[{"_id":"5402","year":"2013","date_created":"2018-12-12T11:39:07Z","page":"16","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Linearizability requires that the outcome of calls by competing threads to a concurrent data structure is the same as some sequential execution where each thread has exclusive access to the data structure. In an ordered data structure, such as a queue or a stack, linearizability is ensured by requiring threads commit in the order dictated by the sequential semantics of the data structure; e.g., in a concurrent queue implementation a dequeue can only remove the oldest element. \r\nIn this paper, we investigate the impact of this strict ordering, by comparing what linearizability allows to what existing implementations do. We first give an operational definition for linearizability which allows us to build the most general linearizable implementation as a transition system for any given sequential specification. We then use this operational definition to categorize linearizable implementations based on whether they are bound or free. In a bound implementation, whenever all threads observe the same logical state, the updates to the logical state and the temporal order of commits coincide. All existing queue implementations we know of are bound. We then proceed to present, to the best of our knowledge, the first ever free queue implementation. Our experiments show that free implementations have the potential for better performance by suffering less from contention."}],"file":[{"date_updated":"2020-07-14T12:46:45Z","relation":"main_file","date_created":"2018-12-12T11:53:19Z","file_id":"5480","file_name":"IST-2013-123-v1+1_main-concur2013.pdf","creator":"system","access_level":"open_access","file_size":249790,"content_type":"application/pdf","checksum":"ce580605ae9756a8c99d7b403ebb8eed"}],"month":"06","publisher":"IST Austria","department":[{"_id":"ToHe"}],"publication_status":"published","oa":1,"publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"12","file_date_updated":"2020-07-14T12:46:45Z","citation":{"ama":"Henzinger TA, Sezgin A. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">10.15479/AT:IST-2013-123-v1-1</a>","apa":"Henzinger, T. A., &#38; Sezgin, A. (2013). <i>How free is your linearizable concurrent data structure?</i> IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">https://doi.org/10.15479/AT:IST-2013-123-v1-1</a>","ieee":"T. A. Henzinger and A. Sezgin, <i>How free is your linearizable concurrent data structure?</i> IST Austria, 2013.","mla":"Henzinger, Thomas A., and Ali Sezgin. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">10.15479/AT:IST-2013-123-v1-1</a>.","ista":"Henzinger TA, Sezgin A. 2013. How free is your linearizable concurrent data structure?, IST Austria, 16p.","chicago":"Henzinger, Thomas A, and Ali Sezgin. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">https://doi.org/10.15479/AT:IST-2013-123-v1-1</a>.","short":"T.A. Henzinger, A. Sezgin, How Free Is Your Linearizable Concurrent Data Structure?, IST Austria, 2013."},"type":"technical_report","author":[{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sezgin","first_name":"Ali","full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2020-07-14T23:04:47Z","pubrep_id":"123","ddc":["000","004"],"alternative_title":["IST Austria Technical Report"],"has_accepted_license":"1","title":"How free is your linearizable concurrent data structure?","status":"public","language":[{"iso":"eng"}],"date_published":"2013-06-12T00:00:00Z","doi":"10.15479/AT:IST-2013-123-v1-1"},{"pubrep_id":"126","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"}],"type":"technical_report","date_updated":"2023-02-23T12:22:53Z","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, Qualitative Analysis of Concurrent Mean-Payoff Games, IST Austria, 2013.","ieee":"K. Chatterjee and R. Ibsen-Jensen, <i>Qualitative analysis of concurrent mean-payoff games</i>. IST Austria, 2013.","ama":"Chatterjee K, Ibsen-Jensen R. <i>Qualitative Analysis of Concurrent Mean-Payoff Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">10.15479/AT:IST-2013-126-v1-1</a>","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). <i>Qualitative analysis of concurrent mean-payoff games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">https://doi.org/10.15479/AT:IST-2013-126-v1-1</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>Qualitative Analysis of Concurrent Mean-Payoff Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">10.15479/AT:IST-2013-126-v1-1</a>.","ista":"Chatterjee K, Ibsen-Jensen R. 2013. Qualitative analysis of concurrent mean-payoff games, IST Austria, 33p.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>Qualitative Analysis of Concurrent Mean-Payoff Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">https://doi.org/10.15479/AT:IST-2013-126-v1-1</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"oa":1,"day":"03","file_date_updated":"2020-07-14T12:46:45Z","language":[{"iso":"eng"}],"status":"public","title":"Qualitative analysis of concurrent mean-payoff games","doi":"10.15479/AT:IST-2013-126-v1-1","date_published":"2013-07-03T00:00:00Z","alternative_title":["IST Austria Technical Report"],"ddc":["000","005"],"has_accepted_license":"1","page":"33","year":"2013","_id":"5403","date_created":"2018-12-12T11:39:08Z","file":[{"file_id":"5510","relation":"main_file","date_created":"2018-12-12T11:53:49Z","file_name":"IST-2013-126-v1+1_soda_full.pdf","date_updated":"2020-07-14T12:46:45Z","file_size":434523,"content_type":"application/pdf","checksum":"063868c665beec37bf28160e2a695746","access_level":"open_access","creator":"system"}],"abstract":[{"lang":"eng","text":"We consider concurrent games played by two-players on a finite state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to every transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of mean-payoff games) that is not known to be in polynomial time."}],"publisher":"IST Austria","related_material":{"record":[{"status":"public","id":"524","relation":"later_version"}]},"publication_status":"published","department":[{"_id":"KrCh"}],"month":"07","oa_version":"Published Version"},{"date_created":"2018-12-12T11:39:08Z","_id":"5404","year":"2013","page":"29","oa_version":"Published Version","month":"07","department":[{"_id":"KrCh"}],"publisher":"IST Austria","publication_status":"published","related_material":{"record":[{"relation":"later_version","id":"2162","status":"public"}]},"abstract":[{"lang":"eng","text":"We study finite-state two-player (zero-sum) concurrent mean-payoff games played on a graph. We focus on the important sub-class of ergodic games where all states are visited infinitely often with probability 1. The algorithmic study of ergodic games was initiated in a seminal work of Hoffman and Karp in 1966, but all basic complexity questions have remained unresolved. Our main results for ergodic games are as follows: We establish (1) an optimal exponential bound on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy); (2) the approximation problem lie in FNP; (3) the approximation problem is at least as hard as the decision problem for simple stochastic games (for which NP and coNP is the long-standing best known bound). We show that the exact value can be expressed in the existential theory of the reals, and also establish square-root sum hardness for a related class of games."}],"file":[{"file_name":"IST-2013-127-v1+1_ergodic.pdf","file_id":"5496","relation":"main_file","date_created":"2018-12-12T11:53:35Z","date_updated":"2020-07-14T12:46:45Z","checksum":"79ee5e677a82611ce06e0360c69d494a","content_type":"application/pdf","file_size":517275,"access_level":"open_access","creator":"system"}],"file_date_updated":"2020-07-14T12:46:45Z","day":"03","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"type":"technical_report","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, The Complexity of Ergodic Games, IST Austria, 2013.","ista":"Chatterjee K, Ibsen-Jensen R. 2013. The complexity of ergodic games, IST Austria, 29p.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>The Complexity of Ergodic Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">https://doi.org/10.15479/AT:IST-2013-127-v1-1</a>.","ieee":"K. Chatterjee and R. Ibsen-Jensen, <i>The complexity of ergodic games</i>. IST Austria, 2013.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). <i>The complexity of ergodic games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">https://doi.org/10.15479/AT:IST-2013-127-v1-1</a>","ama":"Chatterjee K, Ibsen-Jensen R. <i>The Complexity of Ergodic Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">10.15479/AT:IST-2013-127-v1-1</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>The Complexity of Ergodic Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">10.15479/AT:IST-2013-127-v1-1</a>."},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-02-23T10:30:55Z","pubrep_id":"127","has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"ddc":["000","005"],"date_published":"2013-07-03T00:00:00Z","doi":"10.15479/AT:IST-2013-127-v1-1","status":"public","title":"The complexity of ergodic games","language":[{"iso":"eng"}]},{"page":"22","year":"2013","_id":"5405","date_created":"2018-12-12T11:39:09Z","file":[{"relation":"main_file","date_created":"2018-12-12T11:53:54Z","file_id":"5516","file_name":"IST-2013-128-v1+1_full_stoch_mpp.pdf","date_updated":"2020-07-14T12:46:45Z","content_type":"application/pdf","file_size":387467,"checksum":"ede787a10e74e4f7db302fab8f12f3ca","creator":"system","access_level":"open_access"}],"abstract":[{"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).","lang":"eng"}],"department":[{"_id":"KrCh"}],"related_material":{"record":[{"relation":"later_version","id":"2212","status":"public"}]},"publication_status":"published","publisher":"IST Austria","month":"07","oa_version":"Published Version","pubrep_id":"128","citation":{"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>.","ista":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2013. Perfect-information stochastic mean-payoff parity games, IST Austria, 22p.","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>.","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>","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, <i>Perfect-information stochastic mean-payoff parity games</i>. IST Austria, 2013."},"date_updated":"2023-02-23T10:33:08Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"last_name":"Gimbert","first_name":"Hugo","full_name":"Gimbert, Hugo"},{"first_name":"Youssouf","last_name":"Oualhadj","full_name":"Oualhadj, Youssouf"}],"type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"oa":1,"file_date_updated":"2020-07-14T12:46:45Z","day":"08","language":[{"iso":"eng"}],"status":"public","title":"Perfect-information stochastic mean-payoff parity games","doi":"10.15479/AT:IST-2013-128-v1-1","date_published":"2013-07-08T00:00:00Z","alternative_title":["IST Austria Technical Report"],"ddc":["000","005","510"],"has_accepted_license":"1"},{"oa_version":"Published Version","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"IST Austria","publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"1376"}]},"month":"07","file":[{"file_name":"IST-2013-130-v1+1_Distributed_Synthesis.pdf","file_id":"5540","relation":"main_file","date_created":"2018-12-12T11:54:18Z","date_updated":"2020-07-14T12:46:45Z","checksum":"855513ebaf6f72228800c5fdb522f93c","content_type":"application/pdf","file_size":467895,"access_level":"open_access","creator":"system"}],"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"}],"date_created":"2018-12-12T11:39:09Z","year":"2013","_id":"5406","page":"11","has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"ddc":["005"],"doi":"10.15479/AT:IST-2013-130-v1-1","date_published":"2013-07-08T00:00:00Z","language":[{"iso":"eng"}],"title":"Distributed synthesis for LTL Fragments","status":"public","file_date_updated":"2020-07-14T12:46:45Z","day":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"oa":1,"pubrep_id":"130","type":"technical_report","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas"}],"citation":{"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>.","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>","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>","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>.","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL Fragments, IST Austria, 11p.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, Distributed Synthesis for LTL Fragments, IST Austria, 2013."},"date_updated":"2023-02-21T17:01:26Z"},{"month":"09","publisher":"IST Austria","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","id":"2213","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. "}],"file":[{"date_updated":"2020-07-14T12:46:46Z","file_name":"IST-2013-141-v1+1_main-tech-rpt.pdf","file_id":"5477","date_created":"2018-12-12T11:53:16Z","relation":"main_file","access_level":"open_access","creator":"system","checksum":"226bc791124f8d3138379778ce834e86","content_type":"application/pdf","file_size":300481}],"oa_version":"Published Version","page":"17","date_created":"2018-12-12T11:39:10Z","_id":"5408","year":"2013","date_published":"2013-09-12T00:00:00Z","doi":"10.15479/AT:IST-2013-141-v1-1","title":"The complexity of partial-observation stochastic parity games with finite-memory strategies","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"ddc":["000","005"],"type":"technical_report","date_updated":"2023-02-23T10:33:11Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"first_name":"Sumit","last_name":"Nain","full_name":"Nain, Sumit"},{"full_name":"Vardi, Moshe","first_name":"Moshe","last_name":"Vardi"}],"citation":{"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.","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>.","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.","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>","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>","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>.","short":"K. Chatterjee, L. Doyen, S. Nain, M. Vardi, The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies, IST Austria, 2013."},"pubrep_id":"141","day":"12","file_date_updated":"2020-07-14T12:46:46Z","oa":1,"publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"page":"12","year":"2013","_id":"5409","date_created":"2018-12-12T11:39:10Z","file":[{"creator":"system","access_level":"open_access","checksum":"0f7633081ba8299c543322f0ad08571f","file_size":336377,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:46Z","file_name":"IST-2013-144-v1+1_main.pdf","relation":"main_file","date_created":"2018-12-12T11:53:08Z","file_id":"5469"}],"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."}],"department":[{"_id":"KrCh"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"2216"}]},"publication_status":"published","publisher":"IST Austria","month":"10","oa_version":"Published Version","pubrep_id":"144","date_updated":"2023-02-23T10:33:18Z","citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Majumdar R. 2013. Edit distance for timed automata, IST Austria, 12p.","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>.","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>","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>","ieee":"K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, <i>Edit distance for timed automata</i>. IST Austria, 2013.","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."},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Majumdar","first_name":"Rupak","full_name":"Majumdar, Rupak"}],"type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"day":"30","file_date_updated":"2020-07-14T12:46:46Z","language":[{"iso":"eng"}],"title":"Edit distance for timed automata","status":"public","doi":"10.15479/AT:IST-2013-144-v1-1","date_published":"2013-10-30T00:00:00Z","alternative_title":["IST Austria Technical Report"],"ddc":["000"],"has_accepted_license":"1"},{"alternative_title":["IST Austria Technical Report"],"ddc":["000","005"],"has_accepted_license":"1","language":[{"iso":"eng"}],"title":"Automatic generation of alternative starting positions for traditional board games","status":"public","doi":"10.15479/AT:IST-2013-146-v1-1","date_published":"2013-12-03T00:00:00Z","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"day":"03","file_date_updated":"2020-07-14T12:46:46Z","pubrep_id":"146","type":"technical_report","author":[{"full_name":"Ahmed, Umair","last_name":"Ahmed","first_name":"Umair"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Gulwani, Sumit","last_name":"Gulwani","first_name":"Sumit"}],"citation":{"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>","ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, <i>Automatic generation of alternative starting positions for traditional board games</i>. 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>","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>.","ista":"Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative starting positions for traditional board games, IST Austria, 13p.","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>.","short":"U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative Starting Positions for Traditional Board Games, IST Austria, 2013."},"date_updated":"2023-02-23T10:00:50Z","oa_version":"Published Version","file":[{"access_level":"open_access","creator":"system","checksum":"409f3aaaf1184e4057b89cbb449dac80","content_type":"application/pdf","file_size":818189,"date_updated":"2020-07-14T12:46:46Z","file_name":"IST-2013-146-v1+1_main.pdf","file_id":"5528","date_created":"2018-12-12T11:54:06Z","relation":"main_file"}],"abstract":[{"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. ","lang":"eng"}],"publication_status":"published","publisher":"IST Austria","related_material":{"record":[{"status":"public","id":"1481","relation":"later_version"}]},"department":[{"_id":"KrCh"}],"month":"12","year":"2013","_id":"5410","date_created":"2018-12-12T11:39:10Z","page":"13"},{"publication":"Computer Aided Verification","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642397981","9783642397998"],"issn":["0302-9743"]},"oa":1,"author":[{"full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","last_name":"Dragoi","first_name":"Cezara"},{"first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"date_updated":"2023-09-05T14:16:07Z","citation":{"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.","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>","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>","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>.","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.","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>.","short":"C. Dragoi, A. Gupta, T.A. Henzinger, in:, Computer Aided Verification, Springer Berlin Heidelberg, Berlin, Heidelberg, 2013, pp. 174–190."},"has_accepted_license":"1","project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"}],"title":"Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates","year":"2013","_id":"5747","date_created":"2018-12-18T13:10:21Z","ec_funded":1,"series_title":"CAV","oa_version":"None","article_processing_charge":"No","quality_controlled":"1","file":[{"date_updated":"2020-07-14T12:47:10Z","file_id":"5748","relation":"main_file","date_created":"2018-12-18T13:13:33Z","file_name":"2013_CAV_Dragoi.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":236480,"checksum":"a901cc6b71db08b61c0d4c0cbacc6287"}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:47:10Z","volume":8044,"pubrep_id":"195","type":"book_chapter","ddc":["005"],"intvolume":"      8044","language":[{"iso":"eng"}],"status":"public","doi":"10.1007/978-3-642-39799-8_11","date_published":"2013-01-01T00:00:00Z","scopus_import":"1","place":"Berlin, Heidelberg","conference":{"end_date":"2013-07-19","start_date":"2013-07-13","name":"CAV 2013","location":"Saint Petersburg, Russia"},"page":"174-190","publisher":"Springer Berlin Heidelberg","department":[{"_id":"ToHe"}]},{"day":"13","file_date_updated":"2020-07-14T12:47:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"oa":1,"pubrep_id":"124","author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali"}],"date_updated":"2020-07-14T23:06:19Z","type":"technical_report","citation":{"short":"T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation to Achieve Scalable Lock-Free FIFO Queues , 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>.","ista":"Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation to achieve scalable lock-free FIFO queues , IST Austria, 23p.","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.","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>","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>"},"has_accepted_license":"1","alternative_title":["IST Austria Technical Report"],"ddc":["000","005"],"doi":"10.15479/AT:IST-2013-124-v1-1","date_published":"2013-06-13T00:00:00Z","language":[{"iso":"eng"}],"status":"public","title":"Replacing competition with cooperation to achieve scalable lock-free FIFO queues ","date_created":"2019-05-13T14:13:27Z","year":"2013","_id":"6440","page":"23","oa_version":"Published Version","publisher":"IST Austria","publication_status":"published","department":[{"_id":"ToHe"}],"month":"06","file":[{"date_updated":"2020-07-14T12:47:30Z","relation":"main_file","date_created":"2019-05-13T14:11:39Z","file_id":"6441","file_name":"2013_TechRep_Henzinger.pdf","creator":"dernst","access_level":"open_access","file_size":549684,"content_type":"application/pdf","checksum":"a219ba4eada6cd62befed52262ee15d4"}],"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"}]},{"date_created":"2018-12-11T11:48:43Z","ec_funded":1,"_id":"827","year":"2013","quality_controlled":"1","oa_version":"Published Version","publication_status":"published","abstract":[{"lang":"eng","text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed."}],"file":[{"file_name":"2013_FrontiersPlant_OBrien.pdf","file_id":"5903","relation":"main_file","date_created":"2019-01-31T10:40:38Z","date_updated":"2020-07-14T12:48:11Z","checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","file_size":953299,"content_type":"application/pdf","access_level":"open_access","creator":"dernst"}],"publist_id":"6821","day":"19","oa":1,"publication":"Frontiers in Plant Science","citation":{"short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","apa":"O’Brien, J., &#38; Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>","mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>, vol. 4, 451, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>.","ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451.","chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>."},"author":[{"full_name":"O'Brien, José","last_name":"O'Brien","first_name":"José"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"date_updated":"2021-01-12T08:17:50Z","has_accepted_license":"1","article_number":"451","title":"Cytokinin cross talking during biotic and abiotic stress responses","project":[{"grant_number":"207362","call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis"}],"scopus_import":1,"license":"https://creativecommons.org/licenses/by/4.0/","month":"11","publisher":"Frontiers Research Foundation","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:48:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":4,"intvolume":"         4","ddc":["580"],"date_published":"2013-11-19T00:00:00Z","doi":"10.3389/fpls.2013.00451","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}]},{"date_published":"2013-12-26T00:00:00Z","doi":"10.3389/fpls.2013.00537","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"intvolume":"         4","ddc":["580"],"type":"journal_article","volume":4,"file_date_updated":"2020-07-14T12:48:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","department":[{"_id":"EvBe"}],"publisher":"Frontiers Research Foundation","scopus_import":1,"title":"Systems approaches to study root architecture dynamics","project":[{"grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"}],"has_accepted_license":"1","article_number":"537","author":[{"full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","first_name":"Candela","last_name":"Cuesta"},{"orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková"}],"date_updated":"2021-01-12T08:17:52Z","citation":{"short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).","chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>.","ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537.","mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>, vol. 4, 537, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>.","apa":"Cuesta, C., Wabnik, K. T., &#38; Benková, E. (2013). Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>","ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013."},"publist_id":"6820","day":"26","oa":1,"publication":"Frontiers in Plant Science","publication_status":"published","abstract":[{"lang":"eng","text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed."}],"file":[{"date_updated":"2020-07-14T12:48:11Z","file_id":"5902","relation":"main_file","date_created":"2019-01-31T10:36:43Z","file_name":"2013_FrontiersPlant_Cuesta.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":710835,"checksum":"0185b3c4d7df9a94bd3ce5a66d213506"}],"quality_controlled":"1","oa_version":"Published Version","ec_funded":1,"date_created":"2018-12-11T11:48:43Z","_id":"828","year":"2013"},{"year":"2013","_id":"9459","pmid":1,"date_created":"2021-06-04T12:23:28Z","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"}],"publication_status":"published","article_type":"original","oa_version":"Published Version","article_processing_charge":"No","quality_controlled":"1","author":[{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"last_name":"Coleman-Derr","first_name":"Devin","full_name":"Coleman-Derr, Devin"},{"last_name":"Eshed-Williams","first_name":"Leor","full_name":"Eshed-Williams, Leor"},{"full_name":"Thao, Ka","first_name":"Ka","last_name":"Thao"},{"last_name":"Harmer","first_name":"Stacey L.","full_name":"Harmer, Stacey L."},{"last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"citation":{"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.","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>.","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.","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>.","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.","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>"},"date_updated":"2021-12-14T08:25:35Z","publication":"Cell","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"oa":1,"day":"28","external_id":{"pmid":["23540698"]},"title":"The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin","issue":"1","page":"193-205","scopus_import":"1","publisher":"Elsevier","department":[{"_id":"DaZi"}],"month":"03","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.02.033","open_access":"1"}],"volume":153,"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"status":"public","doi":"10.1016/j.cell.2013.02.033","date_published":"2013-03-28T00:00:00Z","intvolume":"       153","extern":"1"},{"pmid":1,"date_created":"2021-06-07T07:31:02Z","year":"2013","_id":"9481","article_type":"original","publication_status":"published","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"}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","keyword":["Multidisciplinary"],"date_updated":"2021-12-14T08:26:44Z","citation":{"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>.","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.","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>.","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>","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.","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."},"author":[{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"full_name":"Ruan, Randy","last_name":"Ruan","first_name":"Randy"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"full_name":"Sharma, Manoj K.","first_name":"Manoj K.","last_name":"Sharma"},{"full_name":"Sharma, Rita","last_name":"Sharma","first_name":"Rita"},{"full_name":"Ronald, Pamela C","first_name":"Pamela C","last_name":"Ronald"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"day":"07","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences","oa":1,"title":"Imprinted expression of genes and small RNA is associated with localized hypomethylation of the maternal genome in rice endosperm","external_id":{"pmid":["23613580"]},"issue":"19","page":"7934-7939","scopus_import":"1","department":[{"_id":"DaZi"}],"publisher":"National Academy of Sciences","month":"05","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1306164110"}],"type":"journal_article","volume":110,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1073/pnas.1306164110","date_published":"2013-05-07T00:00:00Z","language":[{"iso":"eng"}],"status":"public","intvolume":"       110","extern":"1"},{"page":"215-225","scopus_import":"1","month":"02","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2013.01.014"}],"volume":24,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"eng"}],"date_published":"2013-02-11T00:00:00Z","doi":"10.1016/j.devcel.2013.01.014","extern":"1","intvolume":"        24","_id":"9520","year":"2013","date_created":"2021-06-08T06:14:50Z","pmid":1,"abstract":[{"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.","lang":"eng"}],"publication_status":"published","article_type":"review","article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","citation":{"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>","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.","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>","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>.","ista":"Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations: Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.","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>.","short":"X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225."},"date_updated":"2023-05-08T11:00:59Z","author":[{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi"},{"last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"full_name":"Dickinson, Hugh","first_name":"Hugh","last_name":"Dickinson"}],"oa":1,"publication":"Developmental Cell","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"day":"11","external_id":{"pmid":["23410937"]},"title":"A conversation across generations: Soma-germ cell crosstalk in plants","issue":"3"},{"abstract":[{"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.","lang":"eng"}],"month":"12","related_material":{"record":[{"id":"2247","status":"public","relation":"used_in_publication"}]},"publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"article_processing_charge":"No","oa_version":"Published Version","_id":"9749","year":"2013","date_created":"2021-07-28T15:45:07Z","title":"Forgiver triumphs in alternating prisoner's dilemma ","status":"public","date_published":"2013-12-12T00:00:00Z","doi":"10.1371/journal.pone.0080814.s001","date_updated":"2023-02-23T10:34:39Z","type":"research_data_reference","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>","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma .” Public Library of Science, 2013.","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>","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>.","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>.","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>.","short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013)."},"author":[{"last_name":"Zagorsky","first_name":"Benjamin","full_name":"Zagorsky, Benjamin"},{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","first_name":"Johannes"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"12"},{"status":"public","title":"Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection","date_published":"2013-03-21T00:00:00Z","doi":"10.5061/dryad.b1q2n","citation":{"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>.","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>","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.","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>","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>.","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>.","short":"D. Refardt, T. Bergmiller, R. Kümmerli, (2013)."},"type":"research_data_reference","author":[{"first_name":"Dominik","last_name":"Refardt","full_name":"Refardt, Dominik"},{"last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"first_name":"Rolf","last_name":"Kümmerli","full_name":"Kümmerli, Rolf"}],"date_updated":"2023-10-18T06:43:22Z","oa":1,"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"21","abstract":[{"lang":"eng","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."}],"month":"03","department":[{"_id":"CaGu"}],"related_material":{"record":[{"relation":"used_in_publication","id":"2853","status":"public"}]},"publisher":"Dryad","article_processing_charge":"No","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5061/dryad.b1q2n","open_access":"1"}],"_id":"9751","year":"2013","date_created":"2021-07-30T08:08:09Z"},{"main_file_link":[{"url":"https://doi.org/10.5061/dryad.r3r60","open_access":"1"}],"oa_version":"Published Version","article_processing_charge":"No","publisher":"Dryad","related_material":{"record":[{"relation":"used_in_publication","id":"2170","status":"public"}]},"department":[{"_id":"NiBa"}],"month":"10","abstract":[{"lang":"eng","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."}],"date_created":"2021-07-30T08:31:22Z","year":"2013","_id":"9754","doi":"10.5061/dryad.r3r60","date_published":"2013-10-01T00:00:00Z","status":"public","title":"Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies","day":"01","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"author":[{"full_name":"Hearn, Jack","first_name":"Jack","last_name":"Hearn"},{"full_name":"Stone, Graham","first_name":"Graham","last_name":"Stone"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Lohse","first_name":"Konrad","full_name":"Lohse, Konrad"},{"full_name":"Bunnefeld, Lynsey","first_name":"Lynsey","last_name":"Bunnefeld"}],"citation":{"short":"J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).","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>.","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>","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.","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>","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>.","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>."},"date_updated":"2023-02-23T10:31:17Z","type":"research_data_reference"},{"quality_controlled":"1","article_processing_charge":"No","oa_version":"None","month":"07","editor":[{"first_name":"Susan","last_name":"Masino","full_name":"Masino, Susan"},{"last_name":"Boison","first_name":"Detlev","full_name":"Boison, Detlev"}],"publisher":"Springer","publication_status":"published","department":[{"_id":"HaJa"}],"abstract":[{"text":"Under physiological conditions the brain, via the purine salvage pathway, reuses the preformed purine bases hypoxanthine, derived from ATP degradation, and adenine (Ade), derived from polyamine synthesis, to restore its ATP pool. However, the massive degradation of ATP during ischemia, although providing valuable neuroprotective adenosine, results in the accumulation and loss of diffusible purine metabolites and thereby leads to a protracted reduction in the post-ischemic ATP pool size. In vivo, this may both limit the ability to deploy ATP-dependent reparative mechanisms and reduce the subsequent availability of adenosine, whilst in brain slices results in tissue with substantially lower levels of ATP than in vivo. In the present review, we describe the mechanisms by which brain tissue replenishes its ATP, how this can be improved with the clinically tolerated chemicals D-ribose and adenine, and the functional, and potential therapeutic, implications of doing so.","lang":"eng"}],"acknowledgement":"We are grateful to Research into Ageing/Ageing UK and The Dunhill Trust for funding SzN’s graduate studies, and to Prof Nicholas Dale for his valuable input.","place":"New York","date_created":"2022-03-21T07:16:12Z","_id":"10896","year":"2012","scopus_import":"1","page":"109-129","date_published":"2012-07-23T00:00:00Z","doi":"10.1007/978-1-4614-3903-5_6","title":"The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books","status":"public","language":[{"iso":"eng"}],"day":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eisbn":["9781461439035"],"isbn":["9781461439028"]},"publication":"Adenosine","type":"book_chapter","edition":"1","author":[{"full_name":"zur Nedden, Stephanie","id":"3C77F464-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"zur Nedden"},{"full_name":"Doney, Alexander S.","last_name":"Doney","first_name":"Alexander S."},{"last_name":"Frenguelli","first_name":"Bruno G.","full_name":"Frenguelli, Bruno G."}],"citation":{"short":"S. zur Nedden, A.S. Doney, B.G. Frenguelli, in:, S. Masino, D. Boison (Eds.), Adenosine, 1st ed., Springer, New York, 2012, pp. 109–129.","chicago":"Nedden, Stephanie zur, Alexander S. Doney, and Bruno G. Frenguelli. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” In <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., 109–29. New York: Springer, 2012. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>.","ista":"zur Nedden S, Doney AS, Frenguelli BG. 2012.The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Adenosine. , 109–129.","mla":"zur Nedden, Stephanie, et al. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., Springer, 2012, pp. 109–29, doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>.","ama":"zur Nedden S, Doney AS, Frenguelli BG. The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Masino S, Boison D, eds. <i>Adenosine</i>. 1st ed. New York: Springer; 2012:109-129. doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>","apa":"zur Nedden, S., Doney, A. S., &#38; Frenguelli, B. G. (2012). The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In S. Masino &#38; D. Boison (Eds.), <i>Adenosine</i> (1st ed., pp. 109–129). New York: Springer. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>","ieee":"S. zur Nedden, A. S. Doney, and B. G. Frenguelli, “The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books,” in <i>Adenosine</i>, 1st ed., S. Masino and D. Boison, Eds. New York: Springer, 2012, pp. 109–129."},"date_updated":"2022-06-21T11:51:58Z"},{"author":[{"last_name":"Bouajjani","first_name":"Ahmed","full_name":"Bouajjani, Ahmed"},{"full_name":"Dragoi, Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","last_name":"Dragoi"},{"first_name":"Constantin","last_name":"Enea","full_name":"Enea, Constantin"},{"full_name":"Sighireanu, Mihaela","first_name":"Mihaela","last_name":"Sighireanu"}],"citation":{"short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182.","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182.","chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In <i>Automated Technology for Verification and Analysis</i>, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>.","ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>","ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in <i>Automated Technology for Verification and Analysis</i>, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182.","apa":"Bouajjani, A., Dragoi, C., Enea, C., &#38; Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>","mla":"Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer, 2012, pp. 167–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>."},"date_updated":"2023-09-05T14:07:24Z","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642333866"],"isbn":["9783642333859"],"eissn":["1611-3349"]},"publication":"Automated Technology for Verification and Analysis","day":"15","title":"Accurate invariant checking for programs manipulating lists and arrays with infinite data","year":"2012","_id":"10903","date_created":"2022-03-21T07:58:39Z","series_title":"LNCS","abstract":[{"lang":"eng","text":"We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas."}],"publication_status":"published","oa_version":"None","article_processing_charge":"No","quality_controlled":"1","volume":7561,"type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"status":"public","doi":"10.1007/978-3-642-33386-6_14","date_published":"2012-10-15T00:00:00Z","alternative_title":["LNCS"],"intvolume":"      7561","page":"167-182","conference":{"start_date":"2012-10-03","name":"ATVA: Automated Technology for Verification and Analysis","location":"Thiruvananthapuram, India","end_date":"2012-10-06"},"scopus_import":"1","place":"Berlin, Heidelberg","acknowledgement":"This work has been partially supported by the French ANR project Veridyc","department":[{"_id":"ToHe"}],"publisher":"Springer","month":"10"}]