[{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2014","day":"12","corr_author":"1","language":[{"iso":"eng"}],"publist_id":"5043","scopus_import":"1","publication":"Journal of Theoretical Biology","oa_version":"Published Version","pubrep_id":"444","month":"10","acknowledgement":"This work is supported by AFOSR grant FA 9550-11-1-0165, program grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429 (KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically Inspired Engineering. ","status":"public","page":"40 - 54","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"volume":365,"date_updated":"2026-07-07T13:13:09Z","das_tickbox":"1","file_date_updated":"2020-07-14T12:45:25Z","abstract":[{"lang":"eng","text":"Understanding the dynamics of noisy neurons remains an important challenge in neuroscience. Here, we describe a simple probabilistic model that accurately describes the firing behavior in a large class (type II) of neurons. To demonstrate the usefulness of this model, we show how it accurately predicts the interspike interval (ISI) distributions, bursting patterns and mean firing rates found by: (1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental data from squid giant axon with a noisy input current and (3) experimental data on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple model has 6 parameters, however, in some cases, two of these parameters are coupled and only 5 parameters account for much of the known behavior. From these parameters, many properties of spiking can be found through simple calculation. Thus, we show how the complex effects of noise can be understood through a simple and general probabilistic model."}],"_id":"2028","date_published":"2014-10-12T00:00:00Z","article_processing_charge":"No","citation":{"ama":"Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041","mla":"Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology, vol. 365, Academic Press, 2014, pp. 40–54, doi:10.1016/j.jtbi.2014.09.041.","ieee":"K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” Journal of Theoretical Biology, vol. 365. Academic Press, pp. 40–54, 2014.","chicago":"Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology. Academic Press, 2014. https://doi.org/10.1016/j.jtbi.2014.09.041.","apa":"Bodova, K., Paydarfar, D., & Forger, D. (2014). Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. Academic Press. https://doi.org/10.1016/j.jtbi.2014.09.041","short":"K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014) 40–54.","ista":"Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 365, 40–54."},"publisher":"Academic Press","doi":"10.1016/j.jtbi.2014.09.041","oa":1,"quality_controlled":"1","publication_status":"published","type":"journal_article","has_accepted_license":"1","department":[{"_id":"GaTk"}],"external_id":{"isi":["000347267200005"]},"intvolume":" 365","ddc":["570"],"title":"Characterizing spiking in noisy type II neurons","isi":1,"related_material":{"link":[{"url":"https://doi.org/10.1016/j.jtbi.2015.03.013","relation":"erratum"}]},"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:25Z","relation":"main_file","file_id":"5316","date_created":"2018-12-12T10:17:58Z","checksum":"a9dbae18d3233b3dab6944fd3f2cd49e","file_size":2679222,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf"}],"date_created":"2018-12-11T11:55:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bodova","first_name":"Katarina","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bodova, Katarina"},{"last_name":"Paydarfar","first_name":"David","full_name":"Paydarfar, David"},{"full_name":"Forger, Daniel","last_name":"Forger","first_name":"Daniel"}]},{"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"date_created":"2018-12-12T11:39:12Z","file":[{"date_created":"2018-12-12T11:53:36Z","file_id":"5497","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:48Z","file_name":"IST-2014-170-v1+1_main.pdf","checksum":"31f90dcf2cf899c3f8c6427cfcc2b3c7","content_type":"application/pdf","creator":"system","file_size":573457}],"related_material":{"record":[{"id":"5436","status":"public","relation":"later_version"},{"relation":"later_version","id":"1656","status":"public"},{"id":"467","status":"public","relation":"later_version"}]},"date_updated":"2026-07-07T14:01:10Z","title":"Nested weighted automata","ddc":["004"],"page":"27","status":"public","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"month":"02","has_accepted_license":"1","pubrep_id":"170","oa_version":"Published Version","publication_status":"published","type":"technical_report","oa":1,"publisher":"IST Austria","language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2014-170-v1-1","day":"19","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata. IST Austria, 2014.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria; 2014. doi:10.15479/AT:IST-2014-170-v1-1","mla":"Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria, 2014, doi:10.15479/AT:IST-2014-170-v1-1.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria, 2014.","ista":"Chatterjee K, Henzinger TA, Otop J. 2014. Nested weighted automata, IST Austria, 27p.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2014). Nested weighted automata. IST Austria. https://doi.org/10.15479/AT:IST-2014-170-v1-1","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted Automata. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-170-v1-1."},"publication_identifier":{"issn":["2664-1690"]},"date_published":"2014-02-19T00:00:00Z","_id":"5415","year":"2014","file_date_updated":"2020-07-14T12:46:48Z","abstract":[{"lang":"eng","text":"Recently there has been a significant effort to add quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, several basic system properties such as average response time cannot be expressed with weighted automata. In this work, we introduce nested weighted automata as a new formalism for expressing important quantitative properties such as average response time. We establish an almost complete decidability picture for the basic decision problems for nested weighted automata, and illustrate its applicability in several domains. "}]},{"publist_id":"5013","language":[{"iso":"eng"}],"oa_version":"Submitted Version","publication":"ACM Transactions on Computational Logic","scopus_import":"1","year":"2014","day":"16","date_updated":"2026-07-07T14:01:43Z","volume":15,"das_tickbox":"1","acknowledgement":"The research was supported in part by ERC Starting grant 278410 (QUALITY).","status":"public","pubrep_id":"192","month":"09","quality_controlled":"1","doi":"10.1145/2629686","oa":1,"publisher":"ACM","publication_status":"published","type":"journal_article","file_date_updated":"2020-07-14T12:45:26Z","abstract":[{"lang":"eng","text":"Recently, there has been an effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions. At the heart of quantitative objectives lies the accumulation of values along a computation. It is often the accumulated sum, as with energy objectives, or the accumulated average, as with 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 (or Boolean) 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 in time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire infinite computation. We study the border of decidability for such quantitative 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 with both prefix-accumulation assertions, or extending LTL with both path-accumulation assertions, results in temporal logics whose model-checking problem is decidable. Moreover, the prefix-accumulation assertions may be generalized 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 this branching-time logic is, in a sense, the maximal logic with one or both of the prefix-accumulation assertions that permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL, makes the problem undecidable."}],"_id":"2038","ec_funded":1,"article_processing_charge":"No","date_published":"2014-09-16T00:00:00Z","citation":{"ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications with accumulative values,” ACM Transactions on Computational Logic, vol. 15, no. 4. ACM, 2014.","mla":"Boker, Udi, et al. “Temporal Specifications with Accumulative Values.” ACM Transactions on Computational Logic, vol. 15, no. 4, 27, ACM, 2014, doi:10.1145/2629686.","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with accumulative values. ACM Transactions on Computational Logic. 2014;15(4). doi:10.1145/2629686","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2014. Temporal specifications with accumulative values. ACM Transactions on Computational Logic. 15(4), 27.","short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, ACM Transactions on Computational Logic 15 (2014).","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2014). Temporal specifications with accumulative values. ACM Transactions on Computational Logic. ACM. https://doi.org/10.1145/2629686","chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. “Temporal Specifications with Accumulative Values.” ACM Transactions on Computational Logic. ACM, 2014. https://doi.org/10.1145/2629686."},"article_type":"original","isi":1,"file":[{"file_name":"IST-2014-192-v1+1_AccumulativeValues.pdf","checksum":"354c41d37500b56320afce94cf9a99c2","file_size":346184,"creator":"system","content_type":"application/pdf","relation":"main_file","file_id":"4851","date_created":"2018-12-12T10:10:59Z","access_level":"open_access","date_updated":"2020-07-14T12:45:26Z"}],"related_material":{"record":[{"status":"public","id":"5385","relation":"earlier_version"},{"id":"3356","status":"public","relation":"earlier_version"}]},"title":"Temporal specifications with accumulative values","issue":"4","author":[{"last_name":"Boker","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"date_created":"2018-12-11T11:55:21Z","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"has_accepted_license":"1","ddc":["000","004"],"article_number":"27","external_id":{"isi":["000345570700002"]},"intvolume":" 15"},{"day":"01","year":"2014","conference":{"start_date":"2014-08-25","name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2014-08-29","location":"Budapest, Hungary"},"scopus_import":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"corr_author":"1","publist_id":"5192","page":"1 - 4","month":"01","pubrep_id":"141","status":"public","date_updated":"2026-07-07T14:01:25Z","volume":8634,"citation":{"mla":"Chatterjee, Krishnendu. Partial-Observation Stochastic Reachability and Parity Games. Vol. 8634, no. PART 1, Springer, 2014, pp. 1–4, doi:10.1007/978-3-662-44522-8_1.","ama":"Chatterjee K. Partial-observation stochastic reachability and parity games. In: Vol 8634. Springer; 2014:1-4. doi:10.1007/978-3-662-44522-8_1","ieee":"K. Chatterjee, “Partial-observation stochastic reachability and parity games,” presented at the MFCS: Mathematical Foundations of Computer Science, Budapest, Hungary, 2014, vol. 8634, no. PART 1, pp. 1–4.","apa":"Chatterjee, K. (2014). Partial-observation stochastic reachability and parity games (Vol. 8634, pp. 1–4). Presented at the MFCS: Mathematical Foundations of Computer Science, Budapest, Hungary: Springer. https://doi.org/10.1007/978-3-662-44522-8_1","chicago":"Chatterjee, Krishnendu. “Partial-Observation Stochastic Reachability and Parity Games,” 8634:1–4. Springer, 2014. https://doi.org/10.1007/978-3-662-44522-8_1.","ista":"Chatterjee K. 2014. Partial-observation stochastic reachability and parity games. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 8634, 1–4.","short":"K. Chatterjee, in:, Springer, 2014, pp. 1–4."},"date_published":"2014-01-01T00:00:00Z","article_processing_charge":"No","ec_funded":1,"_id":"1903","abstract":[{"lang":"eng","text":"We consider two-player zero-sum partial-observation stochastic games on graphs. Based on the information available to the players these games can be classified as follows: (a) general partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) perfect-observation (both players have complete view of the game). The one-sided partial-observation games subsumes the important special case of one-player partial-observation stochastic games (or partial-observation Markov decision processes (POMDPs)). Based on the randomization available for the strategies, (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. We consider all these classes of games with reachability, and parity objectives that can express all ω-regular objectives. The analysis problems are classified into the qualitative analysis that asks for the existence of a strategy that ensures the objective with probability 1; and the quantitative analysis that asks for the existence of a strategy that ensures the objective with probability at least λ (0,1). In this talk we will cover a wide range of results: for perfect-observation games; for POMDPs; for one-sided partial-observation games; and for general partial-observation games."}],"type":"conference","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15479/AT:IST-2011-0007"}],"doi":"10.1007/978-3-662-44522-8_1","oa":1,"publisher":"Springer","quality_controlled":"1","intvolume":" 8634","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"date_created":"2018-12-11T11:54:38Z","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"issue":"PART 1","title":"Partial-observation stochastic reachability and parity games","OA_place":"repository","OA_type":"green","related_material":{"record":[{"status":"public","id":"5381","relation":"earlier_version"},{"relation":"later_version","status":"public","id":"2211"}]}},{"article_processing_charge":"No","date_published":"2014-04-01T00:00:00Z","citation":{"ista":"Chatterjee K, Doyen L. 2014. Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic. 15(2), 16.","short":"K. Chatterjee, L. Doyen, ACM Transactions on Computational Logic 15 (2014).","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic. ACM, 2014. https://doi.org/10.1145/2579821.","apa":"Chatterjee, K., & Doyen, L. (2014). Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic. ACM. https://doi.org/10.1145/2579821","ieee":"K. Chatterjee and L. Doyen, “Partial-observation stochastic games: How to win when belief fails,” ACM Transactions on Computational Logic, vol. 15, no. 2. ACM, 2014.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” ACM Transactions on Computational Logic, vol. 15, no. 2, 16, ACM, 2014, doi:10.1145/2579821.","ama":"Chatterjee K, Doyen L. Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic. 2014;15(2). doi:10.1145/2579821"},"abstract":[{"lang":"eng","text":"In two-player finite-state stochastic games of partial observation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distribution 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 positively (i.e., with positive probability), no matter the strategy of the second player. We 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. Our main results for pure strategies are as follows: (1) For one-sided games with player 2 having perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strategies are not sufficient, and we present an exponential upper bound on memory 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 algorithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 having perfect observation we show that nonelementarymemory is both necessary and sufficient for both almost-sure and positive 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 nonelementary 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 result exhibit serious flaws in previous results of the literature: we show a nonelementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed."}],"_id":"2211","main_file_link":[{"url":"http://arxiv.org/abs/1107.2141","open_access":"1"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","publisher":"ACM","doi":"10.1145/2579821","oa":1,"article_number":"16","external_id":{"arxiv":["1107.2141"],"isi":["000336005000006"]},"intvolume":" 15","department":[{"_id":"KrCh"}],"issue":"2","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"date_created":"2018-12-11T11:56:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"related_material":{"record":[{"status":"public","id":"5381","relation":"earlier_version"},{"relation":"earlier_version","id":"1903","status":"public"},{"id":"2955","status":"public","relation":"earlier_version"}]},"title":"Partial-observation stochastic games: How to win when belief fails","day":"01","year":"2014","oa_version":"Preprint","publication":"ACM Transactions on Computational Logic","scopus_import":"1","publist_id":"4759","language":[{"iso":"eng"}],"arxiv":1,"status":"public","month":"04","das_tickbox":"1","date_updated":"2026-07-07T14:01:26Z","volume":15},{"abstract":[{"text":"We study two-player concurrent games on finite-state graphs played for an infinite number of rounds, where 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. The objectives are 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). While the qualitative analysis problem for concurrent parity games with infinite-memory, infinite-precision randomized strategies was studied before, 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 (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. Our symbolic algorithms are based on a characterization of the winning sets as μ-calculus formulas, however, our μ-calculus formulas are crucially different from the ones for concurrent parity games (without bounded rationality); and our memoryless witness strategy constructions are significantly different from the infinite-memory witness strategy constructions for concurrent parity games.","lang":"eng"}],"_id":"2054","date_published":"2014-09-01T00:00:00Z","citation":{"mla":"Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded Rationality.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 544–59, doi:10.1007/978-3-662-44584-6_37.","ama":"Chatterjee K. Qualitative concurrent parity games: Bounded rationality. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:544-559. doi:10.1007/978-3-662-44584-6_37","ieee":"K. Chatterjee, “Qualitative concurrent parity games: Bounded rationality,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 544–559.","chicago":"Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded Rationality.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:544–59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_37.","apa":"Chatterjee, K. (2014). Qualitative concurrent parity games: Bounded rationality. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 544–559). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_37","ista":"Chatterjee K. 2014. Qualitative concurrent parity games: Bounded rationality. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 544–559.","short":"K. Chatterjee, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 544–559."},"ec_funded":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.1007/978-3-662-44584-6_37","quality_controlled":"1","publication_status":"published","type":"conference","department":[{"_id":"KrCh"}],"intvolume":" 8704","editor":[{"full_name":"Baldan, Paolo","last_name":"Baldan","first_name":"Paolo"},{"first_name":"Daniele","last_name":"Gorla","full_name":"Gorla, Daniele"}],"title":"Qualitative concurrent parity games: Bounded rationality","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3354"}]},"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"alternative_title":["LNCS"],"date_created":"2018-12-11T11:55:27Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"conference":{"location":"Rome, Italy","end_date":"2014-09-05","name":"CONCUR: Concurrency Theory","start_date":"2014-09-02"},"year":"2014","day":"01","language":[{"iso":"eng"}],"corr_author":"1","publist_id":"4992","scopus_import":"1","oa_version":"None","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","month":"09","status":"public","page":"544 - 559","date_updated":"2026-07-07T14:02:37Z","volume":8704},{"date_created":"2018-12-11T11:47:01Z","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","issue":"3","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Krinninger, Sebastian","last_name":"Krinninger","first_name":"Sebastian"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"}],"title":"Polynomial-time algorithms for energy games with special weight structures","isi":1,"related_material":{"record":[{"relation":"earlier_version","id":"10905","status":"public"}]},"external_id":{"isi":["000340552300005"],"arxiv":["1604.08234"]},"intvolume":" 70","department":[{"_id":"KrCh"}],"type":"journal_article","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08234"}],"oa":1,"publisher":"Springer","doi":"10.1007/s00453-013-9843-7","quality_controlled":"1","date_published":"2014-11-01T00:00:00Z","article_processing_charge":"No","article_type":"original","citation":{"apa":"Chatterjee, K., Henzinger, M., Krinninger, S., & Nanongkai, D. (2014). Polynomial-time algorithms for energy games with special weight structures. Algorithmica. Springer. https://doi.org/10.1007/s00453-013-9843-7","chicago":"Chatterjee, Krishnendu, Monika Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica. Springer, 2014. https://doi.org/10.1007/s00453-013-9843-7.","ista":"Chatterjee K, Henzinger M, Krinninger S, Nanongkai D. 2014. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 70(3), 457–492.","short":"K. Chatterjee, M. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70 (2014) 457–492.","mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica, vol. 70, no. 3, Springer, 2014, pp. 457–92, doi:10.1007/s00453-013-9843-7.","ama":"Chatterjee K, Henzinger M, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 2014;70(3):457-492. doi:10.1007/s00453-013-9843-7","ieee":"K. Chatterjee, M. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” Algorithmica, vol. 70, no. 3. Springer, pp. 457–492, 2014."},"ec_funded":1,"abstract":[{"text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help.","lang":"eng"}],"_id":"535","volume":70,"date_updated":"2026-07-08T05:50:38Z","page":"457 - 492","arxiv":1,"month":"11","status":"public","scopus_import":"1","oa_version":"Preprint","publication":"Algorithmica","language":[{"iso":"eng"}],"publist_id":"7282","day":"01","year":"2014"},{"pubrep_id":"641","month":"01","acknowledgement":"This research was supported in part by the Austrian National Research Network RiSE (S11410-N23).","status":"public","page":"185 - 200","volume":8837,"date_updated":"2026-07-08T06:49:33Z","das_tickbox":"1","conference":{"location":"Sydney, Australia","end_date":"2014-11-07","name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2014-11-03"},"year":"2014","day":"01","language":[{"iso":"eng"}],"publist_id":"5226","scopus_import":"1","oa_version":"Submitted Version","publication":"12th International Symposium on Automated Technology for Verification and Analysis","has_accepted_license":"1","department":[{"_id":"ToHe"}],"intvolume":" 8837","ddc":["000"],"title":"Extensional crisis and proving identity","file":[{"checksum":"af4bd3fc1f4c93075e4dc5cbf625fe7b","creator":"system","content_type":"application/pdf","file_size":244294,"file_name":"IST-2016-641-v1+1_atva2014.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:10:15Z","file_id":"4801","relation":"main_file"}],"alternative_title":["LNCS"],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"}],"date_created":"2018-12-11T11:54:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Gupta","first_name":"Ashutosh","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kovács, Laura","last_name":"Kovács","first_name":"Laura"},{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard","last_name":"Kragl","first_name":"Bernhard","orcid":"0000-0001-7745-9117"},{"full_name":"Voronkov, Andrei","last_name":"Voronkov","first_name":"Andrei"}],"abstract":[{"lang":"eng","text":"Extensionality axioms are common when reasoning about data collections, such as arrays and functions in program analysis, or sets in mathematics. An extensionality axiom asserts that two collections are equal if they consist of the same elements at the same indices. Using extensionality is often required to show that two collections are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly, while humans have no problem with proving such set identities using extensionality, they are very hard for superposition theorem provers because of the calculi they use. In this paper we show how addition of a new inference rule, called extensionality resolution, allows first-order theorem provers to easily solve problems no modern first-order theorem prover can solve. We illustrate this by running the VAMPIRE theorem prover with extensionality resolution on a number of set theory and array problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP library of first-order problems that were never solved before by any prover."}],"file_date_updated":"2020-07-14T12:45:19Z","_id":"1872","date_published":"2014-01-01T00:00:00Z","article_processing_charge":"No","citation":{"ieee":"A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving identity,” in 12th International Symposium on Automated Technology for Verification and Analysis, Sydney, Australia, 2014, vol. 8837, pp. 185–200.","mla":"Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” 12th International Symposium on Automated Technology for Verification and Analysis, vol. 8837, Springer, 2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14.","ama":"Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity. In: 12th International Symposium on Automated Technology for Verification and Analysis. Vol 8837. Springer; 2014:185-200. doi:10.1007/978-3-319-11936-6_14","ista":"Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving identity. 12th International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 185–200.","short":"A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, 12th International Symposium on Automated Technology for Verification and Analysis, Springer, 2014, pp. 185–200.","apa":"Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis and proving identity. In 12th International Symposium on Automated Technology for Verification and Analysis (Vol. 8837, pp. 185–200). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_14","chicago":"Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional Crisis and Proving Identity.” In 12th International Symposium on Automated Technology for Verification and Analysis, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14."},"ec_funded":1,"oa":1,"publisher":"Springer","doi":"10.1007/978-3-319-11936-6_14","quality_controlled":"1","publication_status":"published","type":"conference"},{"publist_id":"5080","language":[{"iso":"eng"}],"corr_author":"1","oa_version":"None","publication":"Current Opinion in Insect Science","scopus_import":"1","year":"2014","day":"01","date_updated":"2026-07-13T22:30:58Z","volume":5,"status":"public","month":"11","page":"1 - 15","quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.cois.2014.09.001","type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","text":"Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses."}],"_id":"1999","ec_funded":1,"article_processing_charge":"No","date_published":"2014-11-01T00:00:00Z","citation":{"ieee":"N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity in social insects,” Current Opinion in Insect Science, vol. 5, no. 1. Elsevier, pp. 1–15, 2014.","mla":"Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” Current Opinion in Insect Science, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:10.1016/j.cois.2014.09.001.","ama":"Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social insects. Current Opinion in Insect Science. 2014;5(1):1-15. doi:10.1016/j.cois.2014.09.001","ista":"Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in social insects. Current Opinion in Insect Science. 5(1), 1–15.","short":"N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect Science 5 (2014) 1–15.","apa":"Stroeymeyt, N., Casillas Perez, B. E., & Cremer, S. (2014). Organisational immunity in social insects. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2014.09.001","chicago":"Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational Immunity in Social Insects.” Current Opinion in Insect Science. Elsevier, 2014. https://doi.org/10.1016/j.cois.2014.09.001."},"isi":1,"related_material":{"record":[{"id":"6383","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"6435","status":"public"}]},"title":"Organisational immunity in social insects","issue":"1","author":[{"full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie","last_name":"Stroeymeyt"},{"first_name":"Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"date_created":"2018-12-11T11:55:08Z","project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"SyCr"}],"intvolume":" 5","external_id":{"isi":["000209578900002"]}},{"license":"https://creativecommons.org/licenses/by/3.0/","year":"2013","publication_identifier":{"issn":["2223-7747"]},"day":"21","corr_author":"1","language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","publication":"Plants","month":"10","status":"public","page":"650-675","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"volume":2,"date_updated":"2024-10-09T21:01:52Z","keyword":["Plant Science","Ecology","Ecology","Evolution","Behavior and Systematics"],"abstract":[{"lang":"eng","text":"Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. "}],"file_date_updated":"2022-03-21T12:12:56Z","_id":"10895","article_processing_charge":"No","date_published":"2013-10-21T00:00:00Z","citation":{"apa":"Vanneste, S., & Friml, J. (2013). Calcium: The missing link in auxin action. Plants. MDPI. https://doi.org/10.3390/plants2040650","chicago":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” Plants. MDPI, 2013. https://doi.org/10.3390/plants2040650.","short":"S. Vanneste, J. Friml, Plants 2 (2013) 650–675.","ista":"Vanneste S, Friml J. 2013. Calcium: The missing link in auxin action. Plants. 2(4), 650–675.","ama":"Vanneste S, Friml J. Calcium: The missing link in auxin action. Plants. 2013;2(4):650-675. doi:10.3390/plants2040650","mla":"Vanneste, Steffen, and Jiří Friml. “Calcium: The Missing Link in Auxin Action.” Plants, vol. 2, no. 4, MDPI, 2013, pp. 650–75, doi:10.3390/plants2040650.","ieee":"S. Vanneste and J. Friml, “Calcium: The missing link in auxin action,” Plants, vol. 2, no. 4. MDPI, pp. 650–675, 2013."},"article_type":"original","pmid":1,"doi":"10.3390/plants2040650","oa":1,"publisher":"MDPI","quality_controlled":"1","type":"journal_article","publication_status":"published","has_accepted_license":"1","department":[{"_id":"JiFr"}],"external_id":{"pmid":["27137397"]},"intvolume":" 2","ddc":["580"],"title":"Calcium: The missing link in auxin action","file":[{"file_name":"2013_Plants_Vanneste.pdf","success":1,"checksum":"fb4ff2e820e344e253c9197544610be6","file_size":670188,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"10916","date_created":"2022-03-21T12:12:56Z","access_level":"open_access","date_updated":"2022-03-21T12:12:56Z"}],"date_created":"2022-03-21T07:13:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","author":[{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}]},{"intvolume":" 7877","department":[{"_id":"HeEd"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7"}],"date_created":"2022-03-21T07:30:33Z","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"}],"series_title":"LNCS","title":"Persistent homology in image processing","citation":{"apa":"Edelsbrunner, H. (2013). Persistent homology in image processing. In Graph-Based Representations in Pattern Recognition (Vol. 7877, pp. 182–183). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-38221-5_19","chicago":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” In Graph-Based Representations in Pattern Recognition, 7877:182–83. LNCS. Berlin, Heidelberg: Springer Nature, 2013. https://doi.org/10.1007/978-3-642-38221-5_19.","ista":"Edelsbrunner H. 2013. Persistent homology in image processing. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNCS vol. 7877, 182–183.","short":"H. Edelsbrunner, in:, Graph-Based Representations in Pattern Recognition, Springer Nature, Berlin, Heidelberg, 2013, pp. 182–183.","mla":"Edelsbrunner, Herbert. “Persistent Homology in Image Processing.” Graph-Based Representations in Pattern Recognition, vol. 7877, Springer Nature, 2013, pp. 182–83, doi:10.1007/978-3-642-38221-5_19.","ama":"Edelsbrunner H. Persistent homology in image processing. In: Graph-Based Representations in Pattern Recognition. Vol 7877. LNCS. Berlin, Heidelberg: Springer Nature; 2013:182-183. doi:10.1007/978-3-642-38221-5_19","ieee":"H. Edelsbrunner, “Persistent homology in image processing,” in Graph-Based Representations in Pattern Recognition, Vienna, Austria, 2013, vol. 7877, pp. 182–183."},"date_published":"2013-06-01T00:00:00Z","article_processing_charge":"No","ec_funded":1,"_id":"10897","abstract":[{"lang":"eng","text":"Taking images is an efficient way to collect data about the physical world. It can be done fast and in exquisite detail. By definition, image processing is the field that concerns itself with the computation aimed at harnessing the information contained in images [10]. This talk is concerned with topological information. Our main thesis is that persistent homology [5] is a useful method to quantify and summarize topological information, building a bridge that connects algebraic topology with applications. We provide supporting evidence for this thesis by touching upon four technical developments in the overlap between persistent homology and image processing."}],"type":"conference","publication_status":"published","doi":"10.1007/978-3-642-38221-5_19","publisher":"Springer Nature","quality_controlled":"1","page":"182-183","place":"Berlin, Heidelberg","month":"06","status":"public","acknowledgement":"This research is partially supported by the European Science Foundation (ESF) under the Research Network Programme, the European Union under the Toposys Project FP7-ICT-318493-STREP, the Russian Government under the Mega Project 11.G34.31.0053.","volume":7877,"date_updated":"2025-04-15T08:37:54Z","day":"01","publication_identifier":{"issn":["0302-9743"],"isbn":["9783642382208"],"eissn":["1611-3349"],"eisbn":["9783642382215"]},"year":"2013","conference":{"start_date":"2013-05-15","name":"GbRPR: Graph-based Representations in Pattern Recognition","end_date":"2013-05-17","location":"Vienna, Austria"},"scopus_import":"1","publication":"Graph-Based Representations in Pattern Recognition","oa_version":"None","corr_author":"1","language":[{"iso":"eng"}]},{"type":"conference","publication_status":"published","quality_controlled":"1","doi":"10.1145/2482767.2482789","publisher":"ACM","ec_funded":1,"citation":{"ama":"Haas A, Lippautz M, Henzinger TA, et al. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In: Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. ACM; 2013. doi:10.1145/2482767.2482789","mla":"Haas, Andreas, et al. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, no. 5, 17, ACM, 2013, doi:10.1145/2482767.2482789.","ieee":"A. Haas et al., “Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation,” in Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, Ischia, Italy, 2013, no. 5.","chicago":"Haas, Andreas, Michael Lippautz, Thomas A Henzinger, Hannes Payer, Ana Sokolova, Christoph M. Kirsch, and Ali Sezgin. “Distributed Queues in Shared Memory: Multicore Performance and Scalability through Quantitative Relaxation.” In Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. ACM, 2013. https://doi.org/10.1145/2482767.2482789.","apa":"Haas, A., Lippautz, M., Henzinger, T. A., Payer, H., Sokolova, A., Kirsch, C. M., & Sezgin, A. (2013). Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. In Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. Ischia, Italy: ACM. https://doi.org/10.1145/2482767.2482789","short":"A. Haas, M. Lippautz, T.A. Henzinger, H. Payer, A. Sokolova, C.M. Kirsch, A. Sezgin, in:, Proceedings of the ACM International Conference on Computing Frontiers - CF ’13, ACM, 2013.","ista":"Haas A, Lippautz M, Henzinger TA, Payer H, Sokolova A, Kirsch CM, Sezgin A. 2013. Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation. Proceedings of the ACM International Conference on Computing Frontiers - CF ’13. CF: Conference on Computing Frontiers, 17."},"article_processing_charge":"No","date_published":"2013-05-14T00:00:00Z","_id":"10898","abstract":[{"lang":"eng","text":"A prominent remedy to multicore scalability issues in concurrent data structure implementations is to relax the sequential specification of the data structure. We present distributed queues (DQ), a new family of relaxed concurrent queue implementations. DQs implement relaxed queues with linearizable emptiness check and either configurable or bounded out-of-order behavior or pool behavior. Our experiments show that DQs outperform and outscale in micro- and macrobenchmarks all strict and relaxed queue as well as pool implementations that we considered."}],"author":[{"first_name":"Andreas","last_name":"Haas","full_name":"Haas, Andreas"},{"last_name":"Lippautz","first_name":"Michael","full_name":"Lippautz, Michael"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Payer, Hannes","first_name":"Hannes","last_name":"Payer"},{"first_name":"Ana","last_name":"Sokolova","full_name":"Sokolova, Ana"},{"first_name":"Christoph M.","last_name":"Kirsch","full_name":"Kirsch, Christoph M."},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali"}],"issue":"5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"date_created":"2022-03-21T07:33:22Z","title":"Distributed queues in shared memory: Multicore performance and scalability through quantitative relaxation","article_number":"17","department":[{"_id":"ToHe"}],"publication":"Proceedings of the ACM International Conference on Computing Frontiers - CF '13","oa_version":"None","scopus_import":"1","language":[{"iso":"eng"}],"day":"14","publication_identifier":{"isbn":["978-145032053-5"]},"year":"2013","conference":{"name":"CF: Conference on Computing Frontiers","start_date":"2013-05-14","end_date":"2013-05-16","location":"Ischia, Italy"},"date_updated":"2025-05-14T11:23:58Z","status":"public","acknowledgement":"This work has been supported by the European Research Council advanced grant on Quantitative Reactive Modeling (QUAREM) and the National Research Network RiSE on Rigorous Systems Engineering (Austrian Science Fund S11402-N23 and S11404-N23).","month":"05"},{"publication":"Encyclopedia of Biodiversity","oa_version":"None","type":"book_chapter","publication_status":"published","scopus_import":"1","quality_controlled":"1","corr_author":"1","edition":"2","language":[{"iso":"eng"}],"doi":"10.1016/b978-0-12-384719-5.00031-9","publisher":"Elsevier","date_published":"2013-01-01T00:00:00Z","publication_identifier":{"isbn":["978-0-12-384720-1"]},"article_processing_charge":"No","day":"01","citation":{"ama":"Barton NH. Differentiation. In: Encyclopedia of Biodiversity. 2nd ed. Elsevier; 2013:508-515. doi:10.1016/b978-0-12-384719-5.00031-9","mla":"Barton, Nicholas H. “Differentiation.” Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–15, doi:10.1016/b978-0-12-384719-5.00031-9.","ieee":"N. H. Barton, “Differentiation,” in Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","apa":"Barton, N. H. (2013). Differentiation. In Encyclopedia of Biodiversity (2nd ed., pp. 508–515). Elsevier. https://doi.org/10.1016/b978-0-12-384719-5.00031-9","chicago":"Barton, Nicholas H. “Differentiation.” In Encyclopedia of Biodiversity, 2nd ed., 508–15. Elsevier, 2013. https://doi.org/10.1016/b978-0-12-384719-5.00031-9.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515."},"_id":"10899","year":"2013","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"date_created":"2022-03-21T07:46:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-09T21:02:37Z","title":"Differentiation","page":"508-515","department":[{"_id":"NiBa"}],"status":"public","month":"01"},{"publication":"Chemokines","oa_version":"None","scopus_import":"1","language":[{"iso":"eng"}],"corr_author":"1","publication_identifier":{"eisbn":["9781627034265"],"eissn":["1940-6029"],"isbn":["9781627034258"],"issn":["1064-3745"]},"day":"03","year":"2013","volume":1013,"date_updated":"2024-10-09T21:02:37Z","place":"Totowa, NJ","page":"215-226","acknowledgement":"We would like to thank Alexander Eichner and Ingrid de Vries for discussion and critical reading of the manuscript, and Mary Frank for assistance with the recording of videos and images in Fig. 1. M.S. is supported through funding from the German Research Foundation (DFG). M.W. acknowledges the Alexander von Humboldt Foundation for funding.","status":"public","month":"04","publication_status":"published","type":"book_chapter","quality_controlled":"1","doi":"10.1007/978-1-62703-426-5_14","publisher":"Humana Press","pmid":1,"article_processing_charge":"No","date_published":"2013-04-03T00:00:00Z","citation":{"ama":"Weber M, Sixt MK. Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Cardona A, Ubogu E, eds. Chemokines. Vol 1013. MIMB. Totowa, NJ: Humana Press; 2013:215-226. doi:10.1007/978-1-62703-426-5_14","mla":"Weber, Michele, and Michael K. Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” Chemokines, edited by Astrid Cardona and Eroboghene Ubogu, vol. 1013, Humana Press, 2013, pp. 215–26, doi:10.1007/978-1-62703-426-5_14.","ieee":"M. Weber and M. K. Sixt, “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations,” in Chemokines, vol. 1013, A. Cardona and E. Ubogu, Eds. Totowa, NJ: Humana Press, 2013, pp. 215–226.","chicago":"Weber, Michele, and Michael K Sixt. “Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations.” In Chemokines, edited by Astrid Cardona and Eroboghene Ubogu, 1013:215–26. MIMB. Totowa, NJ: Humana Press, 2013. https://doi.org/10.1007/978-1-62703-426-5_14.","apa":"Weber, M., & Sixt, M. K. (2013). Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In A. Cardona & E. Ubogu (Eds.), Chemokines (Vol. 1013, pp. 215–226). Totowa, NJ: Humana Press. https://doi.org/10.1007/978-1-62703-426-5_14","short":"M. Weber, M.K. Sixt, in:, A. Cardona, E. Ubogu (Eds.), Chemokines, Humana Press, Totowa, NJ, 2013, pp. 215–226.","ista":"Weber M, Sixt MK. 2013.Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations. In: Chemokines. Methods in Molecular Biology, vol. 1013, 215–226."},"abstract":[{"lang":"eng","text":"Leukocyte migration through the interstitial space is crucial for the maintenance of tolerance and immunity. The main cues for leukocyte trafficking are chemokines thought to directionally guide these cells towards their targets. However, model systems that facilitate quantification of chemokine-guided leukocyte migration in vivo are uncommon. Here we describe an ex vivo crawl-in assay using explanted mouse ears that allows the visualization of chemokine-dependent dendritic cell (DC) motility in the dermal interstitium in real time. We present methods for the preparation of mouse ear sheets and their use in multidimensional confocal imaging experiments to monitor and analyze the directional migration of fluorescently labelled DCs through the dermis and into afferent lymphatic vessels. The assay provides a more physiological approach to study leukocyte migration than in vitro three-dimensional (3D) or 2-dimensional (2D) migration assays such as collagen gels and transwell assays."}],"_id":"10900","author":[{"first_name":"Michele","last_name":"Weber","full_name":"Weber, Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"alternative_title":["Methods in Molecular Biology"],"date_created":"2022-03-21T07:47:41Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Live Cell Imaging of Chemotactic Dendritic Cell Migration in Explanted Mouse Ear Preparations","series_title":"MIMB","editor":[{"full_name":"Cardona, Astrid","first_name":"Astrid","last_name":"Cardona"},{"last_name":"Ubogu","first_name":"Eroboghene","full_name":"Ubogu, Eroboghene"}],"intvolume":" 1013","external_id":{"pmid":["23625502"]},"department":[{"_id":"MiSi"}]},{"date_updated":"2025-07-10T11:50:03Z","volume":7810,"status":"public","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award. Thanks to Gabriele Puppis for suggesting the problem of identifying a deterministic transducer to compute the optimal cost, and to Martin Chmelik for his comments on the introduction.","month":"04","place":"Berlin, Heidelberg","page":"214-225","language":[{"iso":"eng"}],"corr_author":"1","publication":"7th International Conference on Language and Automata Theory and Applications","oa_version":"None","scopus_import":"1","year":"2013","conference":{"end_date":"2013-04-05","start_date":"2013-04-02","name":"LATA: Language and Automata Theory and Applications","location":"Bilbao, Spain"},"day":"15","publication_identifier":{"isbn":["9783642370632"],"issn":["0302-9743"],"eisbn":["9783642370649"],"eissn":["1611-3349"]},"series_title":"LNCS","title":"How to travel between languages","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Siddhesh","last_name":"Chaubal","full_name":"Chaubal, Siddhesh"},{"full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","last_name":"Rubin","first_name":"Sasha"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"alternative_title":["LNCS"],"date_created":"2022-03-21T07:56:21Z","department":[{"_id":"KrCh"}],"intvolume":" 7810","quality_controlled":"1","publisher":"Springer Nature","doi":"10.1007/978-3-642-37064-9_20","type":"conference","publication_status":"published","_id":"10902","abstract":[{"lang":"eng","text":"We consider how to edit strings from a source language so that the edited strings belong to a target language, where the languages are given as deterministic finite automata. Non-streaming (or offline) transducers perform edits given the whole source string. We show that the class of deterministic one-pass transducers with registers along with increment and min operation suffices for computing optimal edit distance, whereas the same class of transducers without the min operation is not sufficient. Streaming (or online) transducers perform edits as the letters of the source string are received. We present a polynomial time algorithm for the partial-repair problem that given a bound α asks for the construction of a deterministic streaming transducer (if one exists) that ensures that the ‘maximum fraction’ η of the strings of the source language are edited, within cost α, to the target language."}],"ec_funded":1,"citation":{"ieee":"K. Chatterjee, S. Chaubal, and S. Rubin, “How to travel between languages,” in 7th International Conference on Language and Automata Theory and Applications, Bilbao, Spain, 2013, vol. 7810, pp. 214–225.","mla":"Chatterjee, Krishnendu, et al. “How to Travel between Languages.” 7th International Conference on Language and Automata Theory and Applications, vol. 7810, Springer Nature, 2013, pp. 214–25, doi:10.1007/978-3-642-37064-9_20.","ama":"Chatterjee K, Chaubal S, Rubin S. How to travel between languages. In: 7th International Conference on Language and Automata Theory and Applications. Vol 7810. LNCS. Berlin, Heidelberg: Springer Nature; 2013:214-225. doi:10.1007/978-3-642-37064-9_20","ista":"Chatterjee K, Chaubal S, Rubin S. 2013. How to travel between languages. 7th International Conference on Language and Automata Theory and Applications. LATA: Language and Automata Theory and ApplicationsLNCS, LNCS, vol. 7810, 214–225.","short":"K. Chatterjee, S. Chaubal, S. Rubin, in:, 7th International Conference on Language and Automata Theory and Applications, Springer Nature, Berlin, Heidelberg, 2013, pp. 214–225.","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Sasha Rubin. “How to Travel between Languages.” In 7th International Conference on Language and Automata Theory and Applications, 7810:214–25. LNCS. Berlin, Heidelberg: Springer Nature, 2013. https://doi.org/10.1007/978-3-642-37064-9_20.","apa":"Chatterjee, K., Chaubal, S., & Rubin, S. (2013). How to travel between languages. In 7th International Conference on Language and Automata Theory and Applications (Vol. 7810, pp. 214–225). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-37064-9_20"},"article_processing_charge":"No","date_published":"2013-04-15T00:00:00Z"},{"volume":23,"date_updated":"2024-10-14T11:23:44Z","page":"112-117","status":"public","extern":"1","month":"03","publication":"Trends in Cell Biology","oa_version":"None","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-8924"]},"day":"01","year":"2013","issue":"3","author":[{"last_name":"Franks","first_name":"Tobias M.","full_name":"Franks, Tobias M."},{"orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"date_created":"2022-04-07T07:50:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The role of Nup98 in transcription regulation in healthy and diseased cells","intvolume":" 23","external_id":{"pmid":["23246429"]},"publication_status":"published","type":"journal_article","quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.tcb.2012.10.013","pmid":1,"article_processing_charge":"No","date_published":"2013-03-01T00:00:00Z","citation":{"mla":"Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation in Healthy and Diseased Cells.” Trends in Cell Biology, vol. 23, no. 3, Elsevier, 2013, pp. 112–17, doi:10.1016/j.tcb.2012.10.013.","ama":"Franks TM, Hetzer M. The role of Nup98 in transcription regulation in healthy and diseased cells. Trends in Cell Biology. 2013;23(3):112-117. doi:10.1016/j.tcb.2012.10.013","ieee":"T. M. Franks and M. Hetzer, “The role of Nup98 in transcription regulation in healthy and diseased cells,” Trends in Cell Biology, vol. 23, no. 3. Elsevier, pp. 112–117, 2013.","chicago":"Franks, Tobias M., and Martin Hetzer. “The Role of Nup98 in Transcription Regulation in Healthy and Diseased Cells.” Trends in Cell Biology. Elsevier, 2013. https://doi.org/10.1016/j.tcb.2012.10.013.","apa":"Franks, T. M., & Hetzer, M. (2013). The role of Nup98 in transcription regulation in healthy and diseased cells. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2012.10.013","ista":"Franks TM, Hetzer M. 2013. The role of Nup98 in transcription regulation in healthy and diseased cells. Trends in Cell Biology. 23(3), 112–117.","short":"T.M. Franks, M. Hetzer, Trends in Cell Biology 23 (2013) 112–117."},"article_type":"letter_note","abstract":[{"text":"Nuclear pore complex (NPC) proteins are known for their critical roles in regulating nucleocytoplasmic traffic of macromolecules across the nuclear envelope. However, recent findings suggest that some nucleoporins (Nups), including Nup98, have additional functions in developmental gene regulation. Nup98, which exhibits transcription-dependent mobility at the NPC but can also bind chromatin away from the nuclear envelope, is frequently involved in chromosomal translocations in a subset of patients suffering from acute myeloid leukemia (AML). A common paradigm suggests that Nup98 translocations cause aberrant transcription when they are recuited to aberrant genomic loci. Importantly, this model fails to account for the potential loss of wild type (WT) Nup98 function in the presence of Nup98 translocation mutants. Here we examine how the cell might regulate Nup98 nucleoplasmic protein levels to control transcription in healthy cells. In addition, we discuss the possibility that dominant negative Nup98 fusion proteins disrupt the transcriptional activity of WT Nup98 in the nucleoplasm to drive AML.","lang":"eng"}],"_id":"11083","keyword":["Cell Biology"]},{"page":"55-61","status":"public","extern":"1","month":"01","volume":14,"date_updated":"2024-10-14T11:24:09Z","publication_identifier":{"issn":["1471-0072","1471-0080"]},"day":"01","year":"2013","oa_version":"None","publication":"Nature Reviews Molecular Cell Biology","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["23258296"]},"intvolume":" 14","author":[{"full_name":"Toyama, Brandon H.","last_name":"Toyama","first_name":"Brandon H."},{"last_name":"HETZER","first_name":"Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W"}],"date_created":"2022-04-07T07:50:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Protein homeostasis: Live long, won't prosper","pmid":1,"date_published":"2013-01-01T00:00:00Z","article_processing_charge":"No","article_type":"original","citation":{"ieee":"B. H. Toyama and M. Hetzer, “Protein homeostasis: Live long, won’t prosper,” Nature Reviews Molecular Cell Biology, vol. 14. Springer Nature, pp. 55–61, 2013.","mla":"Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t Prosper.” Nature Reviews Molecular Cell Biology, vol. 14, Springer Nature, 2013, pp. 55–61, doi:10.1038/nrm3496.","ama":"Toyama BH, Hetzer M. Protein homeostasis: Live long, won’t prosper. Nature Reviews Molecular Cell Biology. 2013;14:55-61. doi:10.1038/nrm3496","ista":"Toyama BH, Hetzer M. 2013. Protein homeostasis: Live long, won’t prosper. Nature Reviews Molecular Cell Biology. 14, 55–61.","short":"B.H. Toyama, M. Hetzer, Nature Reviews Molecular Cell Biology 14 (2013) 55–61.","chicago":"Toyama, Brandon H., and Martin Hetzer. “Protein Homeostasis: Live Long, Won’t Prosper.” Nature Reviews Molecular Cell Biology. Springer Nature, 2013. https://doi.org/10.1038/nrm3496.","apa":"Toyama, B. H., & Hetzer, M. (2013). Protein homeostasis: Live long, won’t prosper. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/nrm3496"},"abstract":[{"lang":"eng","text":"Protein turnover is an effective way of maintaining a functional proteome, as old and potentially damaged polypeptides are destroyed and replaced by newly synthesized copies. An increasing number of intracellular proteins, however, have been identified that evade this turnover process and instead are maintained over a cell's lifetime. This diverse group of long-lived proteins might be particularly prone to accumulation of damage and thus have a crucial role in the functional deterioration of key regulatory processes during ageing."}],"_id":"11084","keyword":["Cell Biology","Molecular Biology"],"type":"journal_article","publication_status":"published","quality_controlled":"1","doi":"10.1038/nrm3496","publisher":"Springer Nature"},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"doi":"10.1016/j.cell.2013.06.007","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.06.007","open_access":"1"}],"type":"journal_article","publication_status":"published","abstract":[{"lang":"eng","text":"During mitotic exit, missegregated chromosomes can recruit their own nuclear envelope (NE) to form micronuclei (MN). MN have reduced functioning compared to primary nuclei in the same cell, although the two compartments appear to be structurally comparable. Here we show that over 60% of MN undergo an irreversible loss of compartmentalization during interphase due to NE collapse. This disruption of the MN, which is induced by defects in nuclear lamina assembly, drastically reduces nuclear functions and can trigger massive DNA damage. MN disruption is associated with chromatin compaction and invasion of endoplasmic reticulum (ER) tubules into the chromatin. We identified disrupted MN in both major subtypes of human non-small-cell lung cancer, suggesting that disrupted MN could be a useful objective biomarker for genomic instability in solid tumors. Our study shows that NE collapse is a key event underlying MN dysfunction and establishes a link between aberrant NE organization and aneuploidy."}],"_id":"11085","keyword":["General Biochemistry","Genetics and Molecular Biology"],"pmid":1,"article_processing_charge":"No","date_published":"2013-07-03T00:00:00Z","citation":{"ista":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. 2013. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. 154(1), 47–60.","short":"E.M. Hatch, A.H. Fischer, T.J. Deerinck, M. Hetzer, Cell 154 (2013) 47–60.","chicago":"Hatch, Emily M., Andrew H. Fischer, Thomas J. Deerinck, and Martin Hetzer. “Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.06.007.","apa":"Hatch, E. M., Fischer, A. H., Deerinck, T. J., & Hetzer, M. (2013). Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.06.007","ieee":"E. M. Hatch, A. H. Fischer, T. J. Deerinck, and M. Hetzer, “Catastrophic nuclear envelope collapse in cancer cell micronuclei,” Cell, vol. 154, no. 1. Elsevier, pp. 47–60, 2013.","mla":"Hatch, Emily M., et al. “Catastrophic Nuclear Envelope Collapse in Cancer Cell Micronuclei.” Cell, vol. 154, no. 1, Elsevier, 2013, pp. 47–60, doi:10.1016/j.cell.2013.06.007.","ama":"Hatch EM, Fischer AH, Deerinck TJ, Hetzer M. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. 2013;154(1):47-60. doi:10.1016/j.cell.2013.06.007"},"article_type":"original","title":"Catastrophic nuclear envelope collapse in cancer cell micronuclei","issue":"1","author":[{"full_name":"Hatch, Emily M.","first_name":"Emily M.","last_name":"Hatch"},{"first_name":"Andrew H.","last_name":"Fischer","full_name":"Fischer, Andrew H."},{"last_name":"Deerinck","first_name":"Thomas J.","full_name":"Deerinck, Thomas J."},{"full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W"}],"date_created":"2022-04-07T07:50:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["23827674"]},"intvolume":" 154","language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Cell","scopus_import":"1","year":"2013","publication_identifier":{"issn":["0092-8674"]},"day":"03","volume":154,"date_updated":"2024-10-14T11:24:29Z","status":"public","extern":"1","month":"07","page":"47-60"},{"intvolume":" 9","external_id":{"pmid":["23468646"]},"article_number":"e1003308","title":"Dynamic association of NUP98 with the human genome","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-04-07T07:50:59Z","author":[{"full_name":"Liang, Yun","last_name":"Liang","first_name":"Yun"},{"full_name":"Franks, Tobias M.","first_name":"Tobias M.","last_name":"Franks"},{"full_name":"Marchetto, Maria C.","last_name":"Marchetto","first_name":"Maria C."},{"full_name":"Gage, Fred H.","last_name":"Gage","first_name":"Fred H."},{"orcid":"0000-0002-2111-992X","last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"issue":"2","keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"_id":"11086","abstract":[{"lang":"eng","text":"Faithful execution of developmental gene expression programs occurs at multiple levels and involves many different components such as transcription factors, histone-modification enzymes, and mRNA processing proteins. Recent evidence suggests that nucleoporins, well known components that control nucleo-cytoplasmic trafficking, have wide-ranging functions in developmental gene regulation that potentially extend beyond their role in nuclear transport. Whether the unexpected role of nuclear pore proteins in transcription regulation, which initially has been described in fungi and flies, also applies to human cells is unknown. Here we show at a genome-wide level that the nuclear pore protein NUP98 associates with developmentally regulated genes active during human embryonic stem cell differentiation. Overexpression of a dominant negative fragment of NUP98 levels decreases expression levels of NUP98-bound genes. In addition, we identify two modes of developmental gene regulation by NUP98 that are differentiated by the spatial localization of NUP98 target genes. Genes in the initial stage of developmental induction can associate with NUP98 that is embedded in the nuclear pores at the nuclear periphery. Alternatively, genes that are highly induced can interact with NUP98 in the nuclear interior, away from the nuclear pores. This work demonstrates for the first time that NUP98 dynamically associates with the human genome during differentiation, revealing a role of a nuclear pore protein in regulating developmental gene expression programs."}],"citation":{"ama":"Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. Dynamic association of NUP98 with the human genome. PLoS Genetics. 2013;9(2). doi:10.1371/journal.pgen.1003308","mla":"Liang, Yun, et al. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics, vol. 9, no. 2, e1003308, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003308.","ieee":"Y. Liang, T. M. Franks, M. C. Marchetto, F. H. Gage, and M. Hetzer, “Dynamic association of NUP98 with the human genome,” PLoS Genetics, vol. 9, no. 2. Public Library of Science, 2013.","apa":"Liang, Y., Franks, T. M., Marchetto, M. C., Gage, F. H., & Hetzer, M. (2013). Dynamic association of NUP98 with the human genome. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003308","chicago":"Liang, Yun, Tobias M. Franks, Maria C. Marchetto, Fred H. Gage, and Martin Hetzer. “Dynamic Association of NUP98 with the Human Genome.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003308.","short":"Y. Liang, T.M. Franks, M.C. Marchetto, F.H. Gage, M. Hetzer, PLoS Genetics 9 (2013).","ista":"Liang Y, Franks TM, Marchetto MC, Gage FH, Hetzer M. 2013. Dynamic association of NUP98 with the human genome. PLoS Genetics. 9(2), e1003308."},"article_type":"original","date_published":"2013-02-28T00:00:00Z","article_processing_charge":"No","pmid":1,"oa":1,"publisher":"Public Library of Science","doi":"10.1371/journal.pgen.1003308","quality_controlled":"1","type":"journal_article","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1003308"}],"month":"02","extern":"1","status":"public","volume":9,"date_updated":"2024-10-14T11:24:40Z","year":"2013","day":"28","publication_identifier":{"issn":["1553-7404"]},"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","publication":"PLoS Genetics"},{"page":"971-982","status":"public","month":"08","extern":"1","date_updated":"2025-12-15T10:02:46Z","volume":154,"day":"29","publication_identifier":{"issn":["0092-8674"]},"year":"2013","oa_version":"Published Version","publication":"Cell","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["23993091"]},"intvolume":" 154","department":[{"_id":"MaHe"}],"author":[{"full_name":"Toyama, Brandon H.","first_name":"Brandon H.","last_name":"Toyama"},{"full_name":"Savas, Jeffrey N.","first_name":"Jeffrey N.","last_name":"Savas"},{"full_name":"Park, Sung Kyu","last_name":"Park","first_name":"Sung Kyu"},{"last_name":"Harris","first_name":"Michael S.","full_name":"Harris, Michael S."},{"first_name":"Nicholas T.","last_name":"Ingolia","full_name":"Ingolia, Nicholas T."},{"full_name":"Yates, John R.","last_name":"Yates","first_name":"John R."},{"last_name":"HETZER","first_name":"Martin W","orcid":"0000-0002-2111-992X","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W"}],"issue":"5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-04-07T07:51:08Z","title":"Identification of long-lived proteins reveals exceptional stability of essential cellular structures","pmid":1,"citation":{"ieee":"B. H. Toyama et al., “Identification of long-lived proteins reveals exceptional stability of essential cellular structures,” Cell, vol. 154, no. 5. Elsevier, pp. 971–982, 2013.","ama":"Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 2013;154(5):971-982. doi:10.1016/j.cell.2013.07.037","mla":"Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell, vol. 154, no. 5, Elsevier, 2013, pp. 971–82, doi:10.1016/j.cell.2013.07.037.","short":"B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates, M. Hetzer, Cell 154 (2013) 971–982.","ista":"Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 154(5), 971–982.","chicago":"Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris, Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.07.037.","apa":"Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., & Hetzer, M. (2013). Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. Elsevier. https://doi.org/10.1016/j.cell.2013.07.037"},"article_type":"original","date_published":"2013-08-29T00:00:00Z","article_processing_charge":"No","_id":"11087","abstract":[{"lang":"eng","text":"Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process."}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.07.037","open_access":"1"}],"type":"journal_article","publication_status":"published","quality_controlled":"1","doi":"10.1016/j.cell.2013.07.037","oa":1,"publisher":"Elsevier"}]