[{"related_material":{"record":[{"id":"3338","relation":"later_version","status":"public"}]},"oa_version":"Published Version","citation":{"ista":"Chatterjee K. 2011. Bounded rationality in concurrent parity games, IST Austria, 53p.","apa":"Chatterjee, K. (2011). <i>Bounded rationality in concurrent parity games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">https://doi.org/10.15479/AT:IST-2011-0008</a>","short":"K. Chatterjee, Bounded Rationality in Concurrent Parity Games, IST Austria, 2011.","mla":"Chatterjee, Krishnendu. <i>Bounded Rationality in Concurrent Parity Games</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">10.15479/AT:IST-2011-0008</a>.","ama":"Chatterjee K. <i>Bounded Rationality in Concurrent Parity Games</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">10.15479/AT:IST-2011-0008</a>","chicago":"Chatterjee, Krishnendu. <i>Bounded Rationality in Concurrent Parity Games</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">https://doi.org/10.15479/AT:IST-2011-0008</a>.","ieee":"K. Chatterjee, <i>Bounded rationality in concurrent parity games</i>. IST Austria, 2011."},"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"doi":"10.15479/AT:IST-2011-0008","_id":"5380","page":"53","date_updated":"2023-02-23T11:22:53Z","pubrep_id":"16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"file_date_updated":"2020-07-14T12:46:39Z","type":"technical_report","oa":1,"publisher":"IST Austria","date_created":"2018-12-12T11:39:00Z","alternative_title":["IST Austria Technical Report"],"publication_status":"published","file":[{"relation":"main_file","date_created":"2018-12-12T11:54:22Z","checksum":"0fd38186409be819a911c4990fa79d1f","creator":"system","content_type":"application/pdf","file_id":"5544","file_size":500399,"access_level":"open_access","file_name":"IST-2011-0008_IST-2011-0008.pdf","date_updated":"2020-07-14T12:46:39Z"}],"date_published":"2011-07-11T00:00:00Z","abstract":[{"lang":"eng","text":"We consider 2-player games played on a finite state space for an infinite number of rounds.  The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. We study concurrent games with ω-regular winning conditions specified as parity objectives.  We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respectively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). We study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies.  In terms of precision, strategies can be deterministic, uniform, finite-precision or infinite-precision;  and in terms of memory, strategies can be memoryless, finite-memory or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as powerful as infinite-precision finite-memory strategies.  We show that the winning sets can be computed in O(n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. While this complexity is the same as for the simpler class of turn-based parity games, where in each state only one of the two players has a choice of moves, our algorithms,that are obtained by characterization of the winning sets as μ-calculus formulas, are considerably more involved than those for turn-based games."}],"ddc":["000"],"status":"public","day":"11","title":"Bounded rationality in concurrent parity games","year":"2011","has_accepted_license":"1","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"month":"07"},{"publisher":"IST Austria","date_created":"2018-12-12T11:39:00Z","oa":1,"publication_status":"published","alternative_title":["IST Austria Technical Report"],"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"citation":{"ieee":"K. Chatterjee and L. Doyen, <i>Partial-observation stochastic games: How to win when belief fails</i>. IST Austria, 2011.","apa":"Chatterjee, K., &#38; Doyen, L. (2011). <i>Partial-observation stochastic games: How to win when belief fails</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">https://doi.org/10.15479/AT:IST-2011-0007</a>","ista":"Chatterjee K, Doyen L. 2011. Partial-observation stochastic games: How to win when belief fails, IST Austria, 43p.","short":"K. Chatterjee, L. Doyen, Partial-Observation Stochastic Games: How to Win When Belief Fails, IST Austria, 2011.","ama":"Chatterjee K, Doyen L. <i>Partial-Observation Stochastic Games: How to Win When Belief Fails</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">10.15479/AT:IST-2011-0007</a>","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Partial-Observation Stochastic Games: How to Win When Belief Fails</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">10.15479/AT:IST-2011-0007</a>.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Partial-Observation Stochastic Games: How to Win When Belief Fails</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">https://doi.org/10.15479/AT:IST-2011-0007</a>."},"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"1903","relation":"later_version"},{"status":"public","id":"2211","relation":"later_version"},{"id":"2955","relation":"later_version","status":"public"}]},"type":"technical_report","file_date_updated":"2020-07-14T12:46:39Z","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"17","date_updated":"2023-02-23T11:05:48Z","_id":"5381","doi":"10.15479/AT:IST-2011-0007","page":"43","has_accepted_license":"1","year":"2011","month":"07","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"ddc":["000","005"],"abstract":[{"text":"In two-player finite-state stochastic games of partial obser- vation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distri- bution over the successor states. The game is played for infinitely many rounds and thus the players construct an infinite path in the graph. We consider reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1) or pos- itively (i.e., with positive probability), no matter the strategy of the second player.\r\n\r\nWe classify such games according to the information and to the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two- sided with (c) both players having partial observation. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization.\r\n\r\nOur main results for pure strategies are as follows: (1) For one-sided games with player 2 perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strate- gies are not sufficient, and present an exponential upper bound on mem- ory both for almost-sure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete and present symbolic algo- rithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 perfect observation we show that non-elementary memory is both necessary and sufficient for both almost-sure and posi- tive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least non-elementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence re- sult exhibit serious flaws in previous results in the literature: we show a non-elementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed.","lang":"eng"}],"date_published":"2011-07-05T00:00:00Z","file":[{"date_created":"2018-12-12T11:53:27Z","relation":"main_file","checksum":"06bf6dfc97f6006e3fd0e9a3f31bc961","creator":"system","file_id":"5488","content_type":"application/pdf","access_level":"open_access","file_size":574055,"date_updated":"2020-07-14T12:46:39Z","file_name":"IST-2011-0007_IST-2011-0007.pdf"}],"title":"Partial-observation stochastic games: How to win when belief fails","day":"05","status":"public"},{"date_updated":"2023-02-23T11:23:01Z","_id":"5382","doi":"10.15479/AT:IST-2011-0006","page":"18","type":"technical_report","file_date_updated":"2020-07-14T12:46:40Z","pubrep_id":"18","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"later_version","id":"3341"}]},"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"citation":{"ieee":"K. Chatterjee, <i>Robustness of structurally equivalent concurrent parity games</i>. IST Austria, 2011.","chicago":"Chatterjee, Krishnendu. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">https://doi.org/10.15479/AT:IST-2011-0006</a>.","mla":"Chatterjee, Krishnendu. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">10.15479/AT:IST-2011-0006</a>.","ama":"Chatterjee K. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">10.15479/AT:IST-2011-0006</a>","short":"K. Chatterjee, Robustness of Structurally Equivalent Concurrent Parity Games, IST Austria, 2011.","apa":"Chatterjee, K. (2011). <i>Robustness of structurally equivalent concurrent parity games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">https://doi.org/10.15479/AT:IST-2011-0006</a>","ista":"Chatterjee K. 2011. Robustness of structurally equivalent concurrent parity games, IST Austria, 18p."},"oa_version":"Published Version","alternative_title":["IST Austria Technical Report"],"publication_status":"published","publisher":"IST Austria","oa":1,"date_created":"2018-12-12T11:39:00Z","status":"public","title":"Robustness of structurally equivalent concurrent parity games","day":"27","file":[{"file_id":"5546","content_type":"application/pdf","access_level":"open_access","file_size":335997,"file_name":"IST-2011-0006_IST-2011-0006.pdf","date_updated":"2020-07-14T12:46:40Z","date_created":"2018-12-12T11:54:24Z","relation":"main_file","checksum":"1322b652d6ab07eb5248298a3f91c1cf","creator":"system"}],"ddc":["000","005"],"abstract":[{"text":"We consider two-player stochastic games played on a finite state space for an infinite num- ber of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine a probability distribution over the successor states. We also consider the important special case of turn-based stochastic games where players make moves in turns, rather than concurrently. We study concurrent games with ω-regular winning conditions specified as parity objectives. The value for player 1 for a parity objective is the maximal probability with which the player can guarantee the satisfaction of the objective against all strategies of the opponent. We study the problem of continuity and robustness of the value function in concurrent and turn-based stochastic parity games with respect to imprecision in the transition probabilities. We present quantitative bounds on the difference of the value function (in terms of the imprecision of the transition probabilities) and show the value continuity for structurally equivalent concurrent games (two games are structurally equivalent if the support of the transition func- tion is same and the probabilities differ). We also show robustness of optimal strategies for structurally equivalent turn-based stochastic parity games. Finally we show that the value continuity property breaks without the structurally equivalent assumption (even for Markov chains) and show that our quantitative bound is asymptotically optimal. Hence our results are tight (the assumption is both necessary and sufficient) and optimal (our quantitative bound is asymptotically optimal).","lang":"eng"}],"date_published":"2011-06-27T00:00:00Z","month":"06","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"year":"2011","has_accepted_license":"1"},{"year":"2011","has_accepted_license":"1","month":"04","author":[{"full_name":"Wies, Thomas","last_name":"Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Marco","full_name":"Muñiz, Marco","last_name":"Muñiz"},{"first_name":"Viktor","last_name":"Kuncak","full_name":"Kuncak, Viktor"}],"file":[{"relation":"main_file","date_created":"2018-12-12T11:53:01Z","creator":"system","checksum":"b20029184c4a819c5f4466a4a3d238b5","file_size":619053,"access_level":"open_access","content_type":"application/pdf","file_id":"5462","file_name":"IST-2011-0005_IST-2011-0005.pdf","date_updated":"2020-07-14T12:46:40Z"}],"abstract":[{"lang":"eng","text":"We present a new decidable logic called TREX for expressing constraints about imperative tree data structures. In particular, TREX supports a transitive closure operator that can express reachability constraints, which often appear in data structure invariants. We show that our logic is closed under weakest precondition computation, which enables its use for automated software verification. We further show that satisfiability of formulas in TREX is decidable in NP. The low complexity makes it an attractive alternative to more expensive logics such as monadic second-order logic (MSOL) over trees, which have been traditionally used for reasoning about tree data structures."}],"ddc":["000","006"],"date_published":"2011-04-26T00:00:00Z","status":"public","title":"On an efficient decision procedure for imperative tree data structures","day":"26","oa":1,"date_created":"2018-12-12T11:39:01Z","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"later_version","id":"3323"}]},"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"mla":"Wies, Thomas, et al. <i>On an Efficient Decision Procedure for Imperative Tree Data Structures</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">10.15479/AT:IST-2011-0005</a>.","ama":"Wies T, Muñiz M, Kuncak V. <i>On an Efficient Decision Procedure for Imperative Tree Data Structures</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">10.15479/AT:IST-2011-0005</a>","chicago":"Wies, Thomas, Marco Muñiz, and Viktor Kuncak. <i>On an Efficient Decision Procedure for Imperative Tree Data Structures</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">https://doi.org/10.15479/AT:IST-2011-0005</a>.","apa":"Wies, T., Muñiz, M., &#38; Kuncak, V. (2011). <i>On an efficient decision procedure for imperative tree data structures</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">https://doi.org/10.15479/AT:IST-2011-0005</a>","ista":"Wies T, Muñiz M, Kuncak V. 2011. On an efficient decision procedure for imperative tree data structures, IST Austria, 25p.","short":"T. Wies, M. Muñiz, V. Kuncak, On an Efficient Decision Procedure for Imperative Tree Data Structures, IST Austria, 2011.","ieee":"T. Wies, M. Muñiz, and V. Kuncak, <i>On an efficient decision procedure for imperative tree data structures</i>. IST Austria, 2011."},"date_updated":"2023-02-23T11:22:16Z","_id":"5383","doi":"10.15479/AT:IST-2011-0005","page":"25","type":"technical_report","file_date_updated":"2020-07-14T12:46:40Z","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"19"},{"year":"2011","has_accepted_license":"1","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","last_name":"Tracol","full_name":"Tracol, Mathieu"}],"month":"04","file":[{"file_name":"IST-2011-004_IST-2011-0004.pdf","date_updated":"2020-07-14T12:46:40Z","file_size":570827,"access_level":"open_access","content_type":"application/pdf","file_id":"5545","creator":"system","checksum":"f5a0f664fadc335990f5fcf138df19f1","relation":"main_file","date_created":"2018-12-12T11:54:23Z"}],"date_published":"2011-04-11T00:00:00Z","ddc":["000","005"],"abstract":[{"text":"We consider probabilistic automata on infinite words with acceptance defined by parity conditions. We consider three qualitative decision problems: (i) the positive decision problem asks whether there is a word that is accepted with positive probability; (ii) the almost decision problem asks whether there is a word that is accepted with probability 1; and (iii) the limit decision problem asks whether for every ε > 0 there is a word that is accepted with probability at least 1 − ε. We unify and generalize several decidability results for probabilistic automata over infinite words, and identify a robust (closed under union and intersection) subclass of probabilistic automata for which all the qualitative decision problems are decidable for parity conditions. We also show that if the input words are restricted to lasso shape words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions.","lang":"eng"}],"status":"public","day":"11","title":"Decidable problems for probabilistic automata on infinite words","date_created":"2018-12-12T11:39:01Z","publisher":"IST Austria","oa":1,"alternative_title":["IST Austria Technical Report"],"publication_status":"published","related_material":{"record":[{"relation":"later_version","id":"2957","status":"public"}]},"citation":{"ama":"Chatterjee K, Tracol M. <i>Decidable Problems for Probabilistic Automata on Infinite Words</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">10.15479/AT:IST-2011-0004</a>","mla":"Chatterjee, Krishnendu, and Mathieu Tracol. <i>Decidable Problems for Probabilistic Automata on Infinite Words</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">10.15479/AT:IST-2011-0004</a>.","chicago":"Chatterjee, Krishnendu, and Mathieu Tracol. <i>Decidable Problems for Probabilistic Automata on Infinite Words</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">https://doi.org/10.15479/AT:IST-2011-0004</a>.","ista":"Chatterjee K, Tracol M. 2011. Decidable problems for probabilistic automata on infinite words, IST Austria, 30p.","apa":"Chatterjee, K., &#38; Tracol, M. (2011). <i>Decidable problems for probabilistic automata on infinite words</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">https://doi.org/10.15479/AT:IST-2011-0004</a>","short":"K. Chatterjee, M. Tracol, Decidable Problems for Probabilistic Automata on Infinite Words, IST Austria, 2011.","ieee":"K. Chatterjee and M. Tracol, <i>Decidable problems for probabilistic automata on infinite words</i>. IST Austria, 2011."},"oa_version":"Published Version","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"_id":"5384","doi":"10.15479/AT:IST-2011-0004","page":"30","date_updated":"2023-02-23T11:05:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"20","file_date_updated":"2020-07-14T12:46:40Z","type":"technical_report"},{"has_accepted_license":"1","month":"04","author":[{"last_name":"Boker","full_name":"Boker, Udi","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"file":[{"checksum":"8491d0d48c4911620ecd5350b413c11e","creator":"system","relation":"main_file","date_created":"2018-12-12T11:53:00Z","file_name":"IST-2011-0003_IST-2011-0003.pdf","date_updated":"2020-07-14T12:46:41Z","content_type":"application/pdf","file_id":"5461","file_size":366281,"access_level":"open_access"}],"ddc":["000","004"],"abstract":[{"text":"There is recently a significant effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions, aiming for a general and flexible framework for quantitative-oriented specifications. In the heart of quantitative objectives lies the accumulation of values along a computation. It is either the accumulated summation, as with the energy objectives, or the accumulated average, as with the mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point of time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire computation. We study the border of decidability for extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by prefix-accumulation assertions and extending LTL with path-accumulation assertions, result in temporal logics whose model-checking problem is decidable. The extended logics allow to significantly extend the currently known energy and mean-payoff objectives. Moreover, the prefix-accumulation assertions may be refined with “controlled-accumulation”, allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that the fragment we point to is, in a sense, the maximal logic whose extension with prefix-accumulation assertions permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, and in particular CTL and LTL, makes the problem undecidable.","lang":"eng"}],"date_published":"2011-04-04T00:00:00Z","status":"public","publisher":"IST Austria","oa":1,"related_material":{"record":[{"relation":"later_version","id":"2038","status":"public"},{"status":"public","relation":"later_version","id":"3356"}]},"ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"14","doi":"10.15479/AT:IST-2011-0003","type":"technical_report","publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"21","year":"2011","title":"Temporal specifications with accumulative values","day":"04","date_created":"2018-12-12T11:39:02Z","alternative_title":["IST Austria Technical Report"],"publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"citation":{"short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, Temporal Specifications with Accumulative Values, IST Austria, 2011.","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2011. Temporal specifications with accumulative values, IST Austria, 14p.","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., &#38; Kupferman, O. (2011). <i>Temporal specifications with accumulative values</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">https://doi.org/10.15479/AT:IST-2011-0003</a>","chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. <i>Temporal Specifications with Accumulative Values</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">https://doi.org/10.15479/AT:IST-2011-0003</a>.","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. <i>Temporal Specifications with Accumulative Values</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">10.15479/AT:IST-2011-0003</a>","mla":"Boker, Udi, et al. <i>Temporal Specifications with Accumulative Values</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">10.15479/AT:IST-2011-0003</a>.","ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, <i>Temporal specifications with accumulative values</i>. IST Austria, 2011."},"date_updated":"2023-02-23T11:23:41Z","_id":"5385","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Design for Embedded Systems"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:46:41Z"},{"publication_status":"published","alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","date_created":"2018-12-12T11:39:02Z","oa":1,"publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"22","file_date_updated":"2020-07-14T12:46:41Z","type":"technical_report","page":"69","_id":"5386","doi":"10.15479/AT:IST-2011-0002","date_updated":"2023-02-23T11:22:48Z","citation":{"short":"C. Chen, D. Freedman, C. Lampert, Enforcing Topological Constraints in Random Field Image Segmentation, IST Austria, 2011.","apa":"Chen, C., Freedman, D., &#38; Lampert, C. (2011). <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>","ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation, IST Austria, 69p.","chicago":"Chen, Chao, Daniel Freedman, and Christoph Lampert. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>.","ama":"Chen C, Freedman D, Lampert C. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>","mla":"Chen, Chao, et al. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>.","ieee":"C. Chen, D. Freedman, and C. Lampert, <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria, 2011."},"oa_version":"Published Version","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"3336","relation":"later_version","status":"public"}]},"author":[{"full_name":"Chen, Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao"},{"last_name":"Freedman","full_name":"Freedman, Daniel","first_name":"Daniel"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph"}],"month":"03","has_accepted_license":"1","year":"2011","day":"28","title":"Enforcing topological constraints in random field image segmentation","status":"public","date_published":"2011-03-28T00:00:00Z","abstract":[{"lang":"eng","text":"We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks."}],"ddc":["000"],"file":[{"date_updated":"2020-07-14T12:46:41Z","file_name":"IST-2011-0002_IST-2011-0002.pdf","access_level":"open_access","file_size":26390601,"file_id":"5495","content_type":"application/pdf","creator":"system","checksum":"ad64c2add5fe2ad10e9d5c669f3f9526","date_created":"2018-12-12T11:53:34Z","relation":"main_file"}]},{"type":"technical_report","file_date_updated":"2020-07-14T12:46:41Z","publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T11:23:11Z","_id":"5387","page":"20","doi":"10.15479/AT:IST-2011-0001","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>.","ama":"Chatterjee K, Doyen L. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>.","ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p.","apa":"Chatterjee, K., &#38; Doyen, L. (2011). <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011.","ieee":"K. Chatterjee and L. Doyen, <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria, 2011."},"related_material":{"record":[{"status":"public","relation":"later_version","id":"3345"}]},"publication_status":"published","alternative_title":["IST Austria Technical Report"],"date_created":"2018-12-12T11:39:02Z","publisher":"IST Austria","oa":1,"title":"Energy and mean-payoff parity Markov decision processes","day":"16","status":"public","ddc":["000","005"],"abstract":[{"lang":"eng","text":"We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy parity objectives. In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound."}],"date_published":"2011-02-16T00:00:00Z","file":[{"checksum":"824d6c70e6d3feb3e836b009e0b3cf73","creator":"system","relation":"main_file","date_created":"2018-12-12T11:52:57Z","file_name":"IST-2011-0001_IST-2011-0001.pdf","date_updated":"2020-07-14T12:46:41Z","content_type":"application/pdf","file_id":"5458","file_size":329976,"access_level":"open_access"}],"month":"02","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"has_accepted_license":"1","year":"2011"},{"date_published":"2011-11-16T00:00:00Z","abstract":[{"text":"We report the switching behavior of the full bacterial flagellum system that includes the filament and the motor in wild-type Escherichia coli cells. In sorting the motor behavior by the clockwise bias, we find that the distributions of the clockwise (CW) and counterclockwise (CCW) intervals are either exponential or nonexponential with long tails. At low bias, CW intervals are exponentially distributed and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and CCW intervals are mainly exponentially distributed. A simple model suggests that these two distinct switching behaviors are governed by the presence of signaling noise within the chemotaxis network. Low noise yields exponentially distributed intervals, whereas large noise yields nonexponential behavior with long tails. These drastically different motor statistics may play a role in optimizing bacterial behavior for a wide range of environmental conditions.","lang":"eng"}],"quality_controlled":"1","status":"public","author":[{"full_name":"Park, Heungwon","last_name":"Park","first_name":"Heungwon"},{"first_name":"Panos","last_name":"Oikonomou","full_name":"Oikonomou, Panos"},{"last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Philippe","full_name":"Cluzel, Philippe","last_name":"Cluzel"}],"month":"11","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","publication":"Biophysical Journal","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0006-3495"]},"type":"journal_article","doi":"10.1016/j.bpj.2011.09.040","page":"2336-2340","intvolume":"       101","oa":1,"publisher":"Elsevier","volume":101,"day":"16","title":"Noise underlies switching behavior of the bacterial flagellum","external_id":{"pmid":["22098731"]},"issue":"10","year":"2011","citation":{"ieee":"H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching behavior of the bacterial flagellum,” <i>Biophysical Journal</i>, vol. 101, no. 10. Elsevier, pp. 2336–2340, 2011.","short":"H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.","ista":"Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.","apa":"Park, H., Oikonomou, P., Guet, C. C., &#38; Cluzel, P. (2011). Noise underlies switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">https://doi.org/10.1016/j.bpj.2011.09.040</a>","chicago":"Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">https://doi.org/10.1016/j.bpj.2011.09.040</a>.","mla":"Park, Heungwon, et al. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>, vol. 101, no. 10, Elsevier, 2011, pp. 2336–40, doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">10.1016/j.bpj.2011.09.040</a>.","ama":"Park H, Oikonomou P, Guet CC, Cluzel P. Noise underlies switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. 2011;101(10):2336-2340. doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">10.1016/j.bpj.2011.09.040</a>"},"department":[{"_id":"CaGu"}],"_id":"6496","date_updated":"2021-04-16T11:54:49Z","pmid":1,"date_created":"2019-05-28T11:54:29Z","publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/","open_access":"1"}]},{"language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Proceedings of the National Academy of Sciences","extern":"1","type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"page":"1755-1762","doi":"10.1073/pnas.1019273108","intvolume":"       108","oa":1,"publisher":"National Academy of Sciences","abstract":[{"text":"Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development.","lang":"eng"}],"date_published":"2011-02-01T00:00:00Z","quality_controlled":"1","status":"public","article_type":"original","month":"02","author":[{"last_name":"Hsieh","full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu"},{"full_name":"Shin, Juhyun","last_name":"Shin","first_name":"Juhyun"},{"first_name":"Rie","full_name":"Uzawa, Rie","last_name":"Uzawa"},{"full_name":"Silva, Pedro","last_name":"Silva","first_name":"Pedro"},{"full_name":"Cohen, Stephanie","last_name":"Cohen","first_name":"Stephanie"},{"first_name":"Matthew J.","last_name":"Bauer","full_name":"Bauer, Matthew J."},{"first_name":"Meryl","full_name":"Hashimoto, Meryl","last_name":"Hashimoto"},{"last_name":"Kirkbride","full_name":"Kirkbride, Ryan C.","first_name":"Ryan C."},{"last_name":"Harada","full_name":"Harada, John J.","first_name":"John J."},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"}],"scopus_import":"1","article_processing_charge":"No","department":[{"_id":"DaZi"}],"citation":{"ieee":"T.-F. Hsieh <i>et al.</i>, “Regulation of imprinted gene expression in Arabidopsis endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011.","ista":"Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5), 1755–1762.","apa":"Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>","short":"T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto, R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 108 (2011) 1755–1762.","ama":"Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(5):1755-1762. doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>","mla":"Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>.","chicago":"Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>."},"date_updated":"2021-12-14T08:33:49Z","_id":"9483","pmid":1,"date_created":"2021-06-07T07:40:38Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1019273108"}],"publication_status":"published","volume":108,"title":"Regulation of imprinted gene expression in Arabidopsis endosperm","day":"01","external_id":{"pmid":["21257907"]},"year":"2011","issue":"5"},{"extern":"1","oa_version":"Published Version","publication":"Developmental Cell","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2011.05.018","page":"735-736","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"other_academic_publication","publisher":"Elsevier","oa":1,"intvolume":"        20","date_published":"2011-06-14T00:00:00Z","abstract":[{"text":"Little is known about chromatin remodeling events immediately after fertilization. A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory pathways that silence transposable elements are responsible for global delayed activation of gene expression in the early Arabidopsis embryo.","lang":"eng"}],"status":"public","quality_controlled":"1","article_processing_charge":"No","author":[{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"month":"06","citation":{"chicago":"Zilberman, Daniel. <i>Balancing Parental Contributions in Plant Embryonic Gene Activation</i>. <i>Developmental Cell</i>. Vol. 20. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">https://doi.org/10.1016/j.devcel.2011.05.018</a>.","ama":"Zilberman D. <i>Balancing Parental Contributions in Plant Embryonic Gene Activation</i>. Vol 20. Elsevier; 2011:735-736. doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">10.1016/j.devcel.2011.05.018</a>","mla":"Zilberman, Daniel. “Balancing Parental Contributions in Plant Embryonic Gene Activation.” <i>Developmental Cell</i>, vol. 20, no. 6, Elsevier, 2011, pp. 735–36, doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">10.1016/j.devcel.2011.05.018</a>.","short":"D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation, Elsevier, 2011.","apa":"Zilberman, D. (2011). <i>Balancing parental contributions in plant embryonic gene activation</i>. <i>Developmental Cell</i> (Vol. 20, pp. 735–736). Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">https://doi.org/10.1016/j.devcel.2011.05.018</a>","ista":"Zilberman D. 2011. Balancing parental contributions in plant embryonic gene activation, Elsevier,p.","ieee":"D. Zilberman, <i>Balancing parental contributions in plant embryonic gene activation</i>, vol. 20, no. 6. Elsevier, 2011, pp. 735–736."},"department":[{"_id":"DaZi"}],"_id":"9522","date_updated":"2021-12-14T08:34:37Z","date_created":"2021-06-08T06:23:39Z","pmid":1,"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2011.05.018","open_access":"1"}],"volume":20,"external_id":{"pmid":["21664571"]},"day":"14","title":"Balancing parental contributions in plant embryonic gene activation","issue":"6","year":"2011"},{"language":[{"iso":"eng"}],"publication":"Computer Analysis of Images and Patterns","oa_version":"Published Version","type":"conference","publication_identifier":{"issn":["03029743"],"isbn":["9783642236716"],"eissn":["16113349"]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","page":"286-293","doi":"10.1007/978-3-642-23672-3_35","intvolume":"      6854","oa":1,"publisher":"Springer Nature","abstract":[{"text":"In this paper, we establish a correspondence between the incremental algorithm for computing AT-models [8,9] and the one for computing persistent homology [6,14,15]. We also present a decremental algorithm for computing AT-models that allows to extend the persistence computation to a wider setting. Finally, we show how to combine incremental and decremental techniques for persistent homology computation.","lang":"eng"}],"date_published":"2011-08-01T00:00:00Z","quality_controlled":"1","status":"public","month":"08","author":[{"last_name":"Gonzalez-Diaz","full_name":"Gonzalez-Diaz, Rocio","first_name":"Rocio"},{"last_name":"Ion","full_name":"Ion, Adrian","first_name":"Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria Jose","full_name":"Jimenez, Maria Jose","last_name":"Jimenez"},{"first_name":"Regina","full_name":"Poyatos, Regina","last_name":"Poyatos"}],"scopus_import":"1","article_processing_charge":"No","department":[{"_id":"HeEd"}],"citation":{"short":"R. Gonzalez-Diaz, A. Ion, M.J. Jimenez, R. Poyatos, in:, Computer Analysis of Images and Patterns, Springer Nature, 2011, pp. 286–293.","ista":"Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. 2011. Incremental-decremental algorithm for computing AT-models and persistent homology. Computer Analysis of Images and Patterns. CAIP: International Conference on Computer Analysis of Images and Patterns, LNCS, vol. 6854, 286–293.","apa":"Gonzalez-Diaz, R., Ion, A., Jimenez, M. J., &#38; Poyatos, R. (2011). Incremental-decremental algorithm for computing AT-models and persistent homology. In <i>Computer Analysis of Images and Patterns</i> (Vol. 6854, pp. 286–293). Seville, Spain: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-23672-3_35\">https://doi.org/10.1007/978-3-642-23672-3_35</a>","chicago":"Gonzalez-Diaz, Rocio, Adrian Ion, Maria Jose Jimenez, and Regina Poyatos. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” In <i>Computer Analysis of Images and Patterns</i>, 6854:286–93. Springer Nature, 2011. <a href=\"https://doi.org/10.1007/978-3-642-23672-3_35\">https://doi.org/10.1007/978-3-642-23672-3_35</a>.","mla":"Gonzalez-Diaz, Rocio, et al. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” <i>Computer Analysis of Images and Patterns</i>, vol. 6854, Springer Nature, 2011, pp. 286–93, doi:<a href=\"https://doi.org/10.1007/978-3-642-23672-3_35\">10.1007/978-3-642-23672-3_35</a>.","ama":"Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. Incremental-decremental algorithm for computing AT-models and persistent homology. In: <i>Computer Analysis of Images and Patterns</i>. Vol 6854. Springer Nature; 2011:286-293. doi:<a href=\"https://doi.org/10.1007/978-3-642-23672-3_35\">10.1007/978-3-642-23672-3_35</a>","ieee":"R. Gonzalez-Diaz, A. Ion, M. J. Jimenez, and R. Poyatos, “Incremental-decremental algorithm for computing AT-models and persistent homology,” in <i>Computer Analysis of Images and Patterns</i>, Seville, Spain, 2011, vol. 6854, pp. 286–293."},"conference":{"end_date":"2011-08-31","name":"CAIP: International Conference on Computer Analysis of Images and Patterns","location":"Seville, Spain","start_date":"2011-08-29"},"date_updated":"2021-08-12T13:53:17Z","_id":"9648","date_created":"2021-07-11T22:01:19Z","main_file_link":[{"url":"http://hdl.handle.net/11441/30766","open_access":"1"}],"publication_status":"published","alternative_title":["LNCS"],"volume":6854,"title":"Incremental-decremental algorithm for computing AT-models and persistent homology","day":"01","year":"2011"},{"oa_version":"Published Version","citation":{"ama":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). 2011. doi:<a href=\"https://doi.org/10.5061/dryad.299h8\">10.5061/dryad.299h8</a>","mla":"Palero, Ferran, et al. <i>Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas)</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.5061/dryad.299h8\">10.5061/dryad.299h8</a>.","chicago":"Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria, 2011. <a href=\"https://doi.org/10.5061/dryad.299h8\">https://doi.org/10.5061/dryad.299h8</a>.","ista":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas), IST Austria, <a href=\"https://doi.org/10.5061/dryad.299h8\">10.5061/dryad.299h8</a>.","apa":"Palero, F., Abello, P., Macpherson, E., Beaumont, M., &#38; Pascual, M. (2011). Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). IST Austria. <a href=\"https://doi.org/10.5061/dryad.299h8\">https://doi.org/10.5061/dryad.299h8</a>","short":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011).","ieee":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas).” IST Austria, 2011."},"department":[{"_id":"NiBa"}],"related_material":{"record":[{"relation":"used_in_publication","id":"3395","status":"public"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","_id":"9762","doi":"10.5061/dryad.299h8","date_updated":"2023-02-23T11:25:25Z","date_created":"2021-08-02T07:11:19Z","publisher":"IST Austria","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.299h8","open_access":"1"}],"date_published":"2011-05-12T00:00:00Z","abstract":[{"lang":"eng","text":"Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data."}],"day":"12","title":"Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)","status":"public","year":"2011","author":[{"first_name":"Ferran","orcid":"0000-0002-0343-8329","id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","last_name":"Palero","full_name":"Palero, Ferran"},{"last_name":"Abello","full_name":"Abello, Pere","first_name":"Pere"},{"full_name":"Macpherson, Enrique","last_name":"Macpherson","first_name":"Enrique"},{"first_name":"Mark","full_name":"Beaumont, Mark","last_name":"Beaumont"},{"full_name":"Pascual, Marta","last_name":"Pascual","first_name":"Marta"}],"month":"05","article_processing_charge":"No"},{"editor":[{"first_name":"Edmund M","last_name":"Clarke","full_name":"Clarke, Edmund M"},{"first_name":"Andrei","full_name":"Voronkov, Andrei","last_name":"Voronkov"}],"scopus_import":"1","article_processing_charge":"No","month":"05","author":[{"full_name":"Blanc, Régis","last_name":"Blanc","first_name":"Régis"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Hottelier, Thibaud","last_name":"Hottelier","first_name":"Thibaud"},{"first_name":"Laura","full_name":"Kovács, Laura","last_name":"Kovács"}],"abstract":[{"lang":"eng","text":"We present ABC, a software tool for automatically computing symbolic upper bounds on the number of iterations of nested program loops. The system combines static analysis of programs with symbolic summation techniques to derive loop invariant relations between program variables. Iteration bounds are obtained from the inferred invariants, by replacing variables with bounds on their greatest values. We have successfully applied ABC to a large number of examples. The derived symbolic bounds express non-trivial polynomial relations over loop variables. We also report on results to automatically infer symbolic expressions over harmonic numbers as upper bounds on loop iteration counts."}],"place":"Berlin, Heidelberg","date_published":"2010-05-01T00:00:00Z","status":"public","series_title":"LNCS","quality_controlled":"1","publisher":"Springer Nature","oa":1,"intvolume":"      6355","language":[{"iso":"eng"}],"oa_version":"Submitted Version","publication":"Logic for Programming, Artificial Intelligence, and Reasoning","page":"103-118","doi":"10.1007/978-3-642-17511-4_7","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642175107"],"eisbn":["9783642175114"],"issn":["0302-9743"]},"year":"2010","acknowledgement":"This work was supported in part by the Swiss NSF. The fourth author is supported by an FWF Hertha Firnberg Research grant (T425-N23).","volume":6355,"title":"ABC: Algebraic Bound Computation for loops","day":"01","date_created":"2022-03-21T08:14:35Z","publication_status":"published","main_file_link":[{"url":"https://infoscience.epfl.ch/record/186096","open_access":"1"}],"department":[{"_id":"ToHe"}],"citation":{"short":"R. Blanc, T.A. Henzinger, T. Hottelier, L. Kovács, in:, E.M. Clarke, A. Voronkov (Eds.), Logic for Programming, Artificial Intelligence, and Reasoning, Springer Nature, Berlin, Heidelberg, 2010, pp. 103–118.","apa":"Blanc, R., Henzinger, T. A., Hottelier, T., &#38; Kovács, L. (2010). ABC: Algebraic Bound Computation for loops. In E. M. Clarke &#38; A. Voronkov (Eds.), <i>Logic for Programming, Artificial Intelligence, and Reasoning</i> (Vol. 6355, pp. 103–118). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">https://doi.org/10.1007/978-3-642-17511-4_7</a>","ista":"Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and ReasoningLNCS vol. 6355, 103–118.","chicago":"Blanc, Régis, Thomas A Henzinger, Thibaud Hottelier, and Laura Kovács. “ABC: Algebraic Bound Computation for Loops.” In <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, edited by Edmund M Clarke and Andrei Voronkov, 6355:103–18. LNCS. Berlin, Heidelberg: Springer Nature, 2010. <a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">https://doi.org/10.1007/978-3-642-17511-4_7</a>.","mla":"Blanc, Régis, et al. “ABC: Algebraic Bound Computation for Loops.” <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, edited by Edmund M Clarke and Andrei Voronkov, vol. 6355, Springer Nature, 2010, pp. 103–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">10.1007/978-3-642-17511-4_7</a>.","ama":"Blanc R, Henzinger TA, Hottelier T, Kovács L. ABC: Algebraic Bound Computation for loops. In: Clarke EM, Voronkov A, eds. <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>. Vol 6355. LNCS. Berlin, Heidelberg: Springer Nature; 2010:103-118. doi:<a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">10.1007/978-3-642-17511-4_7</a>","ieee":"R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound Computation for loops,” in <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, Dakar, Senegal, 2010, vol. 6355, pp. 103–118."},"date_updated":"2022-06-13T07:44:21Z","_id":"10908","conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","end_date":"2010-05-01","start_date":"2010-04-25","location":"Dakar, Senegal"}},{"publisher":"Society for Industrial and Applied Mathematics","date_created":"2022-03-21T08:24:07Z","publication_status":"published","oa_version":"None","citation":{"ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” in <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Austin, TX, United States, 2010, pp. 1594–1604.","short":"C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010, pp. 1594–1604.","apa":"Chen, C., &#38; Freedman, D. (2010). Hardness results for homology localization. In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611973075.129\">https://doi.org/10.1137/1.9781611973075.129</a>","ista":"Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1594–1604.","chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 1594–1604. Society for Industrial and Applied Mathematics, 2010. <a href=\"https://doi.org/10.1137/1.9781611973075.129\">https://doi.org/10.1137/1.9781611973075.129</a>.","ama":"Chen C, Freedman D. Hardness results for homology localization. In: <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2010:1594-1604. doi:<a href=\"https://doi.org/10.1137/1.9781611973075.129\">10.1137/1.9781611973075.129</a>","mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:<a href=\"https://doi.org/10.1137/1.9781611973075.129\">10.1137/1.9781611973075.129</a>."},"publication":"Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"related_material":{"record":[{"id":"3267","relation":"later_version","status":"public"}]},"conference":{"start_date":"2010-01-17","location":"Austin, TX, United States","name":"SODA: Symposium on Discrete Algorithms","end_date":"2010-01-19"},"publication_identifier":{"eisbn":["9781611973075"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"10909","page":"1594-1604","doi":"10.1137/1.9781611973075.129","date_updated":"2023-02-23T11:19:46Z","year":"2010","author":[{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chao"},{"first_name":"Daniel","full_name":"Freedman, Daniel","last_name":"Freedman"}],"month":"02","scopus_import":"1","article_processing_charge":"No","date_published":"2010-02-01T00:00:00Z","abstract":[{"text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the ℤ2 field.","lang":"eng"}],"acknowledgement":"Partially supported by the Austrian Science Fund under grantFSP-S9103-N04 and P20134-N13.","day":"01","quality_controlled":"1","title":"Hardness results for homology localization","status":"public"},{"year":"2010","issue":"14","acknowledgement":"We thank the following for providing mutant lines and reagents: Hong Ma, De Ye, Sacco De Vries, and Rod Scott for providing the pA9::Barnase lines and information on A9 expression patterns. Carla Galinha and Paolo Piazza gave valuable help with in situ hybridisation and qRT-PCR, respectively, and we acknowledge Qing Zhang, Helen Prescott and Matthew Dicks for providing excellent technical assistance. We are indebted to Miltos Tsiantis and Angela Hay for helpful discussion, and the research was funded by Oxford University through a Clarendon Scholarship to X.F., with additional financial support from Magdalen College (Oxford).","volume":137,"external_id":{"pmid":["20570940"]},"title":"Tapetal cell fate, lineage and proliferation in the Arabidopsis anther","day":"15","date_created":"2023-01-16T09:21:54Z","pmid":1,"publication_status":"published","department":[{"_id":"XiFe"}],"citation":{"ieee":"X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation in the Arabidopsis anther,” <i>Development</i>, vol. 137, no. 14. The Company of Biologists, pp. 2409–2416, 2010.","short":"X. Feng, H.G. Dickinson, Development 137 (2010) 2409–2416.","apa":"Feng, X., &#38; Dickinson, H. G. (2010). Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.049320\">https://doi.org/10.1242/dev.049320</a>","ista":"Feng X, Dickinson HG. 2010. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. Development. 137(14), 2409–2416.","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” <i>Development</i>. The Company of Biologists, 2010. <a href=\"https://doi.org/10.1242/dev.049320\">https://doi.org/10.1242/dev.049320</a>.","ama":"Feng X, Dickinson HG. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. <i>Development</i>. 2010;137(14):2409-2416. doi:<a href=\"https://doi.org/10.1242/dev.049320\">10.1242/dev.049320</a>","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” <i>Development</i>, vol. 137, no. 14, The Company of Biologists, 2010, pp. 2409–16, doi:<a href=\"https://doi.org/10.1242/dev.049320\">10.1242/dev.049320</a>."},"date_updated":"2023-05-08T10:57:11Z","_id":"12199","article_processing_charge":"No","scopus_import":"1","month":"07","author":[{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","last_name":"Feng"},{"last_name":"Dickinson","full_name":"Dickinson, Hugh G.","first_name":"Hugh G."}],"abstract":[{"text":"The four microsporangia of the flowering plant anther develop from archesporial cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes are surrounded by concentric monolayers of tapetal, middle layer and endothecial cells. How this intricate array of tissues, each containing relatively few cells, is established in an organ possessing no formal meristems is poorly understood. We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES 1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually for plants, tapetal cells are specified very early in development, and are subsequently stimulated to proliferate by a receptor-like kinase (RLK) complex that includes EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly, these cells continue to develop, isolated at the locular periphery. Mutant and wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the periphery of mutant locules becomes occupied by microsporocytes. However, induction of late expression of EMS1 in the few tapetal initials in ems1 plants results in their proliferation to generate a functional tapetum, and this proliferation suppresses microsporocyte number. Our experiments also show that integrity of the tapetal monolayer is crucial for the maintenance of the polarity of divisions within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the context of tissue development in complex plant organs, where constancy in size, shape and cell number is crucial.","lang":"eng"}],"date_published":"2010-07-15T00:00:00Z","status":"public","article_type":"original","quality_controlled":"1","publisher":"The Company of Biologists","intvolume":"       137","extern":"1","language":[{"iso":"eng"}],"publication":"Development","oa_version":"None","doi":"10.1242/dev.049320","page":"2409-2416","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1477-9129","0950-1991"]},"keyword":["Developmental Biology","Molecular Biology","Anther Tapetum","Arabidopsis","Cell Fate Establishment","EMS1","Reproductive Cell Lineage"]},{"scopus_import":"1","article_processing_charge":"No","month":"03","author":[{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","last_name":"Feng"},{"last_name":"Dickinson","full_name":"Dickinson, Hugh G.","first_name":"Hugh G."}],"status":"public","article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"Key steps in the evolution of the angiosperm anther include the patterning of the concentrically organized microsporangium and the incorporation of four such microsporangia into a leaf-like structure. Mutant studies in the model plant Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the cell lineages culminating in the different cell types present in the microsporangium (the microsporocytes, the tapetum, and the middle and endothecial layers), and (ii) some of the genes responsible for specifying their fates. However, the processes that confer polarity on the developing anther and position the microsporangia within it remain unclear. Certainly, data from a range of experimental strategies suggest that hormones play a central role in establishing polarity and the patterning of the anther initial, and may be responsible for locating the microsporangia. But the fact that microsporangia were originally positioned externally suggests that their development is likely to be autonomous, perhaps with the reproductive cells generating signals controlling the growth and division of the investing anther epidermis. These possibilities are discussed in the context of the expression of genes which initiate and maintain male and female reproductive development, and in the perspective of our current views of anther evolution."}],"date_published":"2010-03-22T00:00:00Z","publisher":"Portland Press Ltd.","intvolume":"        38","doi":"10.1042/bst0380571","page":"571-576","type":"journal_article","publication_identifier":{"issn":["0300-5127","1470-8752"]},"keyword":["Biochemistry","Anther Development","Arabidopsis","Cell Fate","Microsporangium","Polarity","Receptor Kinase"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","language":[{"iso":"eng"}],"oa_version":"None","publication":"Biochemical Society Transactions","year":"2010","issue":"2","external_id":{"pmid":["20298223"]},"title":"Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther","day":"22","volume":38,"publication_status":"published","date_created":"2023-01-16T09:22:18Z","pmid":1,"date_updated":"2023-05-08T10:57:59Z","_id":"12200","department":[{"_id":"XiFe"}],"citation":{"short":"X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576.","ista":"Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. Biochemical Society Transactions. 38(2), 571–576.","apa":"Feng, X., &#38; Dickinson, H. G. (2010). Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. Portland Press Ltd. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>. Portland Press Ltd., 2010. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>.","ama":"Feng X, Dickinson HG. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. 2010;38(2):571-576. doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>, vol. 38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>.","ieee":"X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther,” <i>Biochemical Society Transactions</i>, vol. 38, no. 2. Portland Press Ltd., pp. 571–576, 2010."}},{"intvolume":"         5","publisher":"BioMed Central","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Algorithms for Molecular Biology","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pubrep_id":"939","doi":"10.1186/1748-7188-5-37","article_number":"37","has_accepted_license":"1","month":"12","author":[{"first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Kupczok","full_name":"Kupczok, Anne"},{"first_name":"Heiko","last_name":"Schmidt","full_name":"Schmidt, Heiko"},{"first_name":"Arndt","full_name":"Von Haeseler, Arndt","last_name":"Von Haeseler"}],"scopus_import":1,"ddc":["576"],"abstract":[{"lang":"eng","text":"Background: The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches.\r\n\r\nResults: We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on average, worse results than a single gene phylogeny with complete taxon information.\r\n\r\nConclusions: For some methods, using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict."}],"date_published":"2010-12-06T00:00:00Z","file":[{"date_updated":"2020-07-14T12:45:40Z","file_name":"IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf","content_type":"application/pdf","file_id":"4739","file_size":723929,"access_level":"open_access","checksum":"e2497285388bc4da629bafb46662eb43","creator":"system","relation":"main_file","date_created":"2018-12-12T10:09:16Z"}],"quality_controlled":"1","status":"public","date_created":"2018-12-11T11:57:30Z","publication_status":"published","department":[{"_id":"JoBo"}],"citation":{"apa":"Kupczok, A., Schmidt, H., &#38; Von Haeseler, A. (2010). Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . <i>Algorithms for Molecular Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1748-7188-5-37\">https://doi.org/10.1186/1748-7188-5-37</a>","ista":"Kupczok A, Schmidt H, Von Haeseler A. 2010. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . Algorithms for Molecular Biology. 5(1), 37.","short":"A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology 5 (2010).","mla":"Kupczok, Anne, et al. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” <i>Algorithms for Molecular Biology</i>, vol. 5, no. 1, 37, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1748-7188-5-37\">10.1186/1748-7188-5-37</a>.","ama":"Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . <i>Algorithms for Molecular Biology</i>. 2010;5(1). doi:<a href=\"https://doi.org/10.1186/1748-7188-5-37\">10.1186/1748-7188-5-37</a>","chicago":"Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” <i>Algorithms for Molecular Biology</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1748-7188-5-37\">https://doi.org/10.1186/1748-7188-5-37</a>.","ieee":"A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ,” <i>Algorithms for Molecular Biology</i>, vol. 5, no. 1. BioMed Central, 2010."},"file_date_updated":"2020-07-14T12:45:40Z","date_updated":"2021-01-12T06:57:18Z","_id":"2409","year":"2010","issue":"1","publist_id":"4517","acknowledgement":"Financial support from the Wiener Wissenschafts-, Forschungs- and Technologiefonds (WWTF) is greatly appreciated. A.v.H. acknowledges support from the German Research Foundation (DFG, SPP-1174).","volume":5,"title":"Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ","day":"06"},{"publisher":"Genetics Society of America","oa":1,"intvolume":"       186","language":[{"iso":"eng"}],"ec_funded":1,"publication":"Genetics","oa_version":"Submitted Version","page":"1389 - 1410","doi":"10.1534/genetics.110.123240","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"12","author":[{"last_name":"Weissman","full_name":"Weissman, Daniel","first_name":"Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marcus","last_name":"Feldman","full_name":"Feldman, Marcus"},{"first_name":"Daniel","last_name":"Fisher","full_name":"Fisher, Daniel"}],"abstract":[{"text":"Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. ","lang":"eng"}],"date_published":"2010-12-01T00:00:00Z","status":"public","quality_controlled":"1","date_created":"2018-12-11T12:02:33Z","publication_status":"published","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/","open_access":"1"}],"department":[{"_id":"NiBa"}],"citation":{"short":"D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.","ista":"Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410.","apa":"Weissman, D., Feldman, M., &#38; Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>","chicago":"Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>. Genetics Society of America, 2010. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>.","mla":"Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>.","ama":"Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. 2010;186(4):1389-1410. doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>","ieee":"D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” <i>Genetics</i>, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010."},"date_updated":"2021-01-12T07:42:31Z","_id":"3303","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"year":"2010","issue":"4","acknowledgement":"This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. ","volume":186,"publist_id":"3337","title":"The rate of fitness-valley crossing in sexual populations","day":"01"},{"status":"public","title":"Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland","day":"01","quality_controlled":"1","volume":19,"abstract":[{"lang":"eng","text":"We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ∼1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika-like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales."}],"date_published":"2010-03-01T00:00:00Z","publist_id":"2779","scopus_import":1,"month":"03","author":[{"first_name":"Helen","last_name":"Senn","full_name":"Senn, Helen"},{"first_name":"Simon","full_name":"Goodman, Simon","last_name":"Goodman"},{"full_name":"Swanson, Graeme","last_name":"Swanson","first_name":"Graeme"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Pemberton, Josephine","last_name":"Pemberton","first_name":"Josephine"}],"year":"2010","issue":"5","date_updated":"2021-01-12T07:44:36Z","_id":"3604","doi":"10.1111/j.1365-294X.2009.04497.x","page":"910 - 924","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"citation":{"ista":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 19(5), 910–924.","apa":"Senn, H., Goodman, S., Swanson, G., Barton, N. H., &#38; Pemberton, J. (2010). Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">https://doi.org/10.1111/j.1365-294X.2009.04497.x</a>","short":"H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 910–924.","mla":"Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” <i>Molecular Ecology</i>, vol. 19, no. 5, Wiley-Blackwell, 2010, pp. 910–24, doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">10.1111/j.1365-294X.2009.04497.x</a>.","ama":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. <i>Molecular Ecology</i>. 2010;19(5):910-924. doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">10.1111/j.1365-294X.2009.04497.x</a>","chicago":"Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">https://doi.org/10.1111/j.1365-294X.2009.04497.x</a>.","ieee":"H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,” <i>Molecular Ecology</i>, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010."},"oa_version":"None","publication":"Molecular Ecology","publication_status":"published","date_created":"2018-12-11T12:04:12Z","publisher":"Wiley-Blackwell","intvolume":"        19"}]