[{"issue":"3","_id":"531","intvolume":"        39","publication_status":"published","doi":"10.1007/s10703-011-0131-3","type":"journal_article","isi":1,"corr_author":"1","fulldoi":"https://doi.org/10.1007/s10703-011-0131-3","article_type":"original","quality_controlled":"1","article_processing_charge":"No","publisher":"Springer","citation":{"mla":"Guerraoui, Rachid, et al. “Verification of STM on Relaxed Memory Models.” <i>Formal Methods in System Design</i>, vol. 39, no. 3, Springer, 2011, pp. 297–331, doi:<a href=\"https://doi.org/10.1007/s10703-011-0131-3\">10.1007/s10703-011-0131-3</a>.","ista":"Guerraoui R, Henzinger TA, Singh V. 2011. Verification of STM on relaxed memory models. Formal Methods in System Design. 39(3), 297–331.","short":"R. Guerraoui, T.A. Henzinger, V. Singh, Formal Methods in System Design 39 (2011) 297–331.","ama":"Guerraoui R, Henzinger TA, Singh V. Verification of STM on relaxed memory models. <i>Formal Methods in System Design</i>. 2011;39(3):297-331. doi:<a href=\"https://doi.org/10.1007/s10703-011-0131-3\">10.1007/s10703-011-0131-3</a>","chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Verification of STM on Relaxed Memory Models.” <i>Formal Methods in System Design</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s10703-011-0131-3\">https://doi.org/10.1007/s10703-011-0131-3</a>.","ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Verification of STM on relaxed memory models,” <i>Formal Methods in System Design</i>, vol. 39, no. 3. Springer, pp. 297–331, 2011.","apa":"Guerraoui, R., Henzinger, T. A., &#38; Singh, V. (2011). Verification of STM on relaxed memory models. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-011-0131-3\">https://doi.org/10.1007/s10703-011-0131-3</a>"},"author":[{"full_name":"Guerraoui, Rachid","last_name":"Guerraoui","first_name":"Rachid"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Singh, Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","last_name":"Singh","first_name":"Vasu"}],"main_file_link":[{"url":"https://infoscience.epfl.ch/record/178042/files/art3A10.10072Fs10703-011-0131-3.pdf","open_access":"1"}],"publist_id":"7288","date_created":"2018-12-11T11:47:00Z","day":"01","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"abstract":[{"text":"Software transactional memories (STM) are described in the literature with assumptions of sequentially consistent program execution and atomicity of high level operations like read, write, and abort. However, in a realistic setting, processors use relaxed memory models to optimize hardware performance. Moreover, the atomicity of operations depends on the underlying hardware. This paper presents the first approach to verify STMs under relaxed memory models with atomicity of 32 bit loads and stores, and read-modify-write operations. We describe RML, a simple language for expressing concurrent programs. We develop a semantics of RML parametrized by a relaxed memory model. We then present our tool, FOIL, which takes as input the RML description of an STM algorithm restricted to two threads and two variables, and the description of a memory model, and automatically determines the locations of fences, which if inserted, ensure the correctness of the restricted STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and McRT STM under the memory models of sequential consistency, total store order, partial store order, and relaxed memory order for two threads and two variables. Finally, we extend the verification results for DSTM and TL2 to an arbitrary number of threads and variables by manually proving that the structural properties of STMs are satisfied at the hardware level of atomicity under the considered relaxed memory models.","lang":"eng"}],"oa_version":"Published Version","ddc":["000"],"title":"Verification of STM on relaxed memory models","status":"public","volume":39,"date_updated":"2025-09-30T09:23:08Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"297 - 331","month":"12","date_published":"2011-12-01T00:00:00Z","scopus_import":"1","publication":"Formal Methods in System Design","external_id":{"isi":["000297596900004"]},"year":"2011"},{"fulldoi":"https://doi.org/10.15479/AT:IST-2011-0009","article_processing_charge":"No","file_date_updated":"2020-07-14T12:46:39Z","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"_id":"5379","type":"technical_report","doi":"10.15479/AT:IST-2011-0009","related_material":{"record":[{"relation":"later_version","id":"3165","status":"public"}]},"alternative_title":["IST Austria Technical Report"],"publication_status":"published","date_published":"2011-07-11T00:00:00Z","month":"07","page":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","file":[{"access_level":"open_access","date_created":"2018-12-12T11:53:43Z","checksum":"0b354264229045d982332fd2cb5b9a26","file_size":388665,"date_updated":"2020-07-14T12:46:39Z","creator":"system","file_id":"5504","file_name":"IST-2011-0009_IST-2011-0009.pdf","relation":"main_file","content_type":"application/pdf"}],"pubrep_id":"15","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is ̃O(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the ̃O(n·m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of O(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m > n4/3 an earlier bound of O(min(m1.5, m·n2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n2), which is an improvement over earlier bounds for m > n4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem."}],"oa":1,"date_created":"2018-12-12T11:38:59Z","day":"11","publisher":"IST Austria","citation":{"ieee":"K. Chatterjee and M. Henzinger, <i>An O(n2) time algorithm for alternating Büchi games</i>. IST Austria, 2011.","apa":"Chatterjee, K., &#38; Henzinger, M. (2011). <i>An O(n2) time algorithm for alternating Büchi games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">https://doi.org/10.15479/AT:IST-2011-0009</a>","ista":"Chatterjee K, Henzinger M. 2011. An O(n2) time algorithm for alternating Büchi games, IST Austria, 20p.","mla":"Chatterjee, Krishnendu, and Monika Henzinger. <i>An O(N2) Time Algorithm for Alternating Büchi Games</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">10.15479/AT:IST-2011-0009</a>.","short":"K. Chatterjee, M. Henzinger, An O(N2) Time Algorithm for Alternating Büchi Games, IST Austria, 2011.","ama":"Chatterjee K, Henzinger M. <i>An O(N2) Time Algorithm for Alternating Büchi Games</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">10.15479/AT:IST-2011-0009</a>","chicago":"Chatterjee, Krishnendu, and Monika Henzinger. <i>An O(N2) Time Algorithm for Alternating Büchi Games</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">https://doi.org/10.15479/AT:IST-2011-0009</a>."},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H"}],"date_updated":"2025-07-10T11:52:28Z","title":"An O(n2) time algorithm for alternating Büchi games","status":"public","ddc":["000","004"],"oa_version":"Published Version"},{"fulldoi":"https://doi.org/10.15479/AT:IST-2011-0008","file_date_updated":"2020-07-14T12:46:39Z","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"_id":"5380","type":"technical_report","doi":"10.15479/AT:IST-2011-0008","related_material":{"record":[{"relation":"later_version","status":"public","id":"3338"}]},"alternative_title":["IST Austria Technical Report"],"publication_status":"published","month":"07","date_published":"2011-07-11T00:00:00Z","page":"53","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","file":[{"date_created":"2018-12-12T11:54:22Z","access_level":"open_access","checksum":"0fd38186409be819a911c4990fa79d1f","file_name":"IST-2011-0008_IST-2011-0008.pdf","content_type":"application/pdf","relation":"main_file","file_size":500399,"date_updated":"2020-07-14T12:46:39Z","creator":"system","file_id":"5544"}],"pubrep_id":"16","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"oa":1,"day":"11","date_created":"2018-12-12T11:39:00Z","citation":{"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>","ieee":"K. Chatterjee, <i>Bounded rationality in concurrent parity games</i>. 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>.","ista":"Chatterjee K. 2011. Bounded rationality in concurrent parity games, IST Austria, 53p.","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>.","short":"K. Chatterjee, Bounded Rationality in Concurrent Parity Games, IST Austria, 2011."},"publisher":"IST Austria","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"date_updated":"2025-06-26T09:28:52Z","status":"public","title":"Bounded rationality in concurrent parity games","ddc":["000"],"oa_version":"Published Version"},{"pubrep_id":"18","file":[{"checksum":"1322b652d6ab07eb5248298a3f91c1cf","date_created":"2018-12-12T11:54:24Z","access_level":"open_access","creator":"system","file_id":"5546","date_updated":"2020-07-14T12:46:40Z","file_size":335997,"content_type":"application/pdf","relation":"main_file","file_name":"IST-2011-0006_IST-2011-0006.pdf"}],"year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2011-06-27T00:00:00Z","month":"06","page":"18","ddc":["000","005"],"oa_version":"Published Version","date_updated":"2025-04-15T08:12:24Z","status":"public","title":"Robustness of structurally equivalent concurrent parity games","day":"27","date_created":"2018-12-12T11:39:00Z","publisher":"IST Austria","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"citation":{"ieee":"K. Chatterjee, <i>Robustness of structurally equivalent concurrent parity games</i>. 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>","short":"K. Chatterjee, Robustness of Structurally Equivalent Concurrent Parity Games, IST Austria, 2011.","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>","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>.","ista":"Chatterjee K. 2011. Robustness of structurally equivalent concurrent parity games, IST Austria, 18p."},"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"}],"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"oa":1,"file_date_updated":"2020-07-14T12:46:40Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT:IST-2011-0006","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"status":"public","id":"3341","relation":"later_version"}]},"publication_status":"published","type":"technical_report","doi":"10.15479/AT:IST-2011-0006","_id":"5382","publication_identifier":{"issn":["2664-1690"]}},{"type":"technical_report","doi":"10.15479/AT:IST-2011-0005","related_material":{"record":[{"relation":"later_version","status":"public","id":"3323"}]},"alternative_title":["IST Austria Technical Report"],"publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"_id":"5383","file_date_updated":"2020-07-14T12:46:40Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT:IST-2011-0005","date_updated":"2024-10-09T20:54:31Z","title":"On an efficient decision procedure for imperative tree data structures","status":"public","ddc":["000","006"],"oa_version":"Published Version","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"oa":1,"date_created":"2018-12-12T11:39:01Z","day":"26","publisher":"IST Austria","author":[{"first_name":"Thomas","last_name":"Wies","full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Muñiz, Marco","first_name":"Marco","last_name":"Muñiz"},{"last_name":"Kuncak","first_name":"Viktor","full_name":"Kuncak, Viktor"}],"citation":{"ieee":"T. Wies, M. Muñiz, and V. Kuncak, <i>On an efficient decision procedure for imperative tree data structures</i>. IST Austria, 2011.","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>","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>.","short":"T. Wies, M. Muñiz, V. Kuncak, On an Efficient Decision Procedure for Imperative Tree Data Structures, IST Austria, 2011.","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>.","ista":"Wies T, Muñiz M, Kuncak V. 2011. On an efficient decision procedure for imperative tree data structures, IST Austria, 25p."},"year":"2011","file":[{"checksum":"b20029184c4a819c5f4466a4a3d238b5","access_level":"open_access","date_created":"2018-12-12T11:53:01Z","creator":"system","file_id":"5462","file_size":619053,"date_updated":"2020-07-14T12:46:40Z","relation":"main_file","content_type":"application/pdf","file_name":"IST-2011-0005_IST-2011-0005.pdf"}],"pubrep_id":"19","date_published":"2011-04-26T00:00:00Z","month":"04","page":"25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"5384","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"relation":"later_version","status":"public","id":"2957"}]},"doi":"10.15479/AT:IST-2011-0004","type":"technical_report","corr_author":"1","fulldoi":"https://doi.org/10.15479/AT:IST-2011-0004","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:40Z","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tracol, Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","last_name":"Tracol","first_name":"Mathieu"}],"publisher":"IST Austria","citation":{"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>.","ista":"Chatterjee K, Tracol M. 2011. Decidable problems for probabilistic automata on infinite words, IST Austria, 30p.","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>.","short":"K. Chatterjee, M. Tracol, Decidable Problems for Probabilistic Automata on Infinite Words, IST Austria, 2011.","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>","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>","ieee":"K. Chatterjee and M. Tracol, <i>Decidable problems for probabilistic automata on infinite words</i>. IST Austria, 2011."},"day":"11","date_created":"2018-12-12T11:39:01Z","oa":1,"abstract":[{"lang":"eng","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."}],"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","ddc":["000","005"],"title":"Decidable problems for probabilistic automata on infinite words","status":"public","date_updated":"2025-09-30T08:07:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"30","date_published":"2011-04-11T00:00:00Z","month":"04","pubrep_id":"20","file":[{"checksum":"f5a0f664fadc335990f5fcf138df19f1","access_level":"open_access","date_created":"2018-12-12T11:54:23Z","file_id":"5545","creator":"system","file_size":570827,"date_updated":"2020-07-14T12:46:40Z","relation":"main_file","content_type":"application/pdf","file_name":"IST-2011-004_IST-2011-0004.pdf"}],"year":"2011"},{"pubrep_id":"22","file":[{"date_updated":"2020-07-14T12:46:41Z","file_size":26390601,"creator":"system","file_id":"5495","file_name":"IST-2011-0002_IST-2011-0002.pdf","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T11:53:34Z","access_level":"open_access","checksum":"ad64c2add5fe2ad10e9d5c669f3f9526"}],"year":"2011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"69","month":"03","date_published":"2011-03-28T00:00:00Z","oa_version":"Published Version","ddc":["000"],"status":"public","title":"Enforcing topological constraints in random field image segmentation","date_updated":"2024-10-09T20:54:30Z","publisher":"IST Austria","author":[{"first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"full_name":"Freedman, Daniel","first_name":"Daniel","last_name":"Freedman"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert"}],"citation":{"short":"C. Chen, D. Freedman, C. Lampert, Enforcing Topological Constraints in Random Field Image Segmentation, IST Austria, 2011.","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>","ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation, IST Austria, 69p.","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.","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>"},"date_created":"2018-12-12T11:39:02Z","day":"28","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"ChLa"}],"abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:41Z","fulldoi":"https://doi.org/10.15479/AT:IST-2011-0002","publication_status":"published","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"relation":"later_version","id":"3336","status":"public"}]},"doi":"10.15479/AT:IST-2011-0002","type":"technical_report","_id":"5386","publication_identifier":{"issn":["2664-1690"]}},{"date_published":"2011-02-16T00:00:00Z","month":"02","page":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","pubrep_id":"23","file":[{"date_updated":"2020-07-14T12:46:41Z","file_size":329976,"creator":"system","file_id":"5458","file_name":"IST-2011-0001_IST-2011-0001.pdf","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T11:52:57Z","access_level":"open_access","checksum":"824d6c70e6d3feb3e836b009e0b3cf73"}],"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"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."}],"oa":1,"date_created":"2018-12-12T11:39:02Z","day":"16","publisher":"IST Austria","citation":{"ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p.","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>.","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011.","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>.","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>","ieee":"K. Chatterjee and L. Doyen, <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria, 2011.","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>"},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"date_updated":"2025-04-15T08:12:14Z","status":"public","title":"Energy and mean-payoff parity Markov decision processes","ddc":["000","005"],"oa_version":"Published Version","fulldoi":"https://doi.org/10.15479/AT:IST-2011-0001","file_date_updated":"2020-07-14T12:46:41Z","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"_id":"5387","type":"technical_report","doi":"10.15479/AT:IST-2011-0001","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"id":"3345","status":"public","relation":"later_version"}]},"publication_status":"published"},{"intvolume":"       474","day":"08","date_created":"2018-12-11T11:47:18Z","publist_id":"7224","_id":"580","author":[{"first_name":"Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Onur Hosten"}],"publisher":"Nature Publishing Group","issue":"7350","citation":{"ieee":"O. Hosten, “Quantum physics: How to catch a wave,” <i>Nature</i>, vol. 474, no. 7350. Nature Publishing Group, pp. 170–171, 2011.","apa":"Hosten, O. (2011). Quantum physics: How to catch a wave. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>","ista":"Hosten O. 2011. Quantum physics: How to catch a wave. Nature. 474(7350), 170–171.","mla":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>, vol. 474, no. 7350, Nature Publishing Group, 2011, pp. 170–71, doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>.","chicago":"Hosten, Onur. “Quantum Physics: How to Catch a Wave.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/474170a\">https://doi.org/10.1038/474170a</a>.","short":"O. Hosten, Nature 474 (2011) 170–171.","ama":"Hosten O. Quantum physics: How to catch a wave. <i>Nature</i>. 2011;474(7350):170-171. doi:<a href=\"https://doi.org/10.1038/474170a\">10.1038/474170a</a>"},"date_updated":"2021-01-12T08:03:34Z","volume":474,"type":"journal_article","doi":"10.1038/474170a","title":"Quantum physics: How to catch a wave","status":"public","publication_status":"published","date_published":"2011-06-08T00:00:00Z","month":"06","page":"170 - 171","fulldoi":"https://doi.org/10.1038/474170a","extern":1,"year":"2011","publication":"Nature","quality_controlled":0},{"alternative_title":["Optics InfoBase Conference Papers"],"publication_status":"published","type":"conference","date_updated":"2021-01-12T08:03:44Z","doi":"10.1364/CLEO_AT.2011.JThB130","title":"Methods towards achieving precise birefringent focusing","status":"public","date_created":"2018-12-11T11:47:20Z","publist_id":"7220","day":"01","publisher":"OSA","author":[{"full_name":"Schmid, David","last_name":"Schmid","first_name":"David"},{"first_name":"Shiraz","last_name":"Hazrat","full_name":"Hazrat, Shiraz"},{"full_name":"Rangarajan, Radhika","first_name":"Radhika","last_name":"Rangarajan"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","full_name":"Onur Hosten","last_name":"Hosten","first_name":"Onur"},{"full_name":"Quint, Stephan","last_name":"Quint","first_name":"Stephan"},{"last_name":"Kwiat","first_name":"Paul","full_name":"Kwiat, Paul G"}],"citation":{"ama":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. Methods towards achieving precise birefringent focusing. In: OSA; 2011. doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>","short":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, P. Kwiat, in:, OSA, 2011.","chicago":"Schmid, David, Shiraz Hazrat, Radhika Rangarajan, Onur Hosten, Stephan Quint, and Paul Kwiat. “Methods towards Achieving Precise Birefringent Focusing.” OSA, 2011. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>.","ista":"Schmid D, Hazrat S, Rangarajan R, Hosten O, Quint S, Kwiat P. 2011. Methods towards achieving precise birefringent focusing. QELS: Quantum Electronics and Laser Science, Optics InfoBase Conference Papers, .","mla":"Schmid, David, et al. <i>Methods towards Achieving Precise Birefringent Focusing</i>. OSA, 2011, doi:<a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">10.1364/CLEO_AT.2011.JThB130</a>.","apa":"Schmid, D., Hazrat, S., Rangarajan, R., Hosten, O., Quint, S., &#38; Kwiat, P. (2011). Methods towards achieving precise birefringent focusing. Presented at the QELS: Quantum Electronics and Laser Science, OSA. <a href=\"https://doi.org/10.1364/CLEO_AT.2011.JThB130\">https://doi.org/10.1364/CLEO_AT.2011.JThB130</a>","ieee":"D. Schmid, S. Hazrat, R. Rangarajan, O. Hosten, S. Quint, and P. Kwiat, “Methods towards achieving precise birefringent focusing,” presented at the QELS: Quantum Electronics and Laser Science, 2011."},"_id":"585","abstract":[{"lang":"eng","text":"We present two independent schemes for the precise focusing of orthogonal polarizations of light at arbitrary relative locations. The first scheme uses a polarization Sagnac interferometer, the second a set of three birefringent elements.\n\n"}],"conference":{"name":"QELS: Quantum Electronics and Laser Science"},"quality_controlled":0,"year":"2011","extern":1,"date_published":"2011-01-01T00:00:00Z","month":"01","fulldoi":"https://doi.org/10.1364/CLEO_AT.2011.JThB130"},{"year":"2011","extern":1,"quality_controlled":0,"publication":"Physical Review Letters","fulldoi":"https://doi.org/10.1103/PhysRevLett.107.063904","date_published":"2011-08-04T00:00:00Z","month":"08","title":"Raman lasing with a cold atom gain medium in a high-finesse optical cavity","doi":"10.1103/PhysRevLett.107.063904","status":"public","volume":107,"date_updated":"2021-01-12T08:05:05Z","type":"journal_article","publication_status":"published","abstract":[{"text":"We demonstrate a Raman laser using cold Rb87 atoms as the gain medium in a high-finesse optical cavity. We observe robust continuous wave lasing in the atypical regime where single atoms can considerably affect the cavity field. Consequently, we discover unusual lasing threshold behavior in the system causing jumps in lasing power, and propose a model to explain the effect. We also measure the intermode laser linewidth, and observe values as low as 80Hz. The tunable gain properties of this laser suggest multiple directions for future research.","lang":"eng"}],"publisher":"American Physical Society","issue":"6","author":[{"full_name":"Vrijsen, Geert","last_name":"Vrijsen","first_name":"Geert"},{"full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","first_name":"Onur"},{"first_name":"Jongmin","last_name":"Lee","full_name":"Lee, Jongmin"},{"last_name":"Bernon","first_name":"Simon","full_name":"Bernon, Simon"},{"first_name":"Mark","last_name":"Kasevich","full_name":"Kasevich, Mark A"}],"citation":{"ista":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. 2011. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. Physical Review Letters. 107(6).","mla":"Vrijsen, Geert, et al. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” <i>Physical Review Letters</i>, vol. 107, no. 6, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>.","short":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, M. Kasevich, Physical Review Letters 107 (2011).","chicago":"Vrijsen, Geert, Onur Hosten, Jongmin Lee, Simon Bernon, and Mark Kasevich. “Raman Lasing with a Cold Atom Gain Medium in a High-Finesse Optical Cavity.” <i>Physical Review Letters</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>.","ama":"Vrijsen G, Hosten O, Lee J, Bernon S, Kasevich M. Raman lasing with a cold atom gain medium in a high-finesse optical cavity. <i>Physical Review Letters</i>. 2011;107(6). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">10.1103/PhysRevLett.107.063904</a>","ieee":"G. Vrijsen, O. Hosten, J. Lee, S. Bernon, and M. Kasevich, “Raman lasing with a cold atom gain medium in a high-finesse optical cavity,” <i>Physical Review Letters</i>, vol. 107, no. 6. American Physical Society, 2011.","apa":"Vrijsen, G., Hosten, O., Lee, J., Bernon, S., &#38; Kasevich, M. (2011). Raman lasing with a cold atom gain medium in a high-finesse optical cavity. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.107.063904\">https://doi.org/10.1103/PhysRevLett.107.063904</a>"},"_id":"586","publist_id":"7223","date_created":"2018-12-11T11:47:20Z","intvolume":"       107","day":"04"},{"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly."}],"date_created":"2018-12-11T11:47:24Z","publist_id":"7209","intvolume":"         9","day":"01","publisher":"Public Library of Science","issue":"3","author":[{"orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky"},{"first_name":"Patricia","last_name":"Grob","full_name":"Grob, Patricia"},{"full_name":"Ebmeier, Christopher","first_name":"Christopher","last_name":"Ebmeier"},{"full_name":"Nogales, Eva","last_name":"Nogales","first_name":"Eva"},{"first_name":"Dylan","last_name":"Taatjes","full_name":"Taatjes, Dylan"}],"citation":{"ista":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. 2011. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biology. 9(3).","mla":"Bernecky, Carrie, et al. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>, vol. 9, no. 3, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>.","short":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, D. Taatjes, PLoS Biology 9 (2011).","ama":"Bernecky C, Grob P, Ebmeier C, Nogales E, Taatjes D. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. 2011;9(3). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000603\">10.1371/journal.pbio.1000603</a>","chicago":"Bernecky, Carrie, Patricia Grob, Christopher Ebmeier, Eva Nogales, and Dylan Taatjes. “Molecular Architecture of the Human Mediator-RNA Polymerase II-TFIIF Assembly.” <i>PLoS Biology</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>.","ieee":"C. Bernecky, P. Grob, C. Ebmeier, E. Nogales, and D. Taatjes, “Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly,” <i>PLoS Biology</i>, vol. 9, no. 3. Public Library of Science, 2011.","apa":"Bernecky, C., Grob, P., Ebmeier, C., Nogales, E., &#38; Taatjes, D. (2011). Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000603\">https://doi.org/10.1371/journal.pbio.1000603</a>"},"_id":"597","volume":9,"type":"journal_article","date_updated":"2021-01-12T08:05:25Z","doi":"10.1371/journal.pbio.1000603","title":"Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly","status":"public","publication_status":"published","oa_version":"None","month":"03","date_published":"2011-03-01T00:00:00Z","fulldoi":"https://doi.org/10.1371/journal.pbio.1000603","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","article_processing_charge":"No","extern":"1","publication":"PLoS Biology"},{"type":"journal_article","doi":"10.1073/pnas.1106134109","publication_status":"published","pmid":1,"publication_identifier":{"issn":["0027-8424","1091-6490"]},"intvolume":"       108","issue":"51","_id":"6137","quality_controlled":"1","fulldoi":"https://doi.org/10.1073/pnas.1106134109","date_updated":"2021-01-12T08:06:18Z","volume":108,"title":"Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans","status":"public","oa_version":"Submitted Version","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Variation in food quality and abundance requires animals to decide whether to stay on a poor food patch or leave in search of better food. An important question in behavioral ecology asks when is it optimal for an animal to leave a food patch it is depleting. Although optimal foraging is central to evolutionary success, the neural and molecular mechanisms underlying it are poorly understood. Here we investigate the neuronal basis for adaptive food-leaving behavior in response to resource depletion in Caenorhabditis elegans, and identify several of the signaling pathways involved. The ASE neurons, previously implicated in salt chemoattraction, promote food-leaving behavior via a cGMP pathway as food becomes limited. High ambient O2 promotes food-leaving via the O2-sensing neurons AQR, PQR, and URX. Ectopic activation of these neurons using channelrhodopsin is sufficient to induce high food-leaving behavior. In contrast, the neuropeptide receptor NPR-1, which regulates social behavior on food, acts in the ASE neurons, the nociceptive ASH neurons, and in the RMG interneuron to repress food-leaving. Finally, we show that neuroendocrine signaling by TGF-β/DAF-7 and neuronal insulin signaling are necessary for adaptive food-leaving behavior. We suggest that animals integrate information about their nutritional state with ambient oxygen and gustatory stimuli to formulate optimal foraging strategies."}],"oa":1,"date_created":"2019-03-20T14:30:06Z","day":"20","author":[{"full_name":"Milward, K.","last_name":"Milward","first_name":"K."},{"last_name":"Busch","first_name":"K. E.","full_name":"Busch, K. E."},{"full_name":"Murphy, R. J.","first_name":"R. J.","last_name":"Murphy"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario"},{"full_name":"Olofsson, B.","last_name":"Olofsson","first_name":"B."}],"citation":{"ama":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(51):20672-20677. doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>","chicago":"Milward, K., K. E. Busch, R. J. Murphy, Mario de Bono, and B. Olofsson. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>.","short":"K. Milward, K.E. Busch, R.J. Murphy, M. de Bono, B. Olofsson, Proceedings of the National Academy of Sciences 108 (2011) 20672–20677.","mla":"Milward, K., et al. “Neuronal and Molecular Substrates for Optimal Foraging in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51, National Academy of Sciences, 2011, pp. 20672–77, doi:<a href=\"https://doi.org/10.1073/pnas.1106134109\">10.1073/pnas.1106134109</a>.","ista":"Milward K, Busch KE, Murphy RJ, de Bono M, Olofsson B. 2011. Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 108(51), 20672–20677.","ieee":"K. Milward, K. E. Busch, R. J. Murphy, M. de Bono, and B. Olofsson, “Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 51. National Academy of Sciences, pp. 20672–20677, 2011.","apa":"Milward, K., Busch, K. E., Murphy, R. J., de Bono, M., &#38; Olofsson, B. (2011). Neuronal and molecular substrates for optimal foraging in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1106134109\">https://doi.org/10.1073/pnas.1106134109</a>"},"publisher":"National Academy of Sciences","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3251049/","open_access":"1"}],"year":"2011","extern":"1","external_id":{"pmid":["22135454"]},"publication":"Proceedings of the National Academy of Sciences","month":"12","date_published":"2011-12-20T00:00:00Z","page":"20672-20677","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"status":"public","title":"Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior","date_updated":"2021-01-12T08:06:18Z","volume":69,"citation":{"ama":"Bretscher AJ, Kodama-Namba E, Busch KE, et al. Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. <i>Neuron</i>. 2011;69(6):1099-1113. doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">10.1016/j.neuron.2011.02.023</a>","chicago":"Bretscher, Andrew Jonathan, Eiji Kodama-Namba, Karl Emanuel Busch, Robin Joseph Murphy, Zoltan Soltesz, Patrick Laurent, and Mario de Bono. “Temperature, Oxygen, and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” <i>Neuron</i>. Elsevier BV, 2011. <a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">https://doi.org/10.1016/j.neuron.2011.02.023</a>.","short":"A.J. Bretscher, E. Kodama-Namba, K.E. Busch, R.J. Murphy, Z. Soltesz, P. Laurent, M. de Bono, Neuron 69 (2011) 1099–1113.","mla":"Bretscher, Andrew Jonathan, et al. “Temperature, Oxygen, and Salt-Sensing Neurons in C. Elegans Are Carbon Dioxide Sensors That Control Avoidance Behavior.” <i>Neuron</i>, vol. 69, no. 6, Elsevier BV, 2011, pp. 1099–113, doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">10.1016/j.neuron.2011.02.023</a>.","ista":"Bretscher AJ, Kodama-Namba E, Busch KE, Murphy RJ, Soltesz Z, Laurent P, de Bono M. 2011. Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. Neuron. 69(6), 1099–1113.","ieee":"A. J. Bretscher <i>et al.</i>, “Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior,” <i>Neuron</i>, vol. 69, no. 6. Elsevier BV, pp. 1099–1113, 2011.","apa":"Bretscher, A. J., Kodama-Namba, E., Busch, K. E., Murphy, R. J., Soltesz, Z., Laurent, P., &#38; de Bono, M. (2011). Temperature, oxygen, and salt-sensing neurons in C. elegans are carbon dioxide sensors that control avoidance behavior. <i>Neuron</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.neuron.2011.02.023\">https://doi.org/10.1016/j.neuron.2011.02.023</a>"},"publisher":"Elsevier BV","author":[{"last_name":"Bretscher","first_name":"Andrew Jonathan","full_name":"Bretscher, Andrew Jonathan"},{"full_name":"Kodama-Namba, Eiji","last_name":"Kodama-Namba","first_name":"Eiji"},{"first_name":"Karl Emanuel","last_name":"Busch","full_name":"Busch, Karl Emanuel"},{"full_name":"Murphy, Robin Joseph","last_name":"Murphy","first_name":"Robin Joseph"},{"full_name":"Soltesz, Zoltan","first_name":"Zoltan","last_name":"Soltesz"},{"full_name":"Laurent, Patrick","last_name":"Laurent","first_name":"Patrick"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario"}],"day":"24","date_created":"2019-03-20T15:01:41Z","oa":1,"language":[{"iso":"eng"}],"file":[{"checksum":"547cffd123f4c508ae927c9244b8f92a","date_created":"2019-03-20T15:06:32Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2011_Cell_Bretscher.pdf","creator":"kschuh","file_id":"6139","date_updated":"2020-07-14T12:47:20Z","file_size":2448332}],"publication":"Neuron","external_id":{"pmid":["21435556"]},"extern":"1","year":"2011","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"1099-1113","month":"03","date_published":"2011-03-24T00:00:00Z","publication_status":"published","doi":"10.1016/j.neuron.2011.02.023","type":"journal_article","_id":"6138","license":"https://creativecommons.org/licenses/by/4.0/","issue":"6","intvolume":"        69","publication_identifier":{"issn":["0896-6273"]},"pmid":1,"has_accepted_license":"1","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:20Z","fulldoi":"https://doi.org/10.1016/j.neuron.2011.02.023"},{"ddc":["570"],"oa_version":"Published Version","date_updated":"2021-01-12T08:06:19Z","volume":7,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability","status":"public","day":"17","date_created":"2019-03-20T15:08:23Z","author":[{"full_name":"Arellano-Carbajal, Fausto","last_name":"Arellano-Carbajal","first_name":"Fausto"},{"full_name":"Briseño-Roa, Luis","last_name":"Briseño-Roa","first_name":"Luis"},{"first_name":"Africa","last_name":"Couto","full_name":"Couto, Africa"},{"last_name":"Cheung","first_name":"Benny H. H.","full_name":"Cheung, Benny H. H."},{"first_name":"Michel","last_name":"Labouesse","full_name":"Labouesse, Michel"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario"}],"citation":{"ieee":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B. H. H. Cheung, M. Labouesse, and M. de Bono, “Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability,” <i>PLoS Genetics</i>, vol. 7, no. 3. Public Library of Science, 2011.","apa":"Arellano-Carbajal, F., Briseño-Roa, L., Couto, A., Cheung, B. H. H., Labouesse, M., &#38; de Bono, M. (2011). Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1001341\">https://doi.org/10.1371/journal.pgen.1001341</a>","short":"F. Arellano-Carbajal, L. Briseño-Roa, A. Couto, B.H.H. Cheung, M. Labouesse, M. de Bono, PLoS Genetics 7 (2011).","ama":"Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono M. Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. <i>PLoS Genetics</i>. 2011;7(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1001341\">10.1371/journal.pgen.1001341</a>","chicago":"Arellano-Carbajal, Fausto, Luis Briseño-Roa, Africa Couto, Benny H. H. Cheung, Michel Labouesse, and Mario de Bono. “Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability.” <i>PLoS Genetics</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pgen.1001341\">https://doi.org/10.1371/journal.pgen.1001341</a>.","mla":"Arellano-Carbajal, Fausto, et al. “Macoilin, a Conserved Nervous System–Specific ER Membrane Protein That Regulates Neuronal Excitability.” <i>PLoS Genetics</i>, vol. 7, no. 3, e1001341, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1001341\">10.1371/journal.pgen.1001341</a>.","ista":"Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono M. 2011. Macoilin, a conserved nervous system–specific ER membrane protein that regulates neuronal excitability. PLoS Genetics. 7(3), e1001341."},"publisher":"Public Library of Science","abstract":[{"lang":"eng","text":"Genome sequence comparisons have highlighted many novel gene families that are conserved across animal phyla but whose biological function is unknown. Here, we functionally characterize a member of one such family, the macoilins. Macoilins are characterized by several highly conserved predicted transmembrane domains towards the N-terminus and by coiled-coil regions C-terminally. They are found throughout Eumetazoa but not in other organisms. Mutants for the single Caenorhabditis elegans macoilin, maco-1, exhibit a constellation of behavioral phenotypes, including defects in aggregation, O2 responses, and swimming. MACO-1 protein is expressed broadly and specifically in the nervous system and localizes to the rough endoplasmic reticulum; it is excluded from dendrites and axons. Apart from subtle synapse defects, nervous system development appears wild-type in maco-1 mutants. However, maco-1 animals are resistant to the cholinesterase inhibitor aldicarb and sensitive to levamisole, suggesting pre-synaptic defects. Using in vivo imaging, we show that macoilin is required to evoke Ca2+ transients, at least in some neurons: in maco-1 mutants the O2-sensing neuron PQR is unable to generate a Ca2+ response to a rise in O2. By genetically disrupting neurotransmission, we show that pre-synaptic input is not necessary for PQR to respond to O2, indicating that the response is mediated by cell-intrinsic sensory transduction and amplification. Disrupting the sodium leak channels NCA-1/NCA-2, or the N-,P/Q,R-type voltage-gated Ca2+ channels, also fails to disrupt Ca2+ responses in the PQR cell body to O2 stimuli. By contrast, mutations in egl-19, which encodes the only Caenorhabditis elegans L-type voltage-gated Ca2+ channel α1 subunit, recapitulate the Ca2+ response defect we see in maco-1 mutants, although we do not see defects in localization of EGL-19. Together, our data suggest that macoilin acts in the ER to regulate assembly or traffic of ion channels or ion channel regulators."}],"language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["21437263"]},"publication":"PLoS Genetics","file":[{"checksum":"c609b2ce616d7dafbb617ec5d022f1ea","date_created":"2019-03-20T15:18:11Z","access_level":"open_access","creator":"kschuh","file_id":"6141","file_size":5625063,"date_updated":"2020-07-14T12:47:20Z","content_type":"application/pdf","relation":"main_file","file_name":"2011_PLOS_Arellano-Carbajal.PDF"}],"extern":"1","year":"2011","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2011-03-17T00:00:00Z","month":"03","publication_status":"published","type":"journal_article","doi":"10.1371/journal.pgen.1001341","article_number":"e1001341","intvolume":"         7","_id":"6140","issue":"3","pmid":1,"publication_identifier":{"issn":["1553-7404"]},"file_date_updated":"2020-07-14T12:47:20Z","has_accepted_license":"1","quality_controlled":"1","fulldoi":"https://doi.org/10.1371/journal.pgen.1001341"},{"quality_controlled":"1","publication":"Journal of Biological Chemistry","year":"2011","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2011-07-22T00:00:00Z","month":"07","fulldoi":"https://doi.org/10.1074/jbc.m111.247395","page":"25675-25686","oa_version":"Published Version","publication_status":"published","date_updated":"2021-01-12T08:06:58Z","volume":286,"type":"journal_article","status":"public","doi":"10.1074/jbc.m111.247395","title":"The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers","date_created":"2019-04-11T20:57:43Z","day":"22","intvolume":"       286","author":[{"last_name":"Baranova","first_name":"Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia"},{"full_name":"Nilebäck, Erik","first_name":"Erik","last_name":"Nilebäck"},{"last_name":"Haller","first_name":"F. Michael","full_name":"Haller, F. Michael"},{"first_name":"David C.","last_name":"Briggs","full_name":"Briggs, David C."},{"full_name":"Svedhem, Sofia","first_name":"Sofia","last_name":"Svedhem"},{"last_name":"Day","first_name":"Anthony J.","full_name":"Day, Anthony J."},{"first_name":"Ralf P.","last_name":"Richter","full_name":"Richter, Ralf P."}],"citation":{"apa":"Baranova, N. S., Nilebäck, E., Haller, F. M., Briggs, D. C., Svedhem, S., Day, A. J., &#38; Richter, R. P. (2011). The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.m111.247395\">https://doi.org/10.1074/jbc.m111.247395</a>","ieee":"N. S. Baranova <i>et al.</i>, “The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers,” <i>Journal of Biological Chemistry</i>, vol. 286, no. 29. American Society for Biochemistry &#38; Molecular Biology, pp. 25675–25686, 2011.","chicago":"Baranova, Natalia S., Erik Nilebäck, F. Michael Haller, David C. Briggs, Sofia Svedhem, Anthony J. Day, and Ralf P. Richter. “The Inflammation-Associated Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology, 2011. <a href=\"https://doi.org/10.1074/jbc.m111.247395\">https://doi.org/10.1074/jbc.m111.247395</a>.","short":"N.S. Baranova, E. Nilebäck, F.M. Haller, D.C. Briggs, S. Svedhem, A.J. Day, R.P. Richter, Journal of Biological Chemistry 286 (2011) 25675–25686.","ama":"Baranova NS, Nilebäck E, Haller FM, et al. The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. <i>Journal of Biological Chemistry</i>. 2011;286(29):25675-25686. doi:<a href=\"https://doi.org/10.1074/jbc.m111.247395\">10.1074/jbc.m111.247395</a>","ista":"Baranova NS, Nilebäck E, Haller FM, Briggs DC, Svedhem S, Day AJ, Richter RP. 2011. The inflammation-associated protein TSG-6 cross-links hyaluronan via hyaluronan-induced TSG-6 oligomers. Journal of Biological Chemistry. 286(29), 25675–25686.","mla":"Baranova, Natalia S., et al. “The Inflammation-Associated Protein TSG-6 Cross-Links Hyaluronan via Hyaluronan-Induced TSG-6 Oligomers.” <i>Journal of Biological Chemistry</i>, vol. 286, no. 29, American Society for Biochemistry &#38; Molecular Biology, 2011, pp. 25675–86, doi:<a href=\"https://doi.org/10.1074/jbc.m111.247395\">10.1074/jbc.m111.247395</a>."},"issue":"29","publisher":"American Society for Biochemistry & Molecular Biology","main_file_link":[{"url":"http://www.jbc.org/content/286/29/25675.full.pdf","open_access":"1"}],"_id":"6298","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyalu-ronan (HA)-binding protein that plays important roles ininflammation and ovulation. TSG-6-mediated cross-linking ofHA has been proposed as a functional mechanism (e.g.for regu-lating leukocyte adhesion), but direct evidence for cross-linkingis lacking, and we know very little about its impact on HA ultra-structure. Here we used films of polymeric and oligomeric HAchains, end-grafted to a solid support, and a combination ofsurface-sensitive biophysical techniques to quantify the bindingof TSG-6 into HA films and to correlate binding to morpholog-ical changes. We find that full-length TSG-6 binds with pro-nounced positive cooperativity and demonstrate that it cancross-link HA at physiologically relevant concentrations. Ourdata indicate that cooperative binding of full-length TSG-6arises from HA-induced protein oligomerization and that theTSG-6 oligomers act as cross-linkers. In contrast, the HA-bind-ing domain of TSG-6 (the Link module) alone binds withoutpositive cooperativity and weaker than the full-length protein.Both the Link module and full-length TSG-6 condensed andrigidified HA films, and the degree of condensation scaled withthe affinity between the TSG-6 constructs and HA. We proposethat condensation is the result of protein-mediated HA cross-linking. Our findings firmly establish that TSG-6 is a potent HAcross-linking agent and might hence have important implica-tions for the mechanistic understanding of the biological func-tion of TSG-6 (e.g.in inflammation)."}],"oa":1,"publication_identifier":{"issn":["0021-9258","1083-351X"]}},{"abstract":[{"lang":"eng","text":"\n\nIn Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from the self-organization of MinD, a membrane-binding ATPase, and its activator MinE. For wave propagation, the proteins need to cycle through states of collective membrane binding and unbinding. Although MinD presumably undergoes cooperative membrane attachment, it is unclear how synchronous detachment is coordinated. We used confocal and single-molecule microscopy to elucidate the order of events during Min wave propagation. We propose that protein detachment at the rear of the wave, and the formation of the E-ring, are accomplished by two complementary processes: first, local accumulation of MinE due to rapid rebinding, leading to dynamic instability; and second, a structural change induced by membrane-interaction of MinE in an equimolar MinD-MinE (MinDE) complex, which supports the robustness of pattern formation."}],"intvolume":"        18","day":"01","date_created":"2018-12-11T11:55:03Z","publist_id":"5098","_id":"1985","author":[{"full_name":"Martin Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin"},{"full_name":"Fischer-Friedrich, Elisabeth","last_name":"Fischer Friedrich","first_name":"Elisabeth"},{"full_name":"Herold, Christoph","first_name":"Christoph","last_name":"Herold"},{"full_name":"Kruse, Karsten","first_name":"Karsten","last_name":"Kruse"},{"first_name":"Petra","last_name":"Schwille","full_name":"Schwille, Petra "}],"publisher":"Nature Publishing Group","issue":"5","citation":{"ista":"Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. 2011. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. Nature Structural and Molecular Biology. 18(5), 577–583.","mla":"Loose, Martin, et al. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” <i>Nature Structural and Molecular Biology</i>, vol. 18, no. 5, Nature Publishing Group, 2011, pp. 577–83, doi:<a href=\"https://doi.org/10.1038/nsmb.2037\">10.1038/nsmb.2037</a>.","short":"M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, P. Schwille, Nature Structural and Molecular Biology 18 (2011) 577–583.","ama":"Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. <i>Nature Structural and Molecular Biology</i>. 2011;18(5):577-583. doi:<a href=\"https://doi.org/10.1038/nsmb.2037\">10.1038/nsmb.2037</a>","chicago":"Loose, Martin, Elisabeth Fischer Friedrich, Christoph Herold, Karsten Kruse, and Petra Schwille. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nsmb.2037\">https://doi.org/10.1038/nsmb.2037</a>.","apa":"Loose, M., Fischer Friedrich, E., Herold, C., Kruse, K., &#38; Schwille, P. (2011). Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.2037\">https://doi.org/10.1038/nsmb.2037</a>","ieee":"M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, and P. Schwille, “Min protein patterns emerge from rapid rebinding and membrane interaction of MinE,” <i>Nature Structural and Molecular Biology</i>, vol. 18, no. 5. Nature Publishing Group, pp. 577–583, 2011."},"volume":18,"type":"journal_article","date_updated":"2021-01-12T06:54:31Z","title":"Min protein patterns emerge from rapid rebinding and membrane interaction of MinE","doi":"10.1038/nsmb.2037","status":"public","publication_status":"published","acknowledgement":"This work was also supported by the Max Planck Society (M.L., E.F.-F., P.S.).","date_published":"2011-05-01T00:00:00Z","month":"05","page":"577 - 583","fulldoi":"https://doi.org/10.1038/nsmb.2037","extern":1,"year":"2011","publication":"Nature Structural and Molecular Biology","quality_controlled":0},{"month":"06","date_published":"2011-06-09T00:00:00Z","fulldoi":"https://doi.org/10.1146/annurev-biophys-042910-155332","page":"315 - 336","quality_controlled":0,"publication":"Annual Review of Biophysics","year":"2011","extern":1,"date_created":"2018-12-11T11:55:04Z","publist_id":"5097","day":"09","intvolume":"        40","author":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Martin Loose","first_name":"Martin","last_name":"Loose"},{"full_name":"Kruse, Karsten","last_name":"Kruse","first_name":"Karsten"},{"last_name":"Schwille","first_name":"Petra","full_name":"Schwille, Petra "}],"publisher":"Annual Reviews","issue":"1","citation":{"ista":"Loose M, Kruse K, Schwille P. 2011. Protein self-organization: Lessons from the min system. Annual Review of Biophysics. 40(1), 315–336.","mla":"Loose, Martin, et al. “Protein Self-Organization: Lessons from the Min System.” <i>Annual Review of Biophysics</i>, vol. 40, no. 1, Annual Reviews, 2011, pp. 315–36, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">10.1146/annurev-biophys-042910-155332</a>.","chicago":"Loose, Martin, Karsten Kruse, and Petra Schwille. “Protein Self-Organization: Lessons from the Min System.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2011. <a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">https://doi.org/10.1146/annurev-biophys-042910-155332</a>.","short":"M. Loose, K. Kruse, P. Schwille, Annual Review of Biophysics 40 (2011) 315–336.","ama":"Loose M, Kruse K, Schwille P. Protein self-organization: Lessons from the min system. <i>Annual Review of Biophysics</i>. 2011;40(1):315-336. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">10.1146/annurev-biophys-042910-155332</a>","apa":"Loose, M., Kruse, K., &#38; Schwille, P. (2011). Protein self-organization: Lessons from the min system. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-042910-155332\">https://doi.org/10.1146/annurev-biophys-042910-155332</a>","ieee":"M. Loose, K. Kruse, and P. Schwille, “Protein self-organization: Lessons from the min system,” <i>Annual Review of Biophysics</i>, vol. 40, no. 1. Annual Reviews, pp. 315–336, 2011."},"_id":"1986","abstract":[{"lang":"eng","text":"One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior. One of the best-understood examples of protein self-organization, which has recently been successfully reconstituted in vitro, is represented by the oscillations of the Min proteins in Escherichia coli. In this review, we summarize the current understanding of the mechanism of Min protein self-organization in vivo and in vitro. We discuss the potential of the Min oscillations to sense the geometry of the cell and suggest that spontaneous protein waves could be a general means of intracellular organization. We hypothesize that cooperative membrane binding and unbinding, e.g., as an energy-dependent switch, may act as an important regulatory mechanism for protein oscillations and pattern formation in the cell."}],"publication_status":"published","volume":40,"date_updated":"2021-01-12T06:54:31Z","type":"journal_article","title":"Protein self-organization: Lessons from the min system","status":"public","doi":"10.1146/annurev-biophys-042910-155332"},{"oa_version":"Published Version","ddc":["570"],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"status":"public","title":"Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite","volume":3,"date_updated":"2021-01-12T06:55:08Z","citation":{"apa":"Vicoso, B., &#38; Bachtrog, D. (2011). Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evr010\">https://doi.org/10.1093/gbe/evr010</a>","ieee":"B. Vicoso and D. Bachtrog, “Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite,” <i>Genome Biology and Evolution</i>, vol. 3, no. 1. Oxford University Press, pp. 230–235, 2011.","chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1093/gbe/evr010\">https://doi.org/10.1093/gbe/evr010</a>.","ama":"Vicoso B, Bachtrog D. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. <i>Genome Biology and Evolution</i>. 2011;3(1):230-235. doi:<a href=\"https://doi.org/10.1093/gbe/evr010\">10.1093/gbe/evr010</a>","short":"B. Vicoso, D. Bachtrog, Genome Biology and Evolution 3 (2011) 230–235.","ista":"Vicoso B, Bachtrog D. 2011. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution. 3(1), 230–235.","mla":"Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” <i>Genome Biology and Evolution</i>, vol. 3, no. 1, Oxford University Press, 2011, pp. 230–35, doi:<a href=\"https://doi.org/10.1093/gbe/evr010\">10.1093/gbe/evr010</a>."},"author":[{"last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"},{"full_name":"Bachtrog, Doris","first_name":"Doris","last_name":"Bachtrog"}],"publisher":"Oxford University Press","date_created":"2018-12-11T11:55:33Z","publist_id":"4966","day":"11","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"Many species have morphologically and genetically differentiated sex chromosomes, such as the XY pair of mammals. Y chromosomes are often highly degenerated and carry few functional genes, so that XY males have only one copy of most Xlinked genes (whereas females have two). As a result, chromosome-wide mechanisms of dosage compensation, such as the mammalian X-inactivation, often evolve to reestablish expression balance. A similar phenomenon is expected in femaleheterogametic species, where ZW females should suffer from imbalances due to W-chromosome degeneration. However, no global dosage compensation mechanisms have been detected in the two independent ZW systems that have been studied systematically (birds and silkworm), leading to the suggestion that lack of global dosage compensation may be a general feature of female-heterogametic species. However, analyses of other independently evolved ZW systems are required to test if this is the case. In this study, we use published genomic and expression data to test for the presence of global dosage compensation in Schistosoma mansoni, a trematode parasite that causes schistosomiasis in humans. We find that Z-linked expression is reduced relative to autosomal expression in females but not males, consistent with incomplete or localized dosage compensation. This gives further support to the theory that female-heterogametic species may not require global mechanisms of dosage compensation.","lang":"eng"}],"publication":"Genome Biology and Evolution","file":[{"date_created":"2019-05-10T07:41:28Z","access_level":"open_access","checksum":"7855c134436e4f6a13d63b6606d7e8dd","file_name":"2011_GBE_Vicoso.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:45:27Z","file_size":212547,"file_id":"6395","creator":"dernst"}],"year":"2011","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"230 - 235","date_published":"2011-02-11T00:00:00Z","month":"02","publication_status":"published","doi":"10.1093/gbe/evr010","type":"journal_article","issue":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"2072","intvolume":"         3","quality_controlled":"1","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:27Z","fulldoi":"https://doi.org/10.1093/gbe/evr010"},{"article_processing_charge":"No","quality_controlled":"1","fulldoi":"https://doi.org/10.1039/c1sm05773a","article_type":"original","doi":"10.1039/c1sm05773a","type":"journal_article","publication_status":"published","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"issue":"18","_id":"10389","article_number":"8324","intvolume":"         7","year":"2011","extern":"1","publication":"Soft Matter","external_id":{"arxiv":["1106.2995"]},"month":"08","arxiv":1,"date_published":"2011-08-08T00:00:00Z","acknowledgement":"This work was supported by the National Science Foundation under Career Grant No. DMR-0846426. We thank Josep C. Pàmies and William L. Miller for helpful discussions.","keyword":["condensed matter physics","general chemistry"],"scopus_import":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Soft elastic surfaces as a platform for particle self-assembly","status":"public","volume":7,"date_updated":"2021-11-29T15:12:10Z","oa_version":"Preprint","oa":1,"language":[{"iso":"eng"}],"abstract":[{"text":"We perform numerical simulations to study self-assembly of nanoparticles mediated by an elastic planar surface. We show how the nontrivial elastic response to deformations of these surfaces leads to anisotropic interactions between the particles resulting in aggregates having different geometrical features. The morphology of the patterns can be controlled by the mechanical properties of the surface and the strength of the particle adhesion. We use simple scaling arguments to understand the formation of the different structures, and we show how the adhering particles can cause the underlying elastic substrate to wrinkle if two of its opposite edges are clamped. Finally, we discuss the implications of our results and suggest how elastic surfaces could be used in nanofabrication.","lang":"eng"}],"citation":{"ieee":"A. Šarić and A. Cacciuto, “Soft elastic surfaces as a platform for particle self-assembly,” <i>Soft Matter</i>, vol. 7, no. 18. Royal Society of Chemistry, 2011.","apa":"Šarić, A., &#38; Cacciuto, A. (2011). Soft elastic surfaces as a platform for particle self-assembly. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c1sm05773a\">https://doi.org/10.1039/c1sm05773a</a>","mla":"Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” <i>Soft Matter</i>, vol. 7, no. 18, 8324, Royal Society of Chemistry, 2011, doi:<a href=\"https://doi.org/10.1039/c1sm05773a\">10.1039/c1sm05773a</a>.","ista":"Šarić A, Cacciuto A. 2011. Soft elastic surfaces as a platform for particle self-assembly. Soft Matter. 7(18), 8324.","ama":"Šarić A, Cacciuto A. Soft elastic surfaces as a platform for particle self-assembly. <i>Soft Matter</i>. 2011;7(18). doi:<a href=\"https://doi.org/10.1039/c1sm05773a\">10.1039/c1sm05773a</a>","short":"A. Šarić, A. Cacciuto, Soft Matter 7 (2011).","chicago":"Šarić, Anđela, and Angelo Cacciuto. “Soft Elastic Surfaces as a Platform for Particle Self-Assembly.” <i>Soft Matter</i>. Royal Society of Chemistry, 2011. <a href=\"https://doi.org/10.1039/c1sm05773a\">https://doi.org/10.1039/c1sm05773a</a>."},"author":[{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić"},{"last_name":"Cacciuto","first_name":"Angelo","full_name":"Cacciuto, Angelo"}],"publisher":"Royal Society of Chemistry","main_file_link":[{"url":"https://arxiv.org/abs/1106.2995","open_access":"1"}],"date_created":"2021-11-29T14:33:18Z","day":"08"}]