[{"intvolume":"      5699","ec_funded":1,"date_updated":"2021-01-12T07:59:34Z","date_published":"2009-09-10T00:00:00Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"publist_id":"180","pubrep_id":"39","oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file":[{"checksum":"e8f53abb63579de3f2bff58b2a1188e2","creator":"system","file_size":164428,"date_updated":"2020-07-14T12:46:31Z","date_created":"2018-12-12T10:15:09Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5126","file_name":"IST-2012-39-v1+1_Alternating_Weighted_Automata.pdf"}],"doi":"10.1007/978-3-642-03409-1_2","_id":"4542","title":"Alternating weighted automata","citation":{"ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “Alternating weighted automata,” presented at the FCT: Fundamentals of Computation Theory, Wroclaw, Poland, 2009, vol. 5699, pp. 3–13.","ama":"Chatterjee K, Doyen L, Henzinger TA. Alternating weighted automata. In: Vol 5699. Springer; 2009:3-13. doi:<a href=\"https://doi.org/10.1007/978-3-642-03409-1_2\">10.1007/978-3-642-03409-1_2</a>","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Alternating Weighted Automata,” 5699:3–13. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-03409-1_2\">https://doi.org/10.1007/978-3-642-03409-1_2</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Alternating Weighted Automata</i>. Vol. 5699, Springer, 2009, pp. 3–13, doi:<a href=\"https://doi.org/10.1007/978-3-642-03409-1_2\">10.1007/978-3-642-03409-1_2</a>.","apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). Alternating weighted automata (Vol. 5699, pp. 3–13). Presented at the FCT: Fundamentals of Computation Theory, Wroclaw, Poland: Springer. <a href=\"https://doi.org/10.1007/978-3-642-03409-1_2\">https://doi.org/10.1007/978-3-642-03409-1_2</a>","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 3–13.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2009. Alternating weighted automata. FCT: Fundamentals of Computation Theory, LNCS, vol. 5699, 3–13."},"acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European Combest, Quasimodo, and Gasics projects, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification) funded by the F.R.S.-FNRS.","oa":1,"date_created":"2018-12-11T12:09:23Z","quality_controlled":"1","publisher":"Springer","ddc":["004"],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Weighted automata are finite automata with numerical weights on transitions. Nondeterministic weighted automata define quantitative languages L that assign to each word w a real number L(w) computed as the maximal value of all runs over w, and the value of a run r is a function of the sequence of weights that appear along r. There are several natural functions to consider such as Sup, LimSup, LimInf, limit average, and discounted sum of transition weights.\r\nWe introduce alternating weighted automata in which the transitions of the runs are chosen by two players in a turn-based fashion. Each word is assigned the maximal value of a run that the first player can enforce regardless of the choices made by the second player. We survey the results about closure properties, expressiveness, and decision problems for nondeterministic weighted automata, and we extend these results to alternating weighted automata.\r\nFor quantitative languages L 1 and L 2, we consider the pointwise operations max(L 1,L 2), min(L 1,L 2), 1 − L 1, and the sum L 1 + L 2. We establish the closure properties of all classes of alternating weighted automata with respect to these four operations.\r\nWe next compare the expressive power of the various classes of alternating and nondeterministic weighted automata over infinite words. In particular, for limit average and discounted sum, we show that alternation brings more expressive power than nondeterminism.\r\nFinally, we present decidability results and open questions for the quantitative extension of the classical decision problems in automata theory: emptiness, universality, language inclusion, and language equivalence."}],"status":"public","type":"conference","file_date_updated":"2020-07-14T12:46:31Z","day":"10","month":"09","department":[{"_id":"KrCh"}],"page":"3 - 13","year":"2009","language":[{"iso":"eng"}],"project":[{"grant_number":"214373","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems"},{"name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"215543"}],"volume":5699,"conference":{"location":"Wroclaw, Poland","end_date":"2009-09-04","start_date":"2009-09-02","name":"FCT: Fundamentals of Computation Theory"}},{"abstract":[{"text":"The synthesis of a reactive system with respect to all omega-regular specification requires the solution of a graph game. Such games have been extended in two natural ways. First, a game graph can be equipped with probabilistic choices between alternative transitions, thus allowing the, modeling of uncertain behaviour. These are called stochastic games. Second, a liveness specification can he strengthened to require satisfaction within all unknown but bounded amount of time. These are called finitary objectives. We study. for the first time, the, combination of Stochastic games and finitary objectives. We characterize the requirements on optimal strategies and provide algorithms for Computing the maximal achievable probability of winning stochastic games with finitary parity or Street, objectives. Most notably the set of state's from which a player can win with probability . for a finitary parity objective can he computed in polynomial time even though no polynomial-time algorithm is known in the nonfinitary case.","lang":"eng"}],"type":"conference","status":"public","day":"01","date_created":"2018-12-11T12:09:24Z","quality_controlled":"1","publisher":"Springer","year":"2009","language":[{"iso":"eng"}],"volume":5734,"project":[{"name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems"}],"conference":{"location":"High Tatras, Slovakia","end_date":"2009-08-28","name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2009-08-24"},"month":"08","page":"34 - 54","department":[{"_id":"KrCh"}],"publist_id":"178","oa_version":"None","scopus_import":1,"alternative_title":["LNCS"],"intvolume":"      5734","ec_funded":1,"date_updated":"2021-01-12T07:59:35Z","date_published":"2009-08-01T00:00:00Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"id":"37327ACE-F248-11E8-B48F-1D18A9856A87","full_name":"Horn, Florian","first_name":"Florian","last_name":"Horn"}],"publication_status":"published","doi":"10.1007/978-3-642-03816-7_4","_id":"4543","title":"Stochastic games with finitary objectives","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Stochastic Games with Finitary Objectives,” 5734:34–54. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-03816-7_4\">https://doi.org/10.1007/978-3-642-03816-7_4</a>.","ama":"Chatterjee K, Henzinger TA, Horn F. Stochastic games with finitary objectives. In: Vol 5734. Springer; 2009:34-54. doi:<a href=\"https://doi.org/10.1007/978-3-642-03816-7_4\">10.1007/978-3-642-03816-7_4</a>","ieee":"K. Chatterjee, T. A. Henzinger, and F. Horn, “Stochastic games with finitary objectives,” presented at the MFCS: Mathematical Foundations of Computer Science, High Tatras, Slovakia, 2009, vol. 5734, pp. 34–54.","short":"K. Chatterjee, T.A. Henzinger, F. Horn, in:, Springer, 2009, pp. 34–54.","ista":"Chatterjee K, Henzinger TA, Horn F. 2009. Stochastic games with finitary objectives. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 5734, 34–54.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Horn, F. (2009). Stochastic games with finitary objectives (Vol. 5734, pp. 34–54). Presented at the MFCS: Mathematical Foundations of Computer Science, High Tatras, Slovakia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-03816-7_4\">https://doi.org/10.1007/978-3-642-03816-7_4</a>","mla":"Chatterjee, Krishnendu, et al. <i>Stochastic Games with Finitary Objectives</i>. Vol. 5734, Springer, 2009, pp. 34–54, doi:<a href=\"https://doi.org/10.1007/978-3-642-03816-7_4\">10.1007/978-3-642-03816-7_4</a>."},"acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), and by the European project Combest.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2021-01-12T07:59:35Z","date_created":"2018-12-11T12:09:24Z","date_published":"2009-01-01T00:00:00Z","quality_controlled":0,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"de Alfaro, Luca","first_name":"Luca","last_name":"De Alfaro"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publisher":"SIAM","pubrep_id":"37","publist_id":"176","abstract":[{"text":"We consider concurrent games played on graphs. At every round of a game, each player simultaneously and independently selects a move; the moves jointly determine the transition to a successor state. Two basic objectives are the safety objective to stay forever in a given set of states, and its dual, the reachability objective to reach a given set of states. We present in this paper a strategy improvement algorithm for computing the value of a concurrent safety game, that is, the maximal probability with which player 1 can enforce the safety objective. The algorithm yields a sequence of player-1 strategies which ensure probabilities of winning that converge monotonically to the value of the safety game. Our result is significant because the strategy improvement algorithm provides, for the first time, a way to approximate the value of a concurrent safety game from below. Since a value iteration algorithm, or a strategy improvement algorithm for reachability games, can be used to approximate the same value from above, the combination of both algorithms yields a method for computing a converging sequence of upper and lower bounds for the values of concurrent reachability and safety games. Previous methods could approximate the values of these games only from one direction, and as no rates of convergence are known, they did not provide a practical way to solve these games.","lang":"eng"}],"type":"conference","status":"public","day":"01","extern":1,"file_date_updated":"2020-07-14T12:46:31Z","main_file_link":[{"open_access":"1","url":"https://repository.ist.ac.at/id/eprint/37"}],"month":"01","page":"197 - 206","doi":"10.1137/1.9781611973068.23","file":[{"date_created":"2018-12-12T10:08:03Z","relation":"main_file","date_updated":"2020-07-14T12:46:31Z","checksum":"ce7dc1667502e26b23c07a767ac41ae6","file_size":212369,"creator":"system","file_name":"IST-2012-37-v1+1_Termination_criteria_for_solving_concurrent_safety_and_reachability_games.pdf","content_type":"application/pdf","file_id":"4662","access_level":"open_access"}],"publication_status":"published","year":"2009","title":"Termination criteria for solving concurrent safety and reachability games","_id":"4544","citation":{"chicago":"Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Termination Criteria for Solving Concurrent Safety and Reachability Games,” 197–206. SIAM, 2009. <a href=\"https://doi.org/10.1137/1.9781611973068.23\">https://doi.org/10.1137/1.9781611973068.23</a>.","ama":"Chatterjee K, De Alfaro L, Henzinger TA. Termination criteria for solving concurrent safety and reachability games. In: SIAM; 2009:197-206. doi:<a href=\"https://doi.org/10.1137/1.9781611973068.23\">10.1137/1.9781611973068.23</a>","ieee":"K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Termination criteria for solving concurrent safety and reachability games,” presented at the SODA: Symposium on Discrete Algorithms, 2009, pp. 197–206.","ista":"Chatterjee K, De Alfaro L, Henzinger TA. 2009. Termination criteria for solving concurrent safety and reachability games. SODA: Symposium on Discrete Algorithms, 197–206.","short":"K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, SIAM, 2009, pp. 197–206.","apa":"Chatterjee, K., De Alfaro, L., &#38; Henzinger, T. A. (2009). Termination criteria for solving concurrent safety and reachability games (pp. 197–206). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. <a href=\"https://doi.org/10.1137/1.9781611973068.23\">https://doi.org/10.1137/1.9781611973068.23</a>","mla":"Chatterjee, Krishnendu, et al. <i>Termination Criteria for Solving Concurrent Safety and Reachability Games</i>. SIAM, 2009, pp. 197–206, doi:<a href=\"https://doi.org/10.1137/1.9781611973068.23\">10.1137/1.9781611973068.23</a>."},"oa":1,"conference":{"name":"SODA: Symposium on Discrete Algorithms"}},{"conference":{"end_date":"2009-07-12","location":"Rhodos, Greece","start_date":"2009-07-05","name":"ICALP: Automata, Languages and Programming"},"year":"2009","language":[{"iso":"eng"}],"project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques"}],"volume":5556,"department":[{"_id":"KrCh"}],"page":"1 - 15","month":"06","status":"public","type":"conference","file_date_updated":"2020-07-14T12:46:31Z","day":"24","ddc":["000","005"],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"A stochastic game is a two-player game played oil a graph, where in each state the successor is chosen either by One of the players, or according to a probability distribution. We Survey Stochastic games with limsup and liminf objectives. A real-valued re-ward is assigned to each state, and the value of all infinite path is the limsup (resp. liminf) of all rewards along the path. The value of a stochastic game is the maximal expected value of an infinite path that call he achieved by resolving the decisions of the first player. We present the complexity of computing values of Stochastic games and their subclasses, and the complexity, of optimal strategies in such games. "}],"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T12:09:24Z","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>A Survey of Stochastic Games with Limsup and Liminf Objectives</i>. Vol. 5556, Springer, 2009, pp. 1–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-02930-1_1\">10.1007/978-3-642-02930-1_1</a>.","apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). A survey of stochastic games with limsup and liminf objectives (Vol. 5556, pp. 1–15). Presented at the ICALP: Automata, Languages and Programming, Rhodos, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02930-1_1\">https://doi.org/10.1007/978-3-642-02930-1_1</a>","ista":"Chatterjee K, Doyen L, Henzinger TA. 2009. A survey of stochastic games with limsup and liminf objectives. ICALP: Automata, Languages and Programming, LNCS, vol. 5556, 1–15.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 1–15.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of stochastic games with limsup and liminf objectives,” presented at the ICALP: Automata, Languages and Programming, Rhodos, Greece, 2009, vol. 5556, pp. 1–15.","ama":"Chatterjee K, Doyen L, Henzinger TA. A survey of stochastic games with limsup and liminf objectives. In: Vol 5556. Springer; 2009:1-15. doi:<a href=\"https://doi.org/10.1007/978-3-642-02930-1_1\">10.1007/978-3-642-02930-1_1</a>","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Stochastic Games with Limsup and Liminf Objectives,” 5556:1–15. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02930-1_1\">https://doi.org/10.1007/978-3-642-02930-1_1</a>."},"acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European projects COMBEST, Quasimodo, Gasics, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification) funded by the F.R.S.-FNRS.","oa":1,"publication_status":"published","file":[{"checksum":"dabb6d24428a000254c95493d9c492e6","file_size":187419,"creator":"system","relation":"main_file","date_created":"2018-12-12T10:13:11Z","date_updated":"2020-07-14T12:46:31Z","access_level":"open_access","file_name":"IST-2012-38-v1+1_A_survey_of_stochastic_games_with_limsup_and_liminf_objectives.pdf","content_type":"application/pdf","file_id":"4992"}],"doi":"10.1007/978-3-642-02930-1_1","title":"A survey of stochastic games with limsup and liminf objectives","_id":"4545","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"alternative_title":["LNCS"],"pubrep_id":"38","publist_id":"177","oa_version":"Submitted Version","date_published":"2009-06-24T00:00:00Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"ec_funded":1,"intvolume":"      5556","date_updated":"2021-01-12T07:59:35Z"},{"conference":{"start_date":"2009-06-26","name":"CAV: Computer Aided Verification","end_date":"2009-07-02","location":"Grenoble, France"},"year":"2009","language":[{"iso":"eng"}],"project":[{"name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"}],"volume":5643,"department":[{"_id":"KrCh"}],"page":"140 - 156","month":"06","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0904.2638"}],"status":"public","type":"conference","day":"19","abstract":[{"text":"Most specification languages express only qualitative constraints. However, among two implementations that satisfy a given specification, one may be preferred to another. For example, if a specification asks that every request is followed by a response, one may prefer an implementation that generates responses quickly but does not generate unnecessary responses. We use quantitative properties to measure the “goodness” of an implementation. Using games with corresponding quantitative objectives, we can synthesize “optimal” implementations, which are preferred among the set of possible implementations that satisfy a given specification.\r\nIn particular, we show how automata with lexicographic mean-payoff conditions can be used to express many interesting quantitative properties for reactive systems. In this framework, the synthesis of optimal implementations requires the solution of lexicographic mean-payoff games (for safety requirements), and the solution of games with both lexicographic mean-payoff and parity objectives (for liveness requirements). We present algorithms for solving both kinds of novel graph games.","lang":"eng"}],"quality_controlled":"1","publisher":"Springer","external_id":{"arxiv":["0904.2638"]},"date_created":"2018-12-11T12:09:31Z","citation":{"chicago":"Bloem, Roderick, Krishnendu Chatterjee, Thomas A Henzinger, and Barbara Jobstmann. “Better Quality in Synthesis through Quantitative Objectives,” 5643:140–56. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">https://doi.org/10.1007/978-3-642-02658-4_14</a>.","ama":"Bloem R, Chatterjee K, Henzinger TA, Jobstmann B. Better quality in synthesis through quantitative objectives. In: Vol 5643. Springer; 2009:140-156. doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">10.1007/978-3-642-02658-4_14</a>","ieee":"R. Bloem, K. Chatterjee, T. A. Henzinger, and B. Jobstmann, “Better quality in synthesis through quantitative objectives,” presented at the CAV: Computer Aided Verification, Grenoble, France, 2009, vol. 5643, pp. 140–156.","mla":"Bloem, Roderick, et al. <i>Better Quality in Synthesis through Quantitative Objectives</i>. Vol. 5643, Springer, 2009, pp. 140–56, doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">10.1007/978-3-642-02658-4_14</a>.","apa":"Bloem, R., Chatterjee, K., Henzinger, T. A., &#38; Jobstmann, B. (2009). Better quality in synthesis through quantitative objectives (Vol. 5643, pp. 140–156). Presented at the CAV: Computer Aided Verification, Grenoble, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">https://doi.org/10.1007/978-3-642-02658-4_14</a>","ista":"Bloem R, Chatterjee K, Henzinger TA, Jobstmann B. 2009. Better quality in synthesis through quantitative objectives. CAV: Computer Aided Verification, LNCS, vol. 5643, 140–156.","short":"R. Bloem, K. Chatterjee, T.A. Henzinger, B. Jobstmann, in:, Springer, 2009, pp. 140–156."},"arxiv":1,"acknowledgement":"This research was supported by the Swiss National Science Foundation (Indo-Swiss Research Program and NCCR MICS) and the European Union projects COMBEST and COCONUT.","oa":1,"publication_status":"published","doi":"10.1007/978-3-642-02658-4_14","_id":"4569","title":"Better quality in synthesis through quantitative objectives","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"publist_id":"141","oa_version":"Preprint","date_published":"2009-06-19T00:00:00Z","author":[{"full_name":"Bloem, Roderick","first_name":"Roderick","last_name":"Bloem"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Barbara","full_name":"Jobstmann, Barbara","last_name":"Jobstmann"}],"ec_funded":1,"intvolume":"      5643","date_updated":"2021-01-12T07:59:46Z"},{"_id":"4580","title":"Alpaga: A tool for solving parity games with imperfect information","volume":5505,"doi":"10.1007/978-3-642-00768-2_7","year":"2009","publication_status":"published","file":[{"relation":"main_file","date_created":"2018-12-12T10:15:45Z","date_updated":"2020-07-14T12:46:32Z","checksum":"d52b55a10a47b3e3b0e016ea9bf85c41","file_size":212180,"creator":"system","file_name":"IST-2012-35-v1+1_Alpaga_-_A_tool_for_solving_parity_games_with_imperfect_information.pdf","file_id":"5168","content_type":"application/pdf","access_level":"open_access"}],"oa":1,"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"citation":{"chicago":"Berwanger, Dietmar, Krishnendu Chatterjee, Martin De Wulf, Laurent Doyen, and Thomas A Henzinger. “Alpaga: A Tool for Solving Parity Games with Imperfect Information,” 5505:58–61. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-00768-2_7\">https://doi.org/10.1007/978-3-642-00768-2_7</a>.","ama":"Berwanger D, Chatterjee K, De Wulf M, Doyen L, Henzinger TA. Alpaga: A tool for solving parity games with imperfect information. In: Vol 5505. Springer; 2009:58-61. doi:<a href=\"https://doi.org/10.1007/978-3-642-00768-2_7\">10.1007/978-3-642-00768-2_7</a>","ieee":"D. Berwanger, K. Chatterjee, M. De Wulf, L. Doyen, and T. A. Henzinger, “Alpaga: A tool for solving parity games with imperfect information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, 2009, vol. 5505, pp. 58–61.","ista":"Berwanger D, Chatterjee K, De Wulf M, Doyen L, Henzinger TA. 2009. Alpaga: A tool for solving parity games with imperfect information. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 5505, 58–61.","short":"D. Berwanger, K. Chatterjee, M. De Wulf, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 58–61.","mla":"Berwanger, Dietmar, et al. <i>Alpaga: A Tool for Solving Parity Games with Imperfect Information</i>. Vol. 5505, Springer, 2009, pp. 58–61, doi:<a href=\"https://doi.org/10.1007/978-3-642-00768-2_7\">10.1007/978-3-642-00768-2_7</a>.","apa":"Berwanger, D., Chatterjee, K., De Wulf, M., Doyen, L., &#38; Henzinger, T. A. (2009). Alpaga: A tool for solving parity games with imperfect information (Vol. 5505, pp. 58–61). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Springer. <a href=\"https://doi.org/10.1007/978-3-642-00768-2_7\">https://doi.org/10.1007/978-3-642-00768-2_7</a>"},"main_file_link":[{"url":"https://repository.ist.ac.at/35/","open_access":"1"}],"month":"03","page":"58 - 61","abstract":[{"text":"Alpaga is a solver for two-player parity games with imperfect information. Given the description of a game, it determines whether the first player can ensure to win and, if so, it constructs a winning strategy. The tool provides a symbolic implementation of a recent algorithm based on antichains.","lang":"eng"}],"publist_id":"127","pubrep_id":"35","alternative_title":["LNCS"],"extern":1,"file_date_updated":"2020-07-14T12:46:32Z","day":"09","status":"public","type":"conference","date_updated":"2021-01-12T07:59:52Z","intvolume":"      5505","date_created":"2018-12-11T12:09:35Z","quality_controlled":0,"publisher":"Springer","author":[{"last_name":"Berwanger","full_name":"Berwanger, Dietmar","first_name":"Dietmar"},{"full_name":"Krishnendu Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"De Wulf","full_name":"De Wulf, Martin","first_name":"Martin"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2009-03-09T00:00:00Z"},{"language":[{"iso":"eng"}],"year":"2008","publication_identifier":{"issn":["0885-6087"],"eissn":["1099-1085"]},"volume":22,"page":"3980-3997","article_type":"original","month":"09","status":"public","type":"journal_article","day":"15","extern":"1","abstract":[{"lang":"eng","text":"We use meteorological data from two automatic weather stations (AWS) on Juncal Norte Glacier, central Chile, to investigate the glacier–climate interaction and to test ablation models of different complexity. The semi-arid Central Andes are characterized by dry summers, with precipitation close to zero, low relative humidity and intense solar radiation. We show that katabatic forcing is dominant both on the glacier tongue and in the fore field, and that low humidity and absence of clouds cause strong radiative cooling of the glacier surface. Surface albedo is basically constant for snow and ice, because of the scarcity of solid precipitation. The energy balance of the glacier is simulated for a 2-month period in austral summer using two models of different complexity, which differ in the inclusion of the heat conduction flux into the snowpack and in the parameterization of the incoming longwave radiation. Net shortwave radiation is the dominant component of the energy balance. The sensible heat flux is always positive, while both the net longwave radiation and latent heat flux are negative. Neglecting the subsurface heat flux and corresponding variations in surface temperature leads to an overestimation of ablation of 2% over a total of 3695 mm water equivalent (w.e.) at the end of the season. Correct modelling of incoming longwave radiation is crucial, and we suggest that parameterizations based on vapour pressure and air temperature should be used rather than on computed cloud amount. We also used an enhanced temperature-index model incorporating the shortwave radiation flux, which has two empirical parameters. We apply it both with values of parameters obtained for Alpine glaciers and recalibrated on Juncal Norte. The model recalibrated against the correct energy balance simulations performs very well. The model parameters respond to the meteorological conditions typical of this climatic setting."}],"quality_controlled":"1","publisher":"Wiley","date_created":"2023-02-20T08:18:45Z","citation":{"chicago":"Pellicciotti, Francesca, Jakob Helbing, Andrés Rivera, Vincent Favier, Javier Corripio, José Araos, Jean-Emmanuel Sicart, and Marco Carenzo. “A Study of the Energy Balance and Melt Regime on Juncal Norte Glacier, Semi-Arid Andes of Central Chile, Using Melt Models of Different Complexity.” <i>Hydrological Processes</i>. Wiley, 2008. <a href=\"https://doi.org/10.1002/hyp.7085\">https://doi.org/10.1002/hyp.7085</a>.","ama":"Pellicciotti F, Helbing J, Rivera A, et al. A study of the energy balance and melt regime on Juncal Norte Glacier, semi-arid Andes of central Chile, using melt models of different complexity. <i>Hydrological Processes</i>. 2008;22(19):3980-3997. doi:<a href=\"https://doi.org/10.1002/hyp.7085\">10.1002/hyp.7085</a>","ieee":"F. Pellicciotti <i>et al.</i>, “A study of the energy balance and melt regime on Juncal Norte Glacier, semi-arid Andes of central Chile, using melt models of different complexity,” <i>Hydrological Processes</i>, vol. 22, no. 19. Wiley, pp. 3980–3997, 2008.","mla":"Pellicciotti, Francesca, et al. “A Study of the Energy Balance and Melt Regime on Juncal Norte Glacier, Semi-Arid Andes of Central Chile, Using Melt Models of Different Complexity.” <i>Hydrological Processes</i>, vol. 22, no. 19, Wiley, 2008, pp. 3980–97, doi:<a href=\"https://doi.org/10.1002/hyp.7085\">10.1002/hyp.7085</a>.","apa":"Pellicciotti, F., Helbing, J., Rivera, A., Favier, V., Corripio, J., Araos, J., … Carenzo, M. (2008). A study of the energy balance and melt regime on Juncal Norte Glacier, semi-arid Andes of central Chile, using melt models of different complexity. <i>Hydrological Processes</i>. Wiley. <a href=\"https://doi.org/10.1002/hyp.7085\">https://doi.org/10.1002/hyp.7085</a>","short":"F. Pellicciotti, J. Helbing, A. Rivera, V. Favier, J. Corripio, J. Araos, J.-E. Sicart, M. Carenzo, Hydrological Processes 22 (2008) 3980–3997.","ista":"Pellicciotti F, Helbing J, Rivera A, Favier V, Corripio J, Araos J, Sicart J-E, Carenzo M. 2008. A study of the energy balance and melt regime on Juncal Norte Glacier, semi-arid Andes of central Chile, using melt models of different complexity. Hydrological Processes. 22(19), 3980–3997."},"doi":"10.1002/hyp.7085","publication_status":"published","title":"A study of the energy balance and melt regime on Juncal Norte Glacier, semi-arid Andes of central Chile, using melt models of different complexity","publication":"Hydrological Processes","_id":"12656","article_processing_charge":"No","keyword":["Water Science and Technology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"None","date_published":"2008-09-15T00:00:00Z","author":[{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"last_name":"Helbing","first_name":"Jakob","full_name":"Helbing, Jakob"},{"last_name":"Rivera","first_name":"Andrés","full_name":"Rivera, Andrés"},{"full_name":"Favier, Vincent","first_name":"Vincent","last_name":"Favier"},{"full_name":"Corripio, Javier","first_name":"Javier","last_name":"Corripio"},{"first_name":"José","full_name":"Araos, José","last_name":"Araos"},{"full_name":"Sicart, Jean-Emmanuel","first_name":"Jean-Emmanuel","last_name":"Sicart"},{"full_name":"Carenzo, Marco","first_name":"Marco","last_name":"Carenzo"}],"issue":"19","date_updated":"2023-02-20T08:48:33Z","intvolume":"        22"},{"intvolume":"        18","date_created":"2018-12-11T11:51:13Z","date_updated":"2021-01-12T06:49:42Z","issue":"5","publisher":"Cell Press","quality_controlled":0,"author":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","full_name":"Maximilian Jösch","last_name":"Jösch","orcid":"0000-0002-3937-1330"},{"first_name":"Johannes","full_name":"Plett, Johannes","last_name":"Plett"},{"last_name":"Borst","full_name":"Borst, Alexander","first_name":"Alexander"},{"full_name":"Reiff, Dierk F","first_name":"Dierk","last_name":"Reiff"}],"date_published":"2008-03-11T00:00:00Z","abstract":[{"lang":"eng","text":"The crystalline-like structure of the optic lobes of the fruit fly Drosophila melanogaster has made them a model system for the study of neuronal cell-fate determination, axonal path finding, and target selection. For functional studies, however, the small size of the constituting visual interneurons has so far presented a formidable barrier. We have overcome this problem by establishing in vivo whole-cell recordings [1] from genetically targeted visual interneurons of Drosophila. Here, we describe the response properties of six motion-sensitive large-field neurons in the lobula plate that form a network consisting of individually identifiable, directionally selective cells most sensitive to vertical image motion (VS cells [2, 3]). Individual VS cell responses to visual motion stimuli exhibit all the characteristics that are indicative of presynaptic input from elementary motion detectors of the correlation type [4, 5]. Different VS cells possess distinct receptive fields that are arranged sequentially along the eye's azimuth, corresponding to their characteristic cellular morphology and position within the retinotopically organized lobula plate. In addition, lateral connections between individual VS cells cause strongly overlapping receptive fields that are wider than expected from their dendritic input. Our results suggest that motion vision in different dipteran fly species is accomplished in similar circuitries and according to common algorithmic rules. The underlying neural mechanisms of population coding within the VS cell network and of elementary motion detection, respectively, can now be analyzed by the combination of electrophysiology and genetic intervention in Drosophila."}],"publist_id":"5973","day":"11","extern":1,"type":"journal_article","status":"public","month":"03","page":"368 - 374","publication":"Current Biology","_id":"1296","volume":18,"title":"Response properties of motion sensitive visual interneurons in the Lobula plate of Drosophila melanogaster","publication_status":"published","year":"2008","doi":"10.1016/j.cub.2008.02.022","acknowledgement":"This work was supported by the Max-Planck-Society and by a Human Frontier Science Program (HFSP) grant to K. Ito, A.B., and B. Nelson.","citation":{"short":"M.A. Jösch, J. Plett, A. Borst, D. Reiff, Current Biology 18 (2008) 368–374.","ista":"Jösch MA, Plett J, Borst A, Reiff D. 2008. Response properties of motion sensitive visual interneurons in the Lobula plate of Drosophila melanogaster. Current Biology. 18(5), 368–374.","apa":"Jösch, M. A., Plett, J., Borst, A., &#38; Reiff, D. (2008). Response properties of motion sensitive visual interneurons in the Lobula plate of Drosophila melanogaster. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2008.02.022\">https://doi.org/10.1016/j.cub.2008.02.022</a>","mla":"Jösch, Maximilian A., et al. “Response Properties of Motion Sensitive Visual Interneurons in the Lobula Plate of Drosophila Melanogaster.” <i>Current Biology</i>, vol. 18, no. 5, Cell Press, 2008, pp. 368–74, doi:<a href=\"https://doi.org/10.1016/j.cub.2008.02.022\">10.1016/j.cub.2008.02.022</a>.","ama":"Jösch MA, Plett J, Borst A, Reiff D. Response properties of motion sensitive visual interneurons in the Lobula plate of Drosophila melanogaster. <i>Current Biology</i>. 2008;18(5):368-374. doi:<a href=\"https://doi.org/10.1016/j.cub.2008.02.022\">10.1016/j.cub.2008.02.022</a>","ieee":"M. A. Jösch, J. Plett, A. Borst, and D. Reiff, “Response properties of motion sensitive visual interneurons in the Lobula plate of Drosophila melanogaster,” <i>Current Biology</i>, vol. 18, no. 5. Cell Press, pp. 368–374, 2008.","chicago":"Jösch, Maximilian A, Johannes Plett, Alexander Borst, and Dierk Reiff. “Response Properties of Motion Sensitive Visual Interneurons in the Lobula Plate of Drosophila Melanogaster.” <i>Current Biology</i>. Cell Press, 2008. <a href=\"https://doi.org/10.1016/j.cub.2008.02.022\">https://doi.org/10.1016/j.cub.2008.02.022</a>."}},{"month":"11","_id":"844","publication":"PLoS Genetics","title":"Hypermutable non-synonymous sites are under stronger negative selection","volume":4,"doi":"10.1371/journal.pgen.1000281","publication_status":"published","year":"2008","acknowledgement":"This work was supported in part by NIH grants R01 GM078598 and U54 LM008748.","citation":{"chicago":"Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” <i>PLoS Genetics</i>. Public Library of Science, 2008. <a href=\"https://doi.org/10.1371/journal.pgen.1000281\">https://doi.org/10.1371/journal.pgen.1000281</a>.","ama":"Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. Hypermutable non-synonymous sites are under stronger negative selection. <i>PLoS Genetics</i>. 2008;4(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000281\">10.1371/journal.pgen.1000281</a>","ieee":"S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,” <i>PLoS Genetics</i>, vol. 4, no. 11. Public Library of Science, 2008.","apa":"Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A., &#38; Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger negative selection. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1000281\">https://doi.org/10.1371/journal.pgen.1000281</a>","mla":"Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger Negative Selection.” <i>PLoS Genetics</i>, vol. 4, no. 11, Public Library of Science, 2008, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000281\">10.1371/journal.pgen.1000281</a>.","short":"S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S. Sunyaev, PLoS Genetics 4 (2008).","ista":"Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S. 2008. Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genetics. 4(11)."},"date_updated":"2021-01-12T08:19:16Z","date_created":"2018-12-11T11:48:48Z","intvolume":"         4","issue":"11","quality_controlled":0,"author":[{"first_name":"Steffen","full_name":"Schmidt, Steffen","last_name":"Schmidt"},{"full_name":"Gerasimova, Anna","first_name":"Anna","last_name":"Gerasimova"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Ivan","full_name":"Adzuhbei, Ivan A","last_name":"Adzuhbei"},{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"},{"last_name":"Sunyaev","first_name":"Shamil","full_name":"Sunyaev, Shamil R"}],"publisher":"Public Library of Science","date_published":"2008-11-01T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites.","lang":"eng"}],"publist_id":"6800","extern":1,"day":"01","status":"public","type":"journal_article"},{"date_created":"2020-09-18T10:12:29Z","intvolume":"       380","date_updated":"2021-01-12T08:19:34Z","issue":"4","publisher":"Elsevier","quality_controlled":"1","author":[{"last_name":"Schanda","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"},{"last_name":"Konrat","first_name":"Robert","full_name":"Konrat, Robert"},{"last_name":"Tollinger","full_name":"Tollinger, Martin","first_name":"Martin"}],"date_published":"2008-07-18T00:00:00Z","abstract":[{"lang":"eng","text":"The KIX domain of the transcription co-activator CBP is a three-helix bundle protein that folds via rapid accumulation of an intermediate state, followed by a slower folding phase. Recent NMR relaxation dispersion studies revealed the presence of a low-populated (excited) state of KIX that exists in equilibrium with the natively folded form under non-denaturing conditions, and likely represents the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium exchange measurements using rapid NMR data acquisition techniques with backbone 15N and 13C relaxation dispersion experiments to further investigate the equilibrium folding of the KIX domain. Residual structure within the folding intermediate is detected by both methods, and their combination enables reliable quantification of the amount of persistent residual structure. Three well-defined folding subunits are found, which display variable stability and correspond closely to the individual helices in the native state. While two of the three helices (α2 and α3) are partially formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C), the third helix is disordered. The observed helical content within the excited state exceeds the helical propensities predicted for the corresponding peptide regions, suggesting that the two helices are weakly mutually stabilized, while methyl 13C relaxation dispersion data indicate that a defined packing arrangement is unlikely. Temperature-dependent experiments reveal that the largest enthalpy and entropy changes along the folding reaction occur during the final transition from the intermediate to the native state. Our experimental data are consistent with a folding mechanism where helices α2 and α3 form rapidly, although to different extents, while helix α1 consolidates only as folding proceeds to complete the native state-structure."}],"oa_version":"None","extern":"1","day":"18","type":"journal_article","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Molecular Biology"],"month":"07","article_type":"original","page":"726-741","_id":"8480","volume":380,"publication":"Journal of Molecular Biology","title":"Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy","article_processing_charge":"No","publication_identifier":{"issn":["0022-2836"]},"year":"2008","publication_status":"published","doi":"10.1016/j.jmb.2008.05.040","language":[{"iso":"eng"}],"citation":{"chicago":"Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” <i>Journal of Molecular Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">https://doi.org/10.1016/j.jmb.2008.05.040</a>.","ama":"Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. <i>Journal of Molecular Biology</i>. 2008;380(4):726-741. doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">10.1016/j.jmb.2008.05.040</a>","ieee":"P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,” <i>Journal of Molecular Biology</i>, vol. 380, no. 4. Elsevier, pp. 726–741, 2008.","mla":"Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” <i>Journal of Molecular Biology</i>, vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">10.1016/j.jmb.2008.05.040</a>.","apa":"Schanda, P., Brutscher, B., Konrat, R., &#38; Tollinger, M. (2008). Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">https://doi.org/10.1016/j.jmb.2008.05.040</a>","ista":"Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. 380(4), 726–741.","short":"P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology 380 (2008) 726–741."}},{"citation":{"ista":"Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M, Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. 380(2), 386–403.","short":"B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M. Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403.","apa":"Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J., … Wattiez, R. (2008). Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">https://doi.org/10.1016/j.jmb.2008.05.017</a>","mla":"Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” <i>Journal of Molecular Biology</i>, vol. 380, no. 2, Elsevier, 2008, pp. 386–403, doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">10.1016/j.jmb.2008.05.017</a>.","chicago":"Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” <i>Journal of Molecular Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">https://doi.org/10.1016/j.jmb.2008.05.017</a>.","ieee":"B. Bersch <i>et al.</i>, “Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge,” <i>Journal of Molecular Biology</i>, vol. 380, no. 2. Elsevier, pp. 386–403, 2008.","ama":"Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. <i>Journal of Molecular Biology</i>. 2008;380(2):386-403. doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">10.1016/j.jmb.2008.05.017</a>"},"publication_identifier":{"issn":["0022-2836"]},"_id":"8481","title":"Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge","article_processing_charge":"No","volume":380,"publication":"Journal of Molecular Biology","doi":"10.1016/j.jmb.2008.05.017","language":[{"iso":"eng"}],"publication_status":"published","year":"2008","page":"386-403","keyword":["Molecular Biology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","month":"07","extern":"1","day":"04","status":"public","type":"journal_article","abstract":[{"lang":"eng","text":"The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans CH34 within the complex cop cluster of genes, for which 21 genes have been identified. The expression of the corresponding periplasmic CopK protein is strongly upregulated in the presence of copper, leading to a high periplasmic accumulation. The structure and metal-binding properties of CopK were investigated by NMR and mass spectrometry. The protein is dimeric in the apo state with a dissociation constant in the range of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed that CopK has two high-affinity Cu(I)-binding sites per monomer with different Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific. The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets in perpendicular orientation with an unstructured C-terminal tail. The dimer interface is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion induces a major structural modification involving dissociation of the dimeric apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm the conservation of the N-terminal β-sheet, while the last strand of the C-terminal sheet appears in slow conformational exchange. We hypothesize that the partial disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange data acquired on the apo-protein are consistent with a lower thermodynamic stability of the C-terminal sheet. CopK contains seven methionine residues, five of which appear highly conserved. Chemical shift data suggest implication of two or three methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second Cu(I) ion further increases protein plasticity. Comparison of the structural and metal-binding properties of CopK with other periplasmic copper-binding proteins reveals two conserved features within these functionally related proteins: the all-β fold and the methionine-rich Cu(I)-binding site."}],"oa_version":"None","quality_controlled":"1","author":[{"full_name":"Bersch, Beate","first_name":"Beate","last_name":"Bersch"},{"last_name":"Favier","first_name":"Adrien","full_name":"Favier, Adrien"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul"},{"first_name":"Sébastien","full_name":"van Aelst, Sébastien","last_name":"van Aelst"},{"last_name":"Vallaeys","full_name":"Vallaeys, Tatiana","first_name":"Tatiana"},{"last_name":"Covès","full_name":"Covès, Jacques","first_name":"Jacques"},{"first_name":"Max","full_name":"Mergeay, Max","last_name":"Mergeay"},{"last_name":"Wattiez","first_name":"Ruddy","full_name":"Wattiez, Ruddy"}],"publisher":"Elsevier","date_published":"2008-07-04T00:00:00Z","date_updated":"2021-01-12T08:19:34Z","date_created":"2020-09-18T10:12:37Z","intvolume":"       380","issue":"2"},{"oa_version":"None","abstract":[{"lang":"eng","text":"The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants."}],"status":"public","type":"journal_article","extern":"1","day":"01","issue":"2","date_updated":"2021-01-12T08:19:35Z","date_created":"2020-09-18T10:12:46Z","intvolume":"       190","date_published":"2008-02-01T00:00:00Z","author":[{"first_name":"Thomas","full_name":"Kern, Thomas","last_name":"Kern"},{"first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"first_name":"Bernhard","full_name":"Brutscher, Bernhard","last_name":"Brutscher"}],"quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.jmr.2007.11.015","language":[{"iso":"eng"}],"publication_status":"published","year":"2008","publication_identifier":{"issn":["1090-7807"]},"article_processing_charge":"No","_id":"8482","title":"Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load","volume":190,"publication":"Journal of Magnetic Resonance","citation":{"short":"T. Kern, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 190 (2008) 333–338.","ista":"Kern T, Schanda P, Brutscher B. 2008. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. 190(2), 333–338.","mla":"Kern, Thomas, et al. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” <i>Journal of Magnetic Resonance</i>, vol. 190, no. 2, Elsevier, 2008, pp. 333–38, doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">10.1016/j.jmr.2007.11.015</a>.","apa":"Kern, T., Schanda, P., &#38; Brutscher, B. (2008). Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">https://doi.org/10.1016/j.jmr.2007.11.015</a>","chicago":"Kern, Thomas, Paul Schanda, and Bernhard Brutscher. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">https://doi.org/10.1016/j.jmr.2007.11.015</a>.","ama":"Kern T, Schanda P, Brutscher B. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. <i>Journal of Magnetic Resonance</i>. 2008;190(2):333-338. doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">10.1016/j.jmr.2007.11.015</a>","ieee":"T. Kern, P. Schanda, and B. Brutscher, “Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load,” <i>Journal of Magnetic Resonance</i>, vol. 190, no. 2. Elsevier, pp. 333–338, 2008."},"article_type":"letter_note","month":"02","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"333-338"},{"doi":"10.1137/070703235","language":[{"iso":"eng"}],"publication_status":"published","year":"2008","publication_identifier":{"issn":["0036-1445","1095-7200"]},"_id":"8509","volume":50,"title":"Geometry of Arnold diffusion","publication":"SIAM Review","article_processing_charge":"No","citation":{"apa":"Kaloshin, V., &#38; Levi, M. (2008). Geometry of Arnold diffusion. <i>SIAM Review</i>. Society for Industrial &#38; Applied Mathematics. <a href=\"https://doi.org/10.1137/070703235\">https://doi.org/10.1137/070703235</a>","mla":"Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” <i>SIAM Review</i>, vol. 50, no. 4, Society for Industrial &#38; Applied Mathematics, 2008, pp. 702–20, doi:<a href=\"https://doi.org/10.1137/070703235\">10.1137/070703235</a>.","short":"V. Kaloshin, M. Levi, SIAM Review 50 (2008) 702–720.","ista":"Kaloshin V, Levi M. 2008. Geometry of Arnold diffusion. SIAM Review. 50(4), 702–720.","ama":"Kaloshin V, Levi M. Geometry of Arnold diffusion. <i>SIAM Review</i>. 2008;50(4):702-720. doi:<a href=\"https://doi.org/10.1137/070703235\">10.1137/070703235</a>","ieee":"V. Kaloshin and M. Levi, “Geometry of Arnold diffusion,” <i>SIAM Review</i>, vol. 50, no. 4. Society for Industrial &#38; Applied Mathematics, pp. 702–720, 2008.","chicago":"Kaloshin, Vadim, and Mark Levi. “Geometry of Arnold Diffusion.” <i>SIAM Review</i>. Society for Industrial &#38; Applied Mathematics, 2008. <a href=\"https://doi.org/10.1137/070703235\">https://doi.org/10.1137/070703235</a>."},"article_type":"original","month":"11","keyword":["Theoretical Computer Science","Applied Mathematics","Computational Mathematics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"702-720","oa_version":"None","abstract":[{"lang":"eng","text":"The goal of this paper is to present to nonspecialists what is perhaps the simplest possible geometrical picture explaining the mechanism of Arnold diffusion. We choose to speak of a specific model—that of geometric rays in a periodic optical medium. This model is equivalent to that of a particle in a periodic potential in ${\\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian metric on ${\\mathbb R}^{n} $."}],"type":"journal_article","status":"public","day":"05","extern":"1","issue":"4","date_updated":"2021-01-12T08:19:46Z","intvolume":"        50","date_created":"2020-09-18T10:48:12Z","date_published":"2008-11-05T00:00:00Z","quality_controlled":"1","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"},{"last_name":"Levi","full_name":"Levi, Mark","first_name":"Mark"}],"publisher":"Society for Industrial & Applied Mathematics"},{"extern":"1","day":"01","type":"journal_article","status":"public","abstract":[{"lang":"eng","text":"In this paper, using the ideas of Bessi and Mather, we present a simple mechanical system exhibiting Arnold diffusion. This system of a particle in a small periodic potential can be also interpreted as ray propagation in a periodic optical medium with a near-constant index of refraction. Arnold diffusion in this context manifests itself as an arbitrary finite change of direction for nearly constant index of refraction."}],"oa_version":"None","publisher":"American Mathematical Society","quality_controlled":"1","author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","first_name":"Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628"},{"last_name":"Levi","full_name":"Levi, Mark","first_name":"Mark"}],"date_published":"2008-07-01T00:00:00Z","date_updated":"2021-01-12T08:19:47Z","intvolume":"        45","date_created":"2020-09-18T10:48:20Z","issue":"3","citation":{"mla":"Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” <i>Bulletin of the American Mathematical Society</i>, vol. 45, no. 3, American Mathematical Society, 2008, pp. 409–27, doi:<a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">10.1090/s0273-0979-08-01211-1</a>.","apa":"Kaloshin, V., &#38; Levi, M. (2008). An example of Arnold diffusion for near-integrable Hamiltonians. <i>Bulletin of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">https://doi.org/10.1090/s0273-0979-08-01211-1</a>","short":"V. Kaloshin, M. Levi, Bulletin of the American Mathematical Society 45 (2008) 409–427.","ista":"Kaloshin V, Levi M. 2008. An example of Arnold diffusion for near-integrable Hamiltonians. Bulletin of the American Mathematical Society. 45(3), 409–427.","chicago":"Kaloshin, Vadim, and Mark Levi. “An Example of Arnold Diffusion for Near-Integrable Hamiltonians.” <i>Bulletin of the American Mathematical Society</i>. American Mathematical Society, 2008. <a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">https://doi.org/10.1090/s0273-0979-08-01211-1</a>.","ama":"Kaloshin V, Levi M. An example of Arnold diffusion for near-integrable Hamiltonians. <i>Bulletin of the American Mathematical Society</i>. 2008;45(3):409-427. doi:<a href=\"https://doi.org/10.1090/s0273-0979-08-01211-1\">10.1090/s0273-0979-08-01211-1</a>","ieee":"V. Kaloshin and M. Levi, “An example of Arnold diffusion for near-integrable Hamiltonians,” <i>Bulletin of the American Mathematical Society</i>, vol. 45, no. 3. American Mathematical Society, pp. 409–427, 2008."},"publication_identifier":{"issn":["0273-0979"]},"volume":45,"_id":"8510","publication":"Bulletin of the American Mathematical Society","title":"An example of Arnold diffusion for near-integrable Hamiltonians","article_processing_charge":"No","doi":"10.1090/s0273-0979-08-01211-1","language":[{"iso":"eng"}],"year":"2008","publication_status":"published","page":"409-427","keyword":["Applied Mathematics","General Mathematics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","month":"07"},{"month":"01","doi":"10.1186/1471-2148-8-180","year":"2008","publication_status":"published","_id":"895","volume":8,"title":"Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene","publication":"BMC Evolutionary Biology","citation":{"ieee":"Z. Donaldson <i>et al.</i>, “Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene,” <i>BMC Evolutionary Biology</i>, vol. 8, no. 1. BioMed Central, 2008.","ama":"Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. <i>BMC Evolutionary Biology</i>. 2008;8(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-8-180\">10.1186/1471-2148-8-180</a>","chicago":"Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski, Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2008. <a href=\"https://doi.org/10.1186/1471-2148-8-180\">https://doi.org/10.1186/1471-2148-8-180</a>.","ista":"Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L. 2008. Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1).","short":"Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock, L. Young, BMC Evolutionary Biology 8 (2008).","mla":"Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” <i>BMC Evolutionary Biology</i>, vol. 8, no. 1, BioMed Central, 2008, doi:<a href=\"https://doi.org/10.1186/1471-2148-8-180\">10.1186/1471-2148-8-180</a>.","apa":"Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock, E., &#38; Young, L. (2008). Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-8-180\">https://doi.org/10.1186/1471-2148-8-180</a>"},"acknowledgement":"We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD).\n","issue":"1","date_updated":"2021-01-12T08:21:29Z","intvolume":"         8","date_created":"2018-12-11T11:49:04Z","date_published":"2008-01-01T00:00:00Z","publisher":"BioMed Central","author":[{"last_name":"Donaldson","full_name":"Donaldson, Zoe R","first_name":"Zoe"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Putnam, Andrea S","first_name":"Andrea","last_name":"Putnam"},{"full_name":"Bai, Yaohui","first_name":"Yaohui","last_name":"Bai"},{"last_name":"Stoinski","first_name":"Tara","full_name":"Stoinski, Tara S"},{"last_name":"Hammock","first_name":"Elizabeth","full_name":"Hammock, Elizabeth A"},{"first_name":"Larry","full_name":"Young, Larry","last_name":"Young"}],"quality_controlled":0,"publist_id":"6753","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Background. The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex (CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results. Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion. There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a unique opportunity to assess the functional role of this duplication in contributing to variation in social behavior in primates. While our initial studies show no signs of directional selection on this locus in chimps, pharmacological and genetic association studies support a potential role for this region in influencing V1aR expression and social behavior."}],"type":"journal_article","status":"public","day":"01","extern":1},{"citation":{"chicago":"Assis, Raquel, Alexey Kondrashov, Eugene Koonin, and Fyodor Kondrashov. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” <i>Trends in Genetics</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.tig.2008.08.003\">https://doi.org/10.1016/j.tig.2008.08.003</a>.","ama":"Assis R, Kondrashov A, Koonin E, Kondrashov F. Nested genes and increasing organizational complexity of metazoan genomes. <i>Trends in Genetics</i>. 2008;24(10):475-478. doi:<a href=\"https://doi.org/10.1016/j.tig.2008.08.003\">10.1016/j.tig.2008.08.003</a>","ieee":"R. Assis, A. Kondrashov, E. Koonin, and F. Kondrashov, “Nested genes and increasing organizational complexity of metazoan genomes,” <i>Trends in Genetics</i>, vol. 24, no. 10. Elsevier, pp. 475–478, 2008.","apa":"Assis, R., Kondrashov, A., Koonin, E., &#38; Kondrashov, F. (2008). Nested genes and increasing organizational complexity of metazoan genomes. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2008.08.003\">https://doi.org/10.1016/j.tig.2008.08.003</a>","mla":"Assis, Raquel, et al. “Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” <i>Trends in Genetics</i>, vol. 24, no. 10, Elsevier, 2008, pp. 475–78, doi:<a href=\"https://doi.org/10.1016/j.tig.2008.08.003\">10.1016/j.tig.2008.08.003</a>.","short":"R. Assis, A. Kondrashov, E. Koonin, F. Kondrashov, Trends in Genetics 24 (2008) 475–478.","ista":"Assis R, Kondrashov A, Koonin E, Kondrashov F. 2008. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics. 24(10), 475–478."},"volume":24,"_id":"907","title":"Nested genes and increasing organizational complexity of metazoan genomes","publication":"Trends in Genetics","doi":"10.1016/j.tig.2008.08.003","publication_status":"published","year":"2008","page":"475 - 478","month":"10","extern":1,"day":"01","status":"public","type":"journal_article","abstract":[{"lang":"eng","text":"The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process."}],"publist_id":"6743","publisher":"Elsevier","quality_controlled":0,"author":[{"first_name":"Raquel","full_name":"Assis, Raquel","last_name":"Assis"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey S"},{"last_name":"Koonin","full_name":"Koonin, Eugene V","first_name":"Eugene"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"}],"date_published":"2008-10-01T00:00:00Z","date_updated":"2021-01-12T08:21:49Z","intvolume":"        24","date_created":"2018-12-11T11:49:08Z","issue":"10"},{"volume":54,"_id":"7320","article_processing_charge":"No","title":"Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC","publication":"Electrochimica Acta","publication_identifier":{"issn":["0013-4686"]},"publication_status":"published","year":"2008","language":[{"iso":"eng"}],"doi":"10.1016/j.electacta.2008.07.034","citation":{"ista":"Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. 2008. Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. Electrochimica Acta. 54(2), 551–559.","short":"R. Flückiger, S.A. Freunberger, D. Kramer, A. Wokaun, G.G. Scherer, F.N. Büchi, Electrochimica Acta 54 (2008) 551–559.","apa":"Flückiger, R., Freunberger, S. A., Kramer, D., Wokaun, A., Scherer, G. G., &#38; Büchi, F. N. (2008). Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. <i>Electrochimica Acta</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.electacta.2008.07.034\">https://doi.org/10.1016/j.electacta.2008.07.034</a>","mla":"Flückiger, Reto, et al. “Anisotropic, Effective Diffusivity of Porous Gas Diffusion Layer Materials for PEFC.” <i>Electrochimica Acta</i>, vol. 54, no. 2, Elsevier, 2008, pp. 551–59, doi:<a href=\"https://doi.org/10.1016/j.electacta.2008.07.034\">10.1016/j.electacta.2008.07.034</a>.","ieee":"R. Flückiger, S. A. Freunberger, D. Kramer, A. Wokaun, G. G. Scherer, and F. N. Büchi, “Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC,” <i>Electrochimica Acta</i>, vol. 54, no. 2. Elsevier, pp. 551–559, 2008.","ama":"Flückiger R, Freunberger SA, Kramer D, Wokaun A, Scherer GG, Büchi FN. Anisotropic, effective diffusivity of porous gas diffusion layer materials for PEFC. <i>Electrochimica Acta</i>. 2008;54(2):551-559. doi:<a href=\"https://doi.org/10.1016/j.electacta.2008.07.034\">10.1016/j.electacta.2008.07.034</a>","chicago":"Flückiger, Reto, Stefan Alexander Freunberger, Denis Kramer, Alexander Wokaun, Günther G. Scherer, and Felix N. Büchi. “Anisotropic, Effective Diffusivity of Porous Gas Diffusion Layer Materials for PEFC.” <i>Electrochimica Acta</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.electacta.2008.07.034\">https://doi.org/10.1016/j.electacta.2008.07.034</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","article_type":"original","page":"551-559","abstract":[{"lang":"eng","text":"A comparative, experimental diffusivity study of gas diffusion layer (GDL) materials for polymer electrolyte fuel cells (PEFC) is presented for the first time. The GDL plays an important role for electrochemical losses due to gas transport limitations at high current densities. Characterization and optimization of these layers is therefore essential to improve power density. A recently developed method which allows for fast diffusimetry is applied and data compared to the literature values. Measurements are made as a function of direction and compression and the effect of different binder structures and hydrophobic treatments on effective diffusivities are discussed. A better understanding of the results is gained by including novel GDL cross-section images and a meaningful unit cell model for the interpretation of the data. The diffusivity data is valuable for GDL manufacturers and future PEFC models. The study reveals that a binder–fiber ratio larger than 50% has a negative impact on the effective diffusion properties. The hydrophobic treatment which is necessary to improve the water management can impede diffusion and thus reduce the power density. Furthermore binder has an isotropic effect while compression pronounces the in-plane orientation of the fibers."}],"oa_version":"None","extern":"1","day":"30","status":"public","type":"journal_article","intvolume":"        54","date_created":"2020-01-15T12:21:36Z","date_updated":"2021-01-12T08:13:02Z","issue":"2","publisher":"Elsevier","author":[{"last_name":"Flückiger","first_name":"Reto","full_name":"Flückiger, Reto"},{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"},{"last_name":"Kramer","first_name":"Denis","full_name":"Kramer, Denis"},{"last_name":"Wokaun","first_name":"Alexander","full_name":"Wokaun, Alexander"},{"first_name":"Günther G.","full_name":"Scherer, Günther G.","last_name":"Scherer"},{"last_name":"Büchi","first_name":"Felix N.","full_name":"Büchi, Felix N."}],"quality_controlled":"1","date_published":"2008-12-30T00:00:00Z"},{"oa_version":"None","abstract":[{"text":"Cell interaction phenomena in polymer electrolyte fuel cell stacks that arise from imbalance between adjacent cells are investigated in detail experimentally and theoretically. A specialized two-cell stack with advanced localized diagnostics was developed and used to analyze the mechanism and effect of cell-to-cell coupling as a result of operationally relevant variations in reactant feed flow. Contributions to overall and local voltage changes with respect to uniformly operated cells are scrutinized. Unequal operation of the cells causes in-plane current in the bipolar plate to redistribute current and result in inhomogeneous polarization. Both increasing and decreasing polarization along the air-flow path reduces cell power as compared to isopotential operation. A two-dimensional model based on a commercial computational fluid dynamics code is used to back and extend the experimental results to more general cases. Furthermore, the experimental setup presented allowed for the first time to perform simultaneous localized electrochemical impedance spectroscopy beyond the single-cell level. The mechanism of mutual cell interaction on local and integral spectra is revealed. Results show that virtually identical operation of the cells is essential to obtain meaningful integral spectra.","lang":"eng"}],"type":"journal_article","status":"public","extern":"1","day":"08","issue":"7","date_updated":"2021-01-12T08:13:03Z","date_created":"2020-01-15T12:21:47Z","intvolume":"       155","date_published":"2008-05-08T00:00:00Z","quality_controlled":"1","author":[{"first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger"},{"last_name":"Schneider","first_name":"Ingo A.","full_name":"Schneider, Ingo A."},{"last_name":"Sui","full_name":"Sui, Pang-Chieh","first_name":"Pang-Chieh"},{"last_name":"Wokaun","full_name":"Wokaun, Alexander","first_name":"Alexander"},{"last_name":"Djilali","first_name":"Nedjib","full_name":"Djilali, Nedjib"},{"last_name":"Büchi","first_name":"Felix N.","full_name":"Büchi, Felix N."}],"publisher":"The Electrochemical Society","language":[{"iso":"eng"}],"doi":"10.1149/1.2913095","publication_status":"published","year":"2008","publication_identifier":{"issn":["0013-4651"]},"_id":"7321","publication":"Journal of The Electrochemical Society","volume":155,"article_processing_charge":"No","title":"Cell interaction phenomena in polymer electrolyte fuel cell stacks","article_number":"B704","citation":{"short":"S.A. Freunberger, I.A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, F.N. Büchi, Journal of The Electrochemical Society 155 (2008).","ista":"Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. 2008. Cell interaction phenomena in polymer electrolyte fuel cell stacks. Journal of The Electrochemical Society. 155(7), B704.","mla":"Freunberger, Stefan Alexander, et al. “Cell Interaction Phenomena in Polymer Electrolyte Fuel Cell Stacks.” <i>Journal of The Electrochemical Society</i>, vol. 155, no. 7, B704, The Electrochemical Society, 2008, doi:<a href=\"https://doi.org/10.1149/1.2913095\">10.1149/1.2913095</a>.","apa":"Freunberger, S. A., Schneider, I. A., Sui, P.-C., Wokaun, A., Djilali, N., &#38; Büchi, F. N. (2008). Cell interaction phenomena in polymer electrolyte fuel cell stacks. <i>Journal of The Electrochemical Society</i>. The Electrochemical Society. <a href=\"https://doi.org/10.1149/1.2913095\">https://doi.org/10.1149/1.2913095</a>","ama":"Freunberger SA, Schneider IA, Sui P-C, Wokaun A, Djilali N, Büchi FN. Cell interaction phenomena in polymer electrolyte fuel cell stacks. <i>Journal of The Electrochemical Society</i>. 2008;155(7). doi:<a href=\"https://doi.org/10.1149/1.2913095\">10.1149/1.2913095</a>","ieee":"S. A. Freunberger, I. A. Schneider, P.-C. Sui, A. Wokaun, N. Djilali, and F. N. Büchi, “Cell interaction phenomena in polymer electrolyte fuel cell stacks,” <i>Journal of The Electrochemical Society</i>, vol. 155, no. 7. The Electrochemical Society, 2008.","chicago":"Freunberger, Stefan Alexander, Ingo A. Schneider, Pang-Chieh Sui, Alexander Wokaun, Nedjib Djilali, and Felix N. Büchi. “Cell Interaction Phenomena in Polymer Electrolyte Fuel Cell Stacks.” <i>Journal of The Electrochemical Society</i>. The Electrochemical Society, 2008. <a href=\"https://doi.org/10.1149/1.2913095\">https://doi.org/10.1149/1.2913095</a>."},"article_type":"original","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"issue":"1","date_created":"2020-01-15T12:21:57Z","intvolume":"       612","date_updated":"2021-01-12T08:13:03Z","date_published":"2008-01-01T00:00:00Z","publisher":"Elsevier","quality_controlled":"1","author":[{"last_name":"Kramer","full_name":"Kramer, Denis","first_name":"Denis"},{"full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","orcid":"0000-0003-2902-5319"},{"first_name":"Reto","full_name":"Flückiger, Reto","last_name":"Flückiger"},{"full_name":"Schneider, Ingo A.","first_name":"Ingo A.","last_name":"Schneider"},{"full_name":"Wokaun, Alexander","first_name":"Alexander","last_name":"Wokaun"},{"full_name":"Büchi, Felix N.","first_name":"Felix N.","last_name":"Büchi"},{"full_name":"Scherer, Günther G.","first_name":"Günther G.","last_name":"Scherer"}],"oa_version":"None","abstract":[{"lang":"eng","text":"The gas diffusion layers (GDLs) of a membrane electrode assembly (MEA) serve as link between flow field and porous electrode within a polymer electrolyte fuel cell. Beside ensuring sufficient electrical and thermal contact between the whole electrode area and the flow field, these typically 200–400 μm thick porous structures enable the access of educts to the electrode area which would be occluded by the flow field lands if the flow field is directly attached to the electrode. Hence, the characterisation of properties pertaining to mass transport of educts and products through these structures is indispensable whilst examining the contribution of the GDLs to the overall electrochemical characteristics of a MEA. A fast and cost effective method to measure the effective diffusivity of a GDL is presented. Electrochemical impedance spectroscopy is applied to measure the effective ionic conductivity of an electrolyte-soaked GDL. Taking advantage of the analogy between Ficks and Ohms law, this provides a measure for the effective diffusivity. The method is described in detail, including experimental as well as theoretical aspects, and selected results, highlighting the anisotropy and dependence on the degree of compression, are shown. Moreover, a two-dimensional model consisting of regularly spaced ellipses is developed to represent the porous structure of the GDL, and by using conformal maps, the agreement between this model and experiment with respect to the sensitivity of the effective diffusivity towards compression is shown."}],"status":"public","type":"journal_article","extern":"1","day":"01","month":"01","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"63-77","publication_status":"published","year":"2008","language":[{"iso":"eng"}],"doi":"10.1016/j.jelechem.2007.09.014","article_processing_charge":"No","_id":"7322","volume":612,"publication":"Journal of Electroanalytical Chemistry","title":"Electrochemical diffusimetry of fuel cell gas diffusion layers","publication_identifier":{"issn":["1572-6657"]},"citation":{"ama":"Kramer D, Freunberger SA, Flückiger R, et al. Electrochemical diffusimetry of fuel cell gas diffusion layers. <i>Journal of Electroanalytical Chemistry</i>. 2008;612(1):63-77. doi:<a href=\"https://doi.org/10.1016/j.jelechem.2007.09.014\">10.1016/j.jelechem.2007.09.014</a>","ieee":"D. Kramer <i>et al.</i>, “Electrochemical diffusimetry of fuel cell gas diffusion layers,” <i>Journal of Electroanalytical Chemistry</i>, vol. 612, no. 1. Elsevier, pp. 63–77, 2008.","chicago":"Kramer, Denis, Stefan Alexander Freunberger, Reto Flückiger, Ingo A. Schneider, Alexander Wokaun, Felix N. Büchi, and Günther G. Scherer. “Electrochemical Diffusimetry of Fuel Cell Gas Diffusion Layers.” <i>Journal of Electroanalytical Chemistry</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jelechem.2007.09.014\">https://doi.org/10.1016/j.jelechem.2007.09.014</a>.","apa":"Kramer, D., Freunberger, S. A., Flückiger, R., Schneider, I. A., Wokaun, A., Büchi, F. N., &#38; Scherer, G. G. (2008). Electrochemical diffusimetry of fuel cell gas diffusion layers. <i>Journal of Electroanalytical Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jelechem.2007.09.014\">https://doi.org/10.1016/j.jelechem.2007.09.014</a>","mla":"Kramer, Denis, et al. “Electrochemical Diffusimetry of Fuel Cell Gas Diffusion Layers.” <i>Journal of Electroanalytical Chemistry</i>, vol. 612, no. 1, Elsevier, 2008, pp. 63–77, doi:<a href=\"https://doi.org/10.1016/j.jelechem.2007.09.014\">10.1016/j.jelechem.2007.09.014</a>.","short":"D. Kramer, S.A. Freunberger, R. Flückiger, I.A. Schneider, A. Wokaun, F.N. Büchi, G.G. Scherer, Journal of Electroanalytical Chemistry 612 (2008) 63–77.","ista":"Kramer D, Freunberger SA, Flückiger R, Schneider IA, Wokaun A, Büchi FN, Scherer GG. 2008. Electrochemical diffusimetry of fuel cell gas diffusion layers. Journal of Electroanalytical Chemistry. 612(1), 63–77."}},{"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"763-765","year":"2008","publication_status":"published","doi":"10.1115/fuelcell2005-74116","language":[{"iso":"eng"}],"publication":"3rd International Conference on Fuel Cell Science, Engineering and Technology","_id":"7425","article_processing_charge":"No","title":"Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks","publication_identifier":{"isbn":["0791837645","0791837572"]},"citation":{"ista":"Santis M, Freunberger SA, Papra M, Büchi FN. 2008. Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. 3rd International Conference on Fuel Cell Science, Engineering and Technology. International conference on fuel cell science, engineering and technology, 763–765.","short":"M. Santis, S.A. Freunberger, M. Papra, F.N. Büchi, in:, 3rd International Conference on Fuel Cell Science, Engineering and Technology, ASMEDC, 2008, pp. 763–765.","apa":"Santis, M., Freunberger, S. A., Papra, M., &#38; Büchi, F. N. (2008). Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. In <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i> (pp. 763–765). Ypsilanti, MI, United States: ASMEDC. <a href=\"https://doi.org/10.1115/fuelcell2005-74116\">https://doi.org/10.1115/fuelcell2005-74116</a>","mla":"Santis, Marco, et al. “Experimental Investigation of the Propagation of Local Current Density Variations to Adjacent Cells in PEFC Stacks.” <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i>, ASMEDC, 2008, pp. 763–65, doi:<a href=\"https://doi.org/10.1115/fuelcell2005-74116\">10.1115/fuelcell2005-74116</a>.","ieee":"M. Santis, S. A. Freunberger, M. Papra, and F. N. Büchi, “Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks,” in <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i>, Ypsilanti, MI, United States, 2008, pp. 763–765.","ama":"Santis M, Freunberger SA, Papra M, Büchi FN. Experimental investigation of the propagation of local current density variations to adjacent cells in PEFC stacks. In: <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i>. ASMEDC; 2008:763-765. doi:<a href=\"https://doi.org/10.1115/fuelcell2005-74116\">10.1115/fuelcell2005-74116</a>","chicago":"Santis, Marco, Stefan Alexander Freunberger, Matthias Papra, and Felix N. Büchi. “Experimental Investigation of the Propagation of Local Current Density Variations to Adjacent Cells in PEFC Stacks.” In <i>3rd International Conference on Fuel Cell Science, Engineering and Technology</i>, 763–65. ASMEDC, 2008. <a href=\"https://doi.org/10.1115/fuelcell2005-74116\">https://doi.org/10.1115/fuelcell2005-74116</a>."},"conference":{"name":"International conference on fuel cell science, engineering and technology","start_date":"2005-05-23","location":"Ypsilanti, MI, United States","end_date":"2005-05-25"},"date_created":"2020-01-31T10:14:45Z","date_updated":"2021-01-12T08:13:33Z","date_published":"2008-10-13T00:00:00Z","publisher":"ASMEDC","author":[{"last_name":"Santis","full_name":"Santis, Marco","first_name":"Marco"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319"},{"first_name":"Matthias","full_name":"Papra, Matthias","last_name":"Papra"},{"full_name":"Büchi, Felix N.","first_name":"Felix N.","last_name":"Büchi"}],"quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"The propagation of single cell performance losses to adjacent cells in a polymer electrolyte fuel cell stack is studied by means of local current density measurements in a two cell stack. In this stack, the working conditions of adjacent cells can be controlled independently in order to deliberately change the performance of one cell (inducing cell) and study the coupling effects to the adjacent cell (response cell), while keeping the working conditions of the later one unchanged. The experiments have shown that changes in the current density distribution caused by lowering of the air stoichiometry in the inducing cell cause changes in the current density distribution of the response cell in the order of 60% of the change of the inducing cell, even when the air stoichiometry of the response cell is kept constant. The losses in cell voltage of the inducing cell cause losses in cell voltage of the response cell in a magnitude between 30 and 50%."}],"status":"public","type":"conference","extern":"1","day":"13"}]