":"published","publisher":"Elsevier","abstract":[{"lang":"eng","text":"Plants undergo alternation of generation in which reproductive cells develop in the plant body (\"sporophytic generation\") and then differentiate into a multicellular gamete-forming \"gametophytic generation.\" Different populations of helper cells assist in this transgenerational journey, with somatic tissues supporting early development and single nurse cells supporting gametogenesis. New data reveal a two-way relationship between early reproductive cells and their helpers involving complex epigenetic and signaling networks determining cell number and fate. Later, the egg cell plays a central role in specifying accessory cells, whereas in both gametophytes, companion cells contribute non-cell-autonomously to the epigenetic landscape of the gamete genomes."}],"publication":"Developmental Cell","status":"public","date_published":"2013-02-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        24","oa_version":"Published Version","scopus_import":"1","extern":"1","date_created":"2021-06-08T06:14:50Z","year":"2013","oa":1,"article_processing_charge":"No","doi":"10.1016/j.devcel.2013.01.014","title":"A conversation across generations: Soma-germ cell crosstalk in plants","external_id":{"pmid":["23410937"]},"day":"11","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"date_updated":"2023-05-08T11:00:59Z","page":"215-225","issue":"3","_id":"9520","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"},{"full_name":"Dickinson, Hugh","first_name":"Hugh","last_name":"Dickinson"}],"month":"02","article_type":"review","citation":{"chicago":"Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>.","ieee":"X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations: Soma-germ cell crosstalk in plants,” <i>Developmental Cell</i>, vol. 24, no. 3. Elsevier, pp. 215–225, 2013.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.","mla":"Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk in Plants.” <i>Developmental Cell</i>, vol. 24, no. 3, Elsevier, 2013, pp. 215–25, doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>.","ama":"Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. 2013;24(3):215-225. doi:<a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">10.1016/j.devcel.2013.01.014</a>","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.","apa":"Feng, X., Zilberman, D., &#38; Dickinson, H. (2013). A conversation across generations: Soma-germ cell crosstalk in plants. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2013.01.014\">https://doi.org/10.1016/j.devcel.2013.01.014</a>"}},{"oa_version":"Published Version","author":[{"full_name":"Zagorsky, Benjamin","first_name":"Benjamin","last_name":"Zagorsky"},{"first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"month":"12","date_created":"2021-07-28T15:45:07Z","citation":{"ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . 2013. doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>","ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma , Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>.","apa":"Zagorsky, B., Reiter, J., Chatterjee, K., &#38; Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>","chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">https://doi.org/10.1371/journal.pone.0080814.s001</a>.","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013.","mla":"Zagorsky, Benjamin, et al. <i>Forgiver Triumphs in Alternating Prisoner’s Dilemma </i>. Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814.s001\">10.1371/journal.pone.0080814.s001</a>.","short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013)."},"abstract":[{"lang":"eng","text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise."}],"date_published":"2013-12-12T00:00:00Z","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9749","doi":"10.1371/journal.pone.0080814.s001","department":[{"_id":"KrCh"}],"title":"Forgiver triumphs in alternating prisoner's dilemma ","day":"12","date_updated":"2023-02-23T10:34:39Z","publisher":"Public Library of Science","related_material":{"record":[{"relation":"used_in_publication","id":"2247","status":"public"}]},"year":"2013","type":"research_data_reference","article_processing_charge":"No"},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"2853"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.b1q2n","open_access":"1"}],"year":"2013","type":"research_data_reference","oa":1,"article_processing_charge":"No","doi":"10.5061/dryad.b1q2n","title":"Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection","department":[{"_id":"CaGu"}],"day":"21","date_updated":"2023-10-18T06:43:22Z","publisher":"Dryad","abstract":[{"text":"High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.","lang":"eng"}],"status":"public","date_published":"2013-03-21T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9751","oa_version":"Published Version","author":[{"full_name":"Refardt, Dominik","first_name":"Dominik","last_name":"Refardt"},{"last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Kümmerli, Rolf","last_name":"Kümmerli","first_name":"Rolf"}],"month":"03","date_created":"2021-07-30T08:08:09Z","citation":{"chicago":"Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>.","ieee":"D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.” Dryad, 2013.","mla":"Refardt, Dominik, et al. <i>Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>.","short":"D. Refardt, T. Bergmiller, R. Kümmerli, (2013).","ama":"Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>","ista":"Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection, Dryad, <a href=\"https://doi.org/10.5061/dryad.b1q2n\">10.5061/dryad.b1q2n</a>.","apa":"Refardt, D., Bergmiller, T., &#38; Kümmerli, R. (2013). Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. Dryad. <a href=\"https://doi.org/10.5061/dryad.b1q2n\">https://doi.org/10.5061/dryad.b1q2n</a>"}},{"type":"research_data_reference","article_processing_charge":"No","oa":1,"related_material":{"record":[{"id":"2170","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r3r60"}],"year":"2013","day":"01","publisher":"Dryad","date_updated":"2023-02-23T10:31:17Z","department":[{"_id":"NiBa"}],"title":"Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies","doi":"10.5061/dryad.r3r60","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9754","abstract":[{"text":"Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.","lang":"eng"}],"date_published":"2013-10-01T00:00:00Z","status":"public","citation":{"apa":"Hearn, J., Stone, G., Barton, N. H., Lohse, K., &#38; Bunnefeld, L. (2013). Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. Dryad. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>","ista":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies, Dryad, <a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>.","ama":"Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies. 2013. doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>","mla":"Hearn, Jack, et al. <i>Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies</i>. Dryad, 2013, doi:<a href=\"https://doi.org/10.5061/dryad.r3r60\">10.5061/dryad.r3r60</a>.","short":"J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).","ieee":"J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies.” Dryad, 2013.","chicago":"Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low Coverage de Novo Genome Assemblies.” Dryad, 2013. <a href=\"https://doi.org/10.5061/dryad.r3r60\">https://doi.org/10.5061/dryad.r3r60</a>."},"date_created":"2021-07-30T08:31:22Z","month":"10","author":[{"last_name":"Hearn","first_name":"Jack","full_name":"Hearn, Jack"},{"first_name":"Graham","last_name":"Stone","full_name":"Stone, Graham"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"},{"full_name":"Bunnefeld, Lynsey","first_name":"Lynsey","last_name":"Bunnefeld"}],"oa_version":"Published Version"},{"date_created":"2018-12-11T11:57:41Z","scopus_import":"1","oa_version":"Published Version","intvolume":"       200","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4460","publication":"New Phytologist","status":"public","date_published":"2013-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery."}],"publisher":"Wiley","publication_status":"published","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"department":[{"_id":"JiFr"}],"type":"journal_article","volume":200,"main_file_link":[{"url":"https://doi.org/10.1111/nph.12437","open_access":"1"}],"ddc":["580"],"citation":{"short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>.","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>"},"article_type":"original","das_tickbox":"1","author":[{"last_name":"Simon","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"last_name":"Kubeš","first_name":"Martin","full_name":"Kubeš, Martin"},{"full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Baster"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"}],"month":"12","language":[{"iso":"eng"}],"_id":"2443","acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","issue":"4","page":"1034 - 1048","date_updated":"2026-06-18T07:49:41Z","day":"01","doi":"10.1111/nph.12437","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","oa":1,"article_processing_charge":"No","year":"2013","ec_funded":1},{"day":"01","date_updated":"2026-06-18T07:50:03Z","title":"Faster algorithms for Markov decision processes with low treewidth","doi":"10.1007/978-3-642-39799-8_36","external_id":{"arxiv":["1304.0084"]},"article_processing_charge":"No","oa":1,"series_title":"Lecture Notes in Computer Science","conference":{"location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification","start_date":"2013-07-13","end_date":"2013-07-19"},"ec_funded":1,"year":"2013","das_tickbox":"1","citation":{"apa":"Chatterjee, K., &#38; Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>","ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558.","ama":"Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.","mla":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. <i>Faster Algorithms for Markov Decision Processes with Low Treewidth</i>. Vol. 8044, Springer, 2013, pp. 543–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>.","ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.","chicago":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>."},"arxiv":1,"ddc":["000"],"month":"07","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Jakub","last_name":"Ła̧Cki","full_name":"Ła̧Cki, Jakub"}],"_id":"2444","language":[{"iso":"eng"}],"page":"543 - 558","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","volume":8044,"type":"conference","main_file_link":[{"url":"http://arxiv.org/abs/1304.0084","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","date_created":"2018-12-11T11:57:42Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      8044","abstract":[{"lang":"eng","text":"We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time."}],"status":"public","date_published":"2013-07-01T00:00:00Z","publist_id":"4459"},{"volume":2,"type":"journal_article","publisher":"MDPI","publication_status":"published","pmid":1,"quality_controlled":"1","department":[{"_id":"JiFr"}],"tmp":{"short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png"},"license":"https://creativecommons.org/licenses/by/3.0/","intvolume":"         2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2013-10-21T00:00:00Z","publication":"Plants","abstract":[{"lang":"eng","text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. "}],"date_created":"2022-03-21T07:13:49Z","scopus_import":"1","oa_version":"Published Version","article_processing_charge":"No","oa":1,"year":"2013","has_accepted_license":"1","date_updated":"2022-03-21T12:15:29Z","publication_identifier":{"issn":["2223-7747"]},"day":"21","external_id":{"pmid":["27137397"]},"title":"Calcium: The missing link in auxin action","doi":"10.3390/plants2040650","_id":"10895","language":[{"iso":"eng"}],"issue":"4","page":"650-675","citation":{"apa":"Vanneste, S., &#38; Friml, J. (2013). Calcium: The missing link in auxin action. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.","ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. <i>Plants</i>. 2013;2(4):650-675. doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:<a href=\"https://doi.org/10.3390/plants2040650\">10.3390/plants2040650</a>.","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675.","ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” <i>Plants</i>, vol. 2, no. 4. MDPI, pp. 650–675, 2013.","chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” <i>Plants</i>. MDPI, 2013. <a href=\"https://doi.org/10.3390/plants2040650\">https://doi.org/10.3390/plants2040650</a>."},"keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"ddc":["580"],"article_type":"original","file_date_updated":"2022-03-21T12:12:56Z","month":"10","author":[{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_size":670188,"file_id":"10916","success":1,"access_level":"open_access","date_created":"2022-03-21T12:12:56Z","date_updated":"2022-03-21T12:12:56Z","content_type":"application/pdf","relation":"main_file","file_name":"2013_Plants_Vanneste.pdf","checksum":"fb4ff2e820e344e253c9197544610be6","creator":"dernst"}]},{"intvolume":"      7877","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2013-06-01T00:00:00Z","status":"public","publication":"Graph-Based Representations in Pattern Recognition","abstract":[{"text":"Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing.","lang":"eng"}],"date_created":"2022-03-21T07:30:33Z","scopus_import":"1","oa_version":"None","volume":7877,"type":"conference","publisher":"Springer Nature","publication_status":"published","project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"quality_controlled":"1","department":[{"_id":"HeEd"}],"acknowledgement":"This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.","language":[{"iso":"eng"}],"_id":"10897","place":"Berlin, Heidelberg","page":"182-183","citation":{"ama":"Edelsbrunner H. Persistent homology in image processing. In: <i>Graph-Based Representations in Pattern Recognition</i>. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>","apa":"Edelsbrunner, H. (2013). Persistent homology in image processing. In <i>Graph-Based Representations in Pattern Recognition</i> (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>","ista":"Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183.","ieee":"H. Edelsbrunner, “Persistent homology in image processing,” in <i>Graph-Based Representations in Pattern Recognition</i>, Vienna, Austria, 2013, vol. 7877, pp. 182–183.","chicago":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In <i>Graph-Based Representations in Pattern Recognition</i>, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. <a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">https://doi.org/10.1007/978-3-642-38221-5_19</a>.","short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.","mla":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” <i>Graph-Based Representations in Pattern Recognition</i>, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:<a href=\"https://doi.org/10.1007/978-3-642-38221-5_19\">10.1007/978-3-642-38221-5_19</a>."},"month":"06","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"article_processing_charge":"No","year":"2013","ec_funded":1,"series_title":"LNCS","conference":{"name":"GbRPR: Graph-based Representations in Pattern Recognition","location":"Vienna, Austria","end_date":"2013-05-17","start_date":"2013-05-15"},"date_updated":"2023-09-05T15:10:20Z","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783642382208"],"eisbn":["9783642382215"]},"day":"01","title":"Persistent homology in image processing","doi":"10.1007/978-3-642-38221-5_19"},{"article_processing_charge":"No","type":"conference","year":"2013","conference":{"start_date":"2013-05-14","end_date":"2013-05-16","location":"Ischia, Italy","name":"CF: Conference on Computing Frontiers"},"publisher":"ACM Press","date_updated":"2022-06-21T08:01:19Z","publication_identifier":{"isbn":["978-145032053-5"]},"publication_status":"published","day":"01","quality_controlled":"1","department":[{"_id":"ToHe"}],"title":"Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation","doi":"10.1145/2482767.2482789","language":[{"iso":"eng"}],"_id":"10898","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-05-01T00:00:00Z","status":"public","publication":"Proceedings of the ACM International Conference on Computing Frontiers - CF '13","issue":"5","abstract":[{"lang":"eng","text":"A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered."}],"citation":{"ista":"Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin A. 2013. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17.","apa":"Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch, C. M., &#38; Sezgin, A. (2013). Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. Ischia, Italy: ACM Press. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>","ama":"Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In: <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM Press; 2013. doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>","short":"A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch, A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, ACM Press, 2013.","mla":"Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, no. 5, 17, ACM Press, 2013, doi:<a href=\"https://doi.org/10.1145/2482767.2482789\">10.1145/2482767.2482789</a>.","chicago":"Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” In <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>. ACM Press, 2013. <a href=\"https://doi.org/10.1145/2482767.2482789\">https://doi.org/10.1145/2482767.2482789</a>.","ieee":"A. Haas <i>et al.</i>, “Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation,” in <i>Proceedings of the ACM International Conference on Computing Frontiers - CF ’13</i>, Ischia, Italy, 2013, no. 5."},"date_created":"2022-03-21T07:33:22Z","scopus_import":"1","article_number":"17","month":"05","oa_version":"None","author":[{"last_name":"Haas","first_name":"Andreas","full_name":"Haas, Andreas"},{"full_name":"Lippautz, Michael","first_name":"Michael","last_name":"Lippautz"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hannes","last_name":"Payer","full_name":"Payer, Hannes"},{"full_name":"Sokolova, Ana","first_name":"Ana","last_name":"Sokolova"},{"last_name":"Kirsch","first_name":"Christoph M.","full_name":"Kirsch, Christoph M."},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","last_name":"Sezgin"}]}]