[{"publication_status":"published","language":[{"iso":"eng"}],"corr_author":"1","publist_id":"4785","department":[{"_id":"ChLa"}],"date_created":"2018-12-11T11:56:13Z","title":"Adaptation de domaine de vote de majorité par auto-étiquetage non itératif","quality_controlled":"1","month":"07","_id":"2189","volume":1,"citation":{"ista":"Morvant E. 2014. Adaptation de domaine de vote de majorité par auto-étiquetage non itératif. CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine Learning French Conference) vol. 1, 49–58.","chicago":"Morvant, Emilie. “Adaptation de Domaine de Vote de Majorité Par Auto-Étiquetage Non Itératif,” 1:49–58. Elsevier, 2014.","apa":"Morvant, E. (2014). Adaptation de domaine de vote de majorité par auto-étiquetage non itératif (Vol. 1, pp. 49–58). Presented at the CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine Learning French Conference), Saint-Etienne, France: Elsevier.","ama":"Morvant E. Adaptation de domaine de vote de majorité par auto-étiquetage non itératif. In: Vol 1. Elsevier; 2014:49-58.","ieee":"E. Morvant, “Adaptation de domaine de vote de majorité par auto-étiquetage non itératif,” presented at the CAP: Conférence Francophone sur l’Apprentissage Automatique (Machine Learning French Conference), Saint-Etienne, France, 2014, vol. 1, pp. 49–58.","mla":"Morvant, Emilie. <i>Adaptation de Domaine de Vote de Majorité Par Auto-Étiquetage Non Itératif</i>. Vol. 1, Elsevier, 2014, pp. 49–58.","short":"E. Morvant, in:, Elsevier, 2014, pp. 49–58."},"abstract":[{"text":"En apprentissage automatique, nous parlons d'adaptation de domaine lorsque les données de test (cibles) et d'apprentissage (sources) sont générées selon différentes distributions. Nous devons donc développer des algorithmes de classification capables de s'adapter à une nouvelle distribution, pour laquelle aucune information sur les étiquettes n'est disponible. Nous attaquons cette problématique sous l'angle de l'approche PAC-Bayésienne qui se focalise sur l'apprentissage de modèles définis comme des votes de majorité sur un ensemble de fonctions. Dans ce contexte, nous introduisons PV-MinCq une version adaptative de l'algorithme (non adaptatif) MinCq. PV-MinCq suit le principe suivant. Nous transférons les étiquettes sources aux points cibles proches pour ensuite appliquer MinCq sur l'échantillon cible ``auto-étiqueté'' (justifié par une borne théorique). Plus précisément, nous définissons un auto-étiquetage non itératif qui se focalise dans les régions où les distributions marginales source et cible sont les plus similaires. Dans un second temps, nous étudions l'influence de notre auto-étiquetage pour en déduire une procédure de validation des hyperparamètres. Finalement, notre approche montre des résultats empiriques prometteurs.","lang":"fre"}],"article_processing_charge":"No","conference":{"name":"CAP: Conférence Francophone sur l'Apprentissage Automatique (Machine Learning French Conference)","location":"Saint-Etienne, France"},"year":"2014","oa_version":"Preprint","date_updated":"2024-10-09T20:55:32Z","date_published":"2014-07-01T00:00:00Z","page":"49-58","intvolume":"         1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-8301-7240","last_name":"Morvant","full_name":"Morvant, Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","first_name":"Emilie"}],"oa":1,"status":"public","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01005776/","open_access":"1"}],"publisher":"Elsevier","day":"01","type":"conference"},{"author":[{"first_name":"Javier","last_name":"Esparza","full_name":"Esparza, Javier"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881"}],"scopus_import":"1","ec_funded":1,"intvolume":"      8559","acknowledgement":"The author is on leave from Faculty of Informatics, Masaryk University, Czech Republic, and partially supported by the Czech Science Foundation, grant No. P202/12/G061.","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1402.3388","open_access":"1"}],"publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"external_id":{"arxiv":["1402.3388"]},"date_created":"2018-12-11T11:56:14Z","language":[{"iso":"eng"}],"corr_author":"1","volume":8559,"quality_controlled":"1","abstract":[{"lang":"eng","text":"We present a new algorithm to construct a (generalized) deterministic Rabin automaton for an LTL formula φ. The automaton is the product of a master automaton and an array of slave automata, one for each G-subformula of φ. The slave automaton for G ψ is in charge of recognizing whether FG ψ holds. As opposed to standard determinization procedures, the states of all our automata have a clear logical structure, which allows for various optimizations. Our construction subsumes former algorithms for fragments of LTL. Experimental results show improvement in the sizes of the resulting automata compared to existing methods."}],"date_published":"2014-01-01T00:00:00Z","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","year":"2014","date_updated":"2025-06-11T08:01:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"192 - 208","status":"public","publisher":"Springer","day":"01","type":"conference","arxiv":1,"publist_id":"4784","doi":"10.1007/978-3-319-08867-9_13","alternative_title":["LNCS"],"_id":"2190","title":"From LTL to deterministic automata: A safraless compositional approach","month":"01","article_processing_charge":"No","conference":{"name":"CAV: Computer Aided Verification"},"citation":{"ieee":"J. Esparza and J. Kretinsky, “From LTL to deterministic automata: A safraless compositional approach,” presented at the CAV: Computer Aided Verification, 2014, vol. 8559, pp. 192–208.","mla":"Esparza, Javier, and Jan Kretinsky. <i>From LTL to Deterministic Automata: A Safraless Compositional Approach</i>. Vol. 8559, Springer, 2014, pp. 192–208, doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_13\">10.1007/978-3-319-08867-9_13</a>.","short":"J. Esparza, J. Kretinsky, in:, Springer, 2014, pp. 192–208.","ista":"Esparza J, Kretinsky J. 2014. From LTL to deterministic automata: A safraless compositional approach. CAV: Computer Aided Verification, LNCS, vol. 8559, 192–208.","chicago":"Esparza, Javier, and Jan Kretinsky. “From LTL to Deterministic Automata: A Safraless Compositional Approach,” 8559:192–208. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_13\">https://doi.org/10.1007/978-3-319-08867-9_13</a>.","apa":"Esparza, J., &#38; Kretinsky, J. (2014). From LTL to deterministic automata: A safraless compositional approach (Vol. 8559, pp. 192–208). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_13\">https://doi.org/10.1007/978-3-319-08867-9_13</a>","ama":"Esparza J, Kretinsky J. From LTL to deterministic automata: A safraless compositional approach. In: Vol 8559. Springer; 2014:192-208. doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_13\">10.1007/978-3-319-08867-9_13</a>"}},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2014-04-01T00:00:00Z","date_updated":"2025-09-30T08:08:45Z","oa_version":"Preprint","year":"2014","issue":"2","publisher":"ACM","day":"01","type":"journal_article","status":"public","publist_id":"4759","doi":"10.1145/2579821","arxiv":1,"article_processing_charge":"No","related_material":{"record":[{"id":"5381","status":"public","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"1903"},{"id":"2955","status":"public","relation":"earlier_version"}]},"citation":{"ieee":"K. Chatterjee and L. Doyen, “Partial-observation stochastic games: How to win when belief fails,” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 15, no. 2. ACM, 2014.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 15, no. 2, 16, ACM, 2014, doi:<a href=\"https://doi.org/10.1145/2579821\">10.1145/2579821</a>.","short":"K. Chatterjee, L. Doyen, ACM Transactions on Computational Logic (TOCL) 15 (2014).","ista":"Chatterjee K, Doyen L. 2014. Partial-observation stochastic games: How to win when belief fails. ACM Transactions on Computational Logic (TOCL). 15(2), 16.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Partial-Observation Stochastic Games: How to Win When Belief Fails.” <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM, 2014. <a href=\"https://doi.org/10.1145/2579821\">https://doi.org/10.1145/2579821</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2014). Partial-observation stochastic games: How to win when belief fails. <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM. <a href=\"https://doi.org/10.1145/2579821\">https://doi.org/10.1145/2579821</a>","ama":"Chatterjee K, Doyen L. Partial-observation stochastic games: How to win when belief fails. <i>ACM Transactions on Computational Logic (TOCL)</i>. 2014;15(2). doi:<a href=\"https://doi.org/10.1145/2579821\">10.1145/2579821</a>"},"_id":"2211","month":"04","title":"Partial-observation stochastic games: How to win when belief fails","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"publication":"ACM Transactions on Computational Logic (TOCL)","scopus_import":"1","isi":1,"intvolume":"        15","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1107.2141"}],"oa":1,"date_created":"2018-12-11T11:56:21Z","department":[{"_id":"KrCh"}],"external_id":{"isi":["000336005000006"],"arxiv":["1107.2141"]},"language":[{"iso":"eng"}],"publication_status":"published","article_number":"16","abstract":[{"lang":"eng","text":"In two-player finite-state stochastic games of partial observation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distribution over the successor states. The game is played for infinitely many rounds and thus the players construct an infinite path in the graph. We consider reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1) or positively (i.e., with positive probability), no matter the strategy of the second player. We classify such games according to the information and to the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two-sided with (c) both players having partial observation. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. Our main results for pure strategies are as follows: (1) For one-sided games with player 2 having perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strategies are not sufficient, and we present an exponential upper bound on memory both for almost-sure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete and present symbolic algorithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 having perfect observation we show that nonelementarymemory is both necessary and sufficient for both almost-sure and positive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least nonelementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence result exhibit serious flaws in previous results of the literature: we show a nonelementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed."}],"volume":15,"quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"The theory of graph games is the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic processes, we use 2 1/2-player games where some transitions of the game graph are controlled by two adversarial players, the System and the Environment, and the other transitions are determined probabilistically. We consider 2 1/2-player games where the objective of the System is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a mean-payoff condition). We establish that the problem of deciding whether the System can ensure that the probability to satisfy the mean-payoff parity objective is at least a given threshold is in NP ∩ coNP, matching the best known bound in the special case of 2-player games (where all transitions are deterministic). We present an algorithm running in time O(d·n2d·MeanGame) to compute the set of almost-sure winning states from which the objective can be ensured with probability 1, where n is the number of states of the game, d the number of priorities of the parity objective, and MeanGame is the complexity to compute the set of almost-sure winning states in 2 1/2-player mean-payoff games. Our results are useful in the synthesis of stochastic reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective). "}],"volume":8412,"quality_controlled":"1","date_created":"2018-12-11T11:56:21Z","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publication_status":"published","acknowledgement":"This research was supported by European project Cassting (FP7-601148).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/128.","scopus_import":1,"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"first_name":"Hugo","full_name":"Gimbert, Hugo","last_name":"Gimbert"},{"full_name":"Oualhadj, Youssouf","last_name":"Oualhadj","first_name":"Youssouf"}],"intvolume":"      8412","ec_funded":1,"conference":{"name":"FoSSaCS: Foundations of Software Science and Computation Structures","start_date":"2014-04-05","location":"Grenoble, France","end_date":"2014-04-13"},"related_material":{"record":[{"id":"5405","relation":"earlier_version","status":"public"}]},"citation":{"ista":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2014. Perfect-information stochastic mean-payoff parity games. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 210–225.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj. “Perfect-Information Stochastic Mean-Payoff Parity Games,” 8412:210–25. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54830-7_14\">https://doi.org/10.1007/978-3-642-54830-7_14</a>.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., &#38; Oualhadj, Y. (2014). Perfect-information stochastic mean-payoff parity games (Vol. 8412, pp. 210–225). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54830-7_14\">https://doi.org/10.1007/978-3-642-54830-7_14</a>","ama":"Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. Perfect-information stochastic mean-payoff parity games. In: Vol 8412. Springer; 2014:210-225. doi:<a href=\"https://doi.org/10.1007/978-3-642-54830-7_14\">10.1007/978-3-642-54830-7_14</a>","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, “Perfect-information stochastic mean-payoff parity games,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 210–225.","mla":"Chatterjee, Krishnendu, et al. <i>Perfect-Information Stochastic Mean-Payoff Parity Games</i>. Vol. 8412, Springer, 2014, pp. 210–25, doi:<a href=\"https://doi.org/10.1007/978-3-642-54830-7_14\">10.1007/978-3-642-54830-7_14</a>.","short":"K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, in:, Springer, 2014, pp. 210–225."},"_id":"2212","month":"04","title":"Perfect-information stochastic mean-payoff parity games","alternative_title":["LNCS"],"publist_id":"4758","doi":"10.1007/978-3-642-54830-7_14","publisher":"Springer","day":"01","type":"conference","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"210 - 225","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"date_published":"2014-04-01T00:00:00Z","date_updated":"2023-02-23T12:24:50Z","year":"2014","oa_version":"None"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"242 - 257","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"date_published":"2014-04-01T00:00:00Z","oa_version":"Preprint","year":"2014","date_updated":"2023-02-23T12:24:58Z","type":"conference","day":"01","publisher":"Springer","status":"public","doi":"10.1007/978-3-642-54830-7_16","publist_id":"4757","alternative_title":["LNCS"],"arxiv":1,"conference":{"end_date":"2014-04-13","location":"Grenoble, France","start_date":"2014-04-05","name":"FoSSaCS: Foundations of Software Science and Computation Structures"},"citation":{"ieee":"K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, “The complexity of partial-observation stochastic parity games with finite-memory strategies,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412, pp. 242–257.","short":"K. Chatterjee, L. Doyen, S. Nain, M. Vardi, in:, Springer, 2014, pp. 242–257.","mla":"Chatterjee, Krishnendu, et al. <i>The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies</i>. Vol. 8412, Springer, 2014, pp. 242–57, doi:<a href=\"https://doi.org/10.1007/978-3-642-54830-7_16\">10.1007/978-3-642-54830-7_16</a>.","ista":"Chatterjee K, Doyen L, Nain S, Vardi M. 2014. The complexity of partial-observation stochastic parity games with finite-memory strategies. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 8412, 242–257.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. “The Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies,” 8412:242–57. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54830-7_16\">https://doi.org/10.1007/978-3-642-54830-7_16</a>.","apa":"Chatterjee, K., Doyen, L., Nain, S., &#38; Vardi, M. (2014). The complexity of partial-observation stochastic parity games with finite-memory strategies (Vol. 8412, pp. 242–257). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54830-7_16\">https://doi.org/10.1007/978-3-642-54830-7_16</a>","ama":"Chatterjee K, Doyen L, Nain S, Vardi M. The complexity of partial-observation stochastic parity games with finite-memory strategies. In: Vol 8412. Springer; 2014:242-257. doi:<a href=\"https://doi.org/10.1007/978-3-642-54830-7_16\">10.1007/978-3-642-54830-7_16</a>"},"related_material":{"record":[{"id":"5408","relation":"earlier_version","status":"public"}]},"_id":"2213","title":"The complexity of partial-observation stochastic parity games with finite-memory strategies","month":"04","scopus_import":1,"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"first_name":"Sumit","last_name":"Nain","full_name":"Nain, Sumit"},{"last_name":"Vardi","full_name":"Vardi, Moshe","first_name":"Moshe"}],"ec_funded":1,"intvolume":"      8412","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.3289"}],"acknowledgement":"This research was supported by European project Cassting (FP7-601148), NSF grants CNS 1049862 and CCF-1139011, by NSF Expe ditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.","oa":1,"external_id":{"arxiv":["1401.3289"]},"department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:56:21Z","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"We consider two-player partial-observation stochastic games on finitestate graphs where player 1 has partial observation and player 2 has perfect observation. The winning condition we study are ε-regular conditions specified as parity objectives. The qualitative-analysis problem given a partial-observation stochastic game and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). These qualitative-analysis problems are known to be undecidable. However in many applications the relevant question is the existence of finite-memory strategies, and the qualitative-analysis problems under finite-memory strategies was recently shown to be decidable in 2EXPTIME.We improve the complexity and show that the qualitative-analysis problems for partial-observation stochastic parity games under finite-memory strategies are EXPTIME-complete; and also establish optimal (exponential) memory bounds for finite-memory strategies required for qualitative analysis."}],"volume":8412,"quality_controlled":"1"},{"author":[{"first_name":"Liat","last_name":"Stoler Barak","full_name":"Stoler Barak, Liat"},{"full_name":"Moussion, Christine","last_name":"Moussion","id":"3356F664-F248-11E8-B48F-1D18A9856A87","first_name":"Christine"},{"first_name":"Elias","last_name":"Shezen","full_name":"Shezen, Elias"},{"last_name":"Hatzav","full_name":"Hatzav, Miki","first_name":"Miki"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"first_name":"Ronen","last_name":"Alon","full_name":"Alon, Ronen"}],"scopus_import":"1","publication":"PLoS One","file_date_updated":"2020-07-14T12:45:33Z","intvolume":"         9","isi":1,"ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"84a8033bda2e07e39405f5acc85f4eca","date_updated":"2020-07-14T12:45:33Z","file_name":"IST-2016-433-v1+1_journal.pone.0085699.pdf","creator":"system","date_created":"2018-12-12T10:07:48Z","file_id":"4646","file_size":12634775}],"acknowledgement":"Michael Sixt's research is supported by the European Research Council (ERC Starting grant).","oa":1,"date_created":"2018-12-11T11:56:22Z","external_id":{"isi":["000330283100061"]},"department":[{"_id":"MiSi"}],"language":[{"iso":"eng"}],"publication_status":"published","article_number":"e85699","abstract":[{"lang":"eng","text":"A hallmark of immune cell trafficking is directional guidance via gradients of soluble or surface bound chemokines. Vascular endothelial cells produce, transport and deposit either their own chemokines or chemokines produced by the underlying stroma. Endothelial heparan sulfate (HS) was suggested to be a critical scaffold for these chemokine pools, but it is unclear how steep chemokine gradients are sustained between the lumenal and ablumenal aspects of blood vessels. Addressing this question by semi-quantitative immunostaining of HS moieties around blood vessels with a pan anti-HS IgM mAb, we found a striking HS enrichment in the basal lamina of resting and inflamed post capillary skin venules, as well as in high endothelial venules (HEVs) of lymph nodes. Staining of skin vessels with a glycocalyx probe further suggested that their lumenal glycocalyx contains much lower HS density than their basolateral extracellular matrix (ECM). This polarized HS pattern was observed also in isolated resting and inflamed microvascular dermal cells. Notably, progressive skin inflammation resulted in massive ECM deposition and in further HS enrichment around skin post capillary venules and their associated pericytes. Inflammation-dependent HS enrichment was not compromised in mice deficient in the main HS degrading enzyme, heparanase. Our results suggest that the blood vasculature patterns steep gradients of HS scaffolds between their lumenal and basolateral endothelial aspects, and that inflammatory processes can further enrich the HS content nearby inflamed vessels. We propose that chemokine gradients between the lumenal and ablumenal sides of vessels could be favored by these sharp HS scaffold gradients."}],"volume":9,"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2014-01-22T00:00:00Z","has_accepted_license":"1","project":[{"call_identifier":"FP7","name":"Stromal Cell-immune Cell Interactions in Health and Disease","grant_number":"289720","_id":"25A76F58-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-09-29T11:30:42Z","year":"2014","oa_version":"Published Version","issue":"1","publisher":"Public Library of Science","day":"22","type":"journal_article","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1371/journal.pone.0085699","publist_id":"4756","ddc":["570"],"pubrep_id":"433","article_processing_charge":"No","citation":{"ista":"Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. 2014. Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. PLoS One. 9(1), e85699.","chicago":"Stoler Barak, Liat, Christine Moussion, Elias Shezen, Miki Hatzav, Michael K Sixt, and Ronen Alon. “Blood Vessels Pattern Heparan Sulfate Gradients between Their Apical and Basolateral Aspects.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0085699\">https://doi.org/10.1371/journal.pone.0085699</a>.","apa":"Stoler Barak, L., Moussion, C., Shezen, E., Hatzav, M., Sixt, M. K., &#38; Alon, R. (2014). Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0085699\">https://doi.org/10.1371/journal.pone.0085699</a>","ama":"Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects. <i>PLoS One</i>. 2014;9(1). doi:<a href=\"https://doi.org/10.1371/journal.pone.0085699\">10.1371/journal.pone.0085699</a>","ieee":"L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M. K. Sixt, and R. Alon, “Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects,” <i>PLoS One</i>, vol. 9, no. 1. Public Library of Science, 2014.","short":"L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M.K. Sixt, R. Alon, PLoS One 9 (2014).","mla":"Stoler Barak, Liat, et al. “Blood Vessels Pattern Heparan Sulfate Gradients between Their Apical and Basolateral Aspects.” <i>PLoS One</i>, vol. 9, no. 1, e85699, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0085699\">10.1371/journal.pone.0085699</a>."},"_id":"2214","month":"01","title":"Blood vessels pattern heparan sulfate gradients between their apical and basolateral aspects"},{"acknowledgement":"J.R. was supported by a Boehringer Ingelheim Fonds PhD stipend.","author":[{"orcid":"0000-0003-2856-3369","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","last_name":"Renkawitz"},{"last_name":"Lademann","full_name":"Lademann, Claudio","first_name":"Claudio"},{"last_name":"Jentsch","full_name":"Jentsch, Stefan","first_name":"Stefan"}],"scopus_import":"1","publication":"Nature Reviews Molecular Cell Biology","intvolume":"        15","isi":1,"volume":15,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events."}],"publication_status":"published","department":[{"_id":"MiSi"}],"external_id":{"isi":["000337245500009"]},"date_created":"2018-12-11T11:56:22Z","language":[{"iso":"eng"}],"status":"public","type":"journal_article","day":"14","publisher":"Nature Publishing Group","issue":"6","date_published":"2014-05-14T00:00:00Z","oa_version":"None","year":"2014","date_updated":"2025-09-29T11:30:10Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"369 - 383","_id":"2215","title":"Mechanisms and principles of homology search during recombination","month":"05","article_processing_charge":"No","citation":{"ista":"Renkawitz J, Lademann C, Jentsch S. 2014. Mechanisms and principles of homology search during recombination. Nature Reviews Molecular Cell Biology. 15(6), 369–383.","chicago":"Renkawitz, Jörg, Claudio Lademann, and Stefan Jentsch. “Mechanisms and Principles of Homology Search during Recombination.” <i>Nature Reviews Molecular Cell Biology</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nrm3805\">https://doi.org/10.1038/nrm3805</a>.","apa":"Renkawitz, J., Lademann, C., &#38; Jentsch, S. (2014). Mechanisms and principles of homology search during recombination. <i>Nature Reviews Molecular Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrm3805\">https://doi.org/10.1038/nrm3805</a>","ama":"Renkawitz J, Lademann C, Jentsch S. Mechanisms and principles of homology search during recombination. <i>Nature Reviews Molecular Cell Biology</i>. 2014;15(6):369-383. doi:<a href=\"https://doi.org/10.1038/nrm3805\">10.1038/nrm3805</a>","ieee":"J. Renkawitz, C. Lademann, and S. Jentsch, “Mechanisms and principles of homology search during recombination,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 15, no. 6. Nature Publishing Group, pp. 369–383, 2014.","short":"J. Renkawitz, C. Lademann, S. Jentsch, Nature Reviews Molecular Cell Biology 15 (2014) 369–383.","mla":"Renkawitz, Jörg, et al. “Mechanisms and Principles of Homology Search during Recombination.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 15, no. 6, Nature Publishing Group, 2014, pp. 369–83, doi:<a href=\"https://doi.org/10.1038/nrm3805\">10.1038/nrm3805</a>."},"publist_id":"4755","doi":"10.1038/nrm3805"},{"related_material":{"record":[{"id":"5409","status":"public","relation":"earlier_version"}]},"citation":{"ista":"Chatterjee K, Ibsen-Jensen R, Majumdar R. 2014. Edit distance for timed automata. HSCC: Hybrid Systems - Computation and Control, 303–312.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Ritankar Majumdar. “Edit Distance for Timed Automata,” 303–12. Springer, 2014. <a href=\"https://doi.org/10.1145/2562059.2562141\">https://doi.org/10.1145/2562059.2562141</a>.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Majumdar, R. (2014). Edit distance for timed automata (pp. 303–312). Presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany: Springer. <a href=\"https://doi.org/10.1145/2562059.2562141\">https://doi.org/10.1145/2562059.2562141</a>","ama":"Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit distance for timed automata. In: Springer; 2014:303-312. doi:<a href=\"https://doi.org/10.1145/2562059.2562141\">10.1145/2562059.2562141</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, “Edit distance for timed automata,” presented at the HSCC: Hybrid Systems - Computation and Control, Berlin, Germany, 2014, pp. 303–312.","short":"K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, in:, Springer, 2014, pp. 303–312.","mla":"Chatterjee, Krishnendu, et al. <i>Edit Distance for Timed Automata</i>. Springer, 2014, pp. 303–12, doi:<a href=\"https://doi.org/10.1145/2562059.2562141\">10.1145/2562059.2562141</a>."},"conference":{"end_date":"2017-04-17","location":"Berlin, Germany","start_date":"2017-04-15","name":"HSCC: Hybrid Systems - Computation and Control"},"abstract":[{"text":"The edit distance between two (untimed) traces is the minimum cost of a sequence of edit operations (insertion, deletion, or substitution) needed to transform one trace to the other. Edit distances have been extensively studied in the untimed setting, and form the basis for approximate matching of sequences in different domains such as coding theory, parsing, and speech recognition. In this paper, we lift the study of edit distances from untimed languages to the timed setting. We define an edit distance between timed words which incorporates both the edit distance between the untimed words and the absolute difference in time stamps. Our edit distance between two timed words is computable in polynomial time. Further, we show that the edit distance between a timed word and a timed language generated by a timed automaton, defined as the edit distance between the word and the closest word in the language, is PSPACE-complete. While computing the edit distance between two timed automata is undecidable, we show that the approximate version, where we decide if the edit distance between two timed automata is either less than a given parameter or more than δ away from the parameter, for δ &gt; 0, can be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques can be generalized to the setting of hybrid systems, and analogous decidability results hold for rectangular automata.","lang":"eng"}],"month":"01","title":"Edit distance for timed automata","quality_controlled":"1","_id":"2216","language":[{"iso":"eng"}],"publist_id":"4752","doi":"10.1145/2562059.2562141","date_created":"2018-12-11T11:56:22Z","department":[{"_id":"KrCh"}],"publication_status":"published","publisher":"Springer","type":"conference","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/citation.cfm?doid=2562059.2562141"}],"day":"01","oa":1,"status":"public","page":"303 - 312","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-4783-0389","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Majumdar, Ritankar","last_name":"Majumdar","first_name":"Ritankar"}],"scopus_import":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-21T06:02:53Z","year":"2014","oa_version":"Submitted Version","date_published":"2014-01-01T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"213 - 222","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"date_published":"2014-04-01T00:00:00Z","date_updated":"2025-06-26T08:32:32Z","year":"2014","oa_version":"Preprint","day":"01","type":"conference","publisher":"Springer","status":"public","OA_type":"green","OA_place":"repository","doi":"10.1145/2562059.2562130","publist_id":"4751","conference":{"start_date":"2014-04-15","name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2014-04-17","location":"Berlin, Germany"},"article_processing_charge":"No","related_material":{"record":[{"id":"5416","relation":"earlier_version","status":"public"}]},"citation":{"chicago":"Henzinger, Thomas A, and Jan Otop. “Model Measuring for Hybrid Systems.” In <i>Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control</i>, 213–22. Springer, 2014. <a href=\"https://doi.org/10.1145/2562059.2562130\">https://doi.org/10.1145/2562059.2562130</a>.","ista":"Henzinger TA, Otop J. 2014. Model measuring for hybrid systems. Proceedings of the 17th international conference on Hybrid systems: computation and control. HSCC: Hybrid Systems - Computation and Control, 213–222.","ama":"Henzinger TA, Otop J. Model measuring for hybrid systems. In: <i>Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control</i>. Springer; 2014:213-222. doi:<a href=\"https://doi.org/10.1145/2562059.2562130\">10.1145/2562059.2562130</a>","apa":"Henzinger, T. A., &#38; Otop, J. (2014). Model measuring for hybrid systems. In <i>Proceedings of the 17th international conference on Hybrid systems: computation and control</i> (pp. 213–222). Berlin, Germany: Springer. <a href=\"https://doi.org/10.1145/2562059.2562130\">https://doi.org/10.1145/2562059.2562130</a>","ieee":"T. A. Henzinger and J. Otop, “Model measuring for hybrid systems,” in <i>Proceedings of the 17th international conference on Hybrid systems: computation and control</i>, Berlin, Germany, 2014, pp. 213–222.","mla":"Henzinger, Thomas A., and Jan Otop. “Model Measuring for Hybrid Systems.” <i>Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control</i>, Springer, 2014, pp. 213–22, doi:<a href=\"https://doi.org/10.1145/2562059.2562130\">10.1145/2562059.2562130</a>.","short":"T.A. Henzinger, J. Otop, in:, Proceedings of the 17th International Conference on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–222."},"_id":"2217","month":"04","title":"Model measuring for hybrid systems","publication":"Proceedings of the 17th international conference on Hybrid systems: computation and control","scopus_import":"1","author":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop"}],"ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.15479/AT:IST-2014-171-v1-1"}],"acknowledgement":"This  work  was  supported  in  part  by  the  Austrian  Science Fund  NFN  RiSE  (Rigorous  Systems  Engineering)  and  by the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).\r\nA Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/171","oa":1,"date_created":"2018-12-11T11:56:23Z","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.\r\n\r\nThe contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem."}],"quality_controlled":"1"},{"volume":8383,"quality_controlled":"1","abstract":[{"text":"Recently, Döttling et al. (ASIACRYPT 2012) proposed the first chosen-ciphertext (IND-CCA) secure public-key encryption scheme from the learning parity with noise (LPN) assumption. In this work we give an alternative scheme which is conceptually simpler and more efficient. At the core of our construction is a trapdoor technique originally proposed for lattices by Micciancio and Peikert (EUROCRYPT 2012), which we adapt to the LPN setting. The main technical tool is a new double-trapdoor mechanism, together with a trapdoor switching lemma based on a computational variant of the leftover hash lemma.","lang":"eng"}],"publication_status":"published","department":[{"_id":"KrPi"}],"date_created":"2018-12-11T11:56:24Z","language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"isbn":["978-364254630-3"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2015/401"}],"author":[{"first_name":"Eike","full_name":"Kiltz, Eike","last_name":"Kiltz"},{"full_name":"Masny, Daniel","last_name":"Masny","first_name":"Daniel"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"}],"scopus_import":1,"intvolume":"      8383","_id":"2219","title":"Simple chosen-ciphertext security from low noise LPN","month":"03","conference":{"name":"IACR: International Conference on Practice and Theory in Public-Key Cryptography"},"citation":{"short":"E. Kiltz, D. Masny, K.Z. Pietrzak, in:, Springer, 2014, pp. 1–18.","mla":"Kiltz, Eike, et al. <i>Simple Chosen-Ciphertext Security from Low Noise LPN</i>. Vol. 8383, Springer, 2014, pp. 1–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_1\">10.1007/978-3-642-54631-0_1</a>.","ieee":"E. Kiltz, D. Masny, and K. Z. Pietrzak, “Simple chosen-ciphertext security from low noise LPN,” presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, 2014, vol. 8383, pp. 1–18.","ama":"Kiltz E, Masny D, Pietrzak KZ. Simple chosen-ciphertext security from low noise LPN. In: Vol 8383. Springer; 2014:1-18. doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_1\">10.1007/978-3-642-54631-0_1</a>","apa":"Kiltz, E., Masny, D., &#38; Pietrzak, K. Z. (2014). Simple chosen-ciphertext security from low noise LPN (Vol. 8383, pp. 1–18). Presented at the IACR: International Conference on Practice and Theory in Public-Key Cryptography, Springer. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_1\">https://doi.org/10.1007/978-3-642-54631-0_1</a>","chicago":"Kiltz, Eike, Daniel Masny, and Krzysztof Z Pietrzak. “Simple Chosen-Ciphertext Security from Low Noise LPN,” 8383:1–18. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_1\">https://doi.org/10.1007/978-3-642-54631-0_1</a>.","ista":"Kiltz E, Masny D, Pietrzak KZ. 2014. Simple chosen-ciphertext security from low noise LPN. IACR: International Conference on Practice and Theory in Public-Key Cryptography, LNCS, vol. 8383, 1–18."},"publist_id":"4748","doi":"10.1007/978-3-642-54631-0_1","alternative_title":["LNCS"],"status":"public","type":"conference","day":"01","publisher":"Springer","date_published":"2014-03-01T00:00:00Z","oa_version":"Submitted Version","year":"2014","date_updated":"2021-01-12T06:56:05Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"1 - 18"},{"abstract":[{"lang":"eng","text":"In this issue of Chemistry & Biology, Cokol and colleagues report a systematic study of drug interactions between antifungal compounds. Suppressive drug interactions occur more frequently than previously realized and come in different flavors with interesting implications."}],"quality_controlled":"1","volume":21,"language":[{"iso":"eng"}],"corr_author":"1","department":[{"_id":"ToBo"}],"external_id":{"pmid":["24766845"],"isi":["000335431300005"]},"date_created":"2018-12-11T11:56:24Z","publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/24766845","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["1074-5521"]},"pmid":1,"intvolume":"        21","isi":1,"author":[{"last_name":"De Vos","full_name":"De Vos, Marjon","first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"}],"publication":"Chemistry and Biology","scopus_import":"1","citation":{"ieee":"M. de Vos and M. T. Bollenbach, “Suppressive drug interactions between antifungals,” <i>Chemistry and Biology</i>, vol. 21, no. 4. Cell Press, pp. 439–440, 2014.","mla":"de Vos, Marjon, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” <i>Chemistry and Biology</i>, vol. 21, no. 4, Cell Press, 2014, pp. 439–40, doi:<a href=\"https://doi.org/10.1016/j.chembiol.2014.04.004\">10.1016/j.chembiol.2014.04.004</a>.","short":"M. de Vos, M.T. Bollenbach, Chemistry and Biology 21 (2014) 439–440.","ista":"de Vos M, Bollenbach MT. 2014. Suppressive drug interactions between antifungals. Chemistry and Biology. 21(4), 439–440.","chicago":"Vos, Marjon de, and Mark Tobias Bollenbach. “Suppressive Drug Interactions between Antifungals.” <i>Chemistry and Biology</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.chembiol.2014.04.004\">https://doi.org/10.1016/j.chembiol.2014.04.004</a>.","apa":"de Vos, M., &#38; Bollenbach, M. T. (2014). Suppressive drug interactions between antifungals. <i>Chemistry and Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.chembiol.2014.04.004\">https://doi.org/10.1016/j.chembiol.2014.04.004</a>","ama":"de Vos M, Bollenbach MT. Suppressive drug interactions between antifungals. <i>Chemistry and Biology</i>. 2014;21(4):439-440. doi:<a href=\"https://doi.org/10.1016/j.chembiol.2014.04.004\">10.1016/j.chembiol.2014.04.004</a>"},"article_processing_charge":"No","title":"Suppressive drug interactions between antifungals","month":"04","_id":"2220","doi":"10.1016/j.chembiol.2014.04.004","publist_id":"4747","day":"24","publisher":"Cell Press","type":"journal_article","issue":"4","status":"public","page":"439 - 440","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","oa_version":"Published Version","date_updated":"2025-09-29T11:28:57Z","date_published":"2014-04-24T00:00:00Z"},{"issue":"4","type":"journal_article","publisher":"Oxford University Press","day":"01","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"750 - 763","date_published":"2014-04-01T00:00:00Z","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-09-29T11:28:27Z","year":"2014","oa_version":"None","article_processing_charge":"No","citation":{"apa":"Naramoto, S., Nodzyński, T., Dainobu, T., Takatsuka, H., Okada, T., Friml, J., &#38; Fukuda, H. (2014). VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcu012\">https://doi.org/10.1093/pcp/pcu012</a>","ama":"Naramoto S, Nodzyński T, Dainobu T, et al. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. <i>Plant and Cell Physiology</i>. 2014;55(4):750-763. doi:<a href=\"https://doi.org/10.1093/pcp/pcu012\">10.1093/pcp/pcu012</a>","ista":"Naramoto S, Nodzyński T, Dainobu T, Takatsuka H, Okada T, Friml J, Fukuda H. 2014. VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis. Plant and Cell Physiology. 55(4), 750–763.","chicago":"Naramoto, Satoshi, Tomasz Nodzyński, Tomoko Dainobu, Hirotomo Takatsuka, Teruyo Okada, Jiří Friml, and Hiroo Fukuda. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/pcp/pcu012\">https://doi.org/10.1093/pcp/pcu012</a>.","mla":"Naramoto, Satoshi, et al. “VAN4 Encodes a Putative TRS120 That Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” <i>Plant and Cell Physiology</i>, vol. 55, no. 4, Oxford University Press, 2014, pp. 750–63, doi:<a href=\"https://doi.org/10.1093/pcp/pcu012\">10.1093/pcp/pcu012</a>.","short":"S. Naramoto, T. Nodzyński, T. Dainobu, H. Takatsuka, T. Okada, J. Friml, H. Fukuda, Plant and Cell Physiology 55 (2014) 750–763.","ieee":"S. Naramoto <i>et al.</i>, “VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis,” <i>Plant and Cell Physiology</i>, vol. 55, no. 4. Oxford University Press, pp. 750–763, 2014."},"_id":"2222","month":"04","title":"VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis","publist_id":"4742","doi":"10.1093/pcp/pcu012","publication_identifier":{"issn":["0032-0781"]},"scopus_import":"1","author":[{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"last_name":"Dainobu","full_name":"Dainobu, Tomoko","first_name":"Tomoko"},{"last_name":"Takatsuka","full_name":"Takatsuka, Hirotomo","first_name":"Hirotomo"},{"first_name":"Teruyo","last_name":"Okada","full_name":"Okada, Teruyo"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Hiroo","full_name":"Fukuda, Hiroo","last_name":"Fukuda"}],"publication":"Plant and Cell Physiology","isi":1,"intvolume":"        55","ec_funded":1,"abstract":[{"lang":"eng","text":"Leaf venation develops complex patterns in angiosperms, but the mechanism underlying this process is largely unknown. To elucidate the molecular mechanisms governing vein pattern formation, we previously isolated vascular network defective (van) mutants that displayed venation discontinuities. Here, we report the phenotypic analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation and subsequent vascular cell differentiation. Reduced shoot and root cell growth is observed in van4 mutants, suggesting that VAN4 function is important for cell growth and the establishment of venation continuity. Consistent with these phenotypes, the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for Rab GTPase involved in regulating vesicle transport, and a known tethering factor that determines the specificity of membrane fusion. VAN4 protein localizes at the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin efflux carrier PIN proteins is observed in van4 mutants. These results suggest that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular development and cell growth in shoot and root. Our identification of VAN4 as a putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases) for continuous vascular development, and provides further evidence for the importance of vesicle transport in leaf vascular formation."}],"volume":55,"quality_controlled":"1","date_created":"2018-12-11T11:56:24Z","department":[{"_id":"JiFr"}],"external_id":{"isi":["000334679500009"]},"language":[{"iso":"eng"}],"publication_status":"published"},{"scopus_import":"1","author":[{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"full_name":"Kitakura, Saeko","last_name":"Kitakura","first_name":"Saeko"},{"last_name":"Feraru","full_name":"Feraru, Mugurel","first_name":"Mugurel"},{"last_name":"Sasabe","full_name":"Sasabe, Michiko","first_name":"Michiko"},{"first_name":"Tomomi","last_name":"Ishikawa","full_name":"Ishikawa, Tomomi"},{"full_name":"Kleine Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"full_name":"Kakimoto, Tatsuo","last_name":"Kakimoto","first_name":"Tatsuo"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí"}],"file_date_updated":"2020-07-14T12:45:34Z","publication":"Plant and Cell Physiology","ec_funded":1,"isi":1,"intvolume":"        55","file":[{"checksum":"b781a76b32ac35a520256453c3ba9433","content_type":"application/pdf","date_updated":"2020-07-14T12:45:34Z","date_created":"2018-12-12T10:14:25Z","file_id":"5076","creator":"system","file_name":"IST-2016-431-v1+1_Plant_Cell_Physiol-2014-Tanaka-737-49.pdf","file_size":2028111,"relation":"main_file","access_level":"open_access"}],"pmid":1,"publication_identifier":{"issn":["0032-0781"]},"oa":1,"department":[{"_id":"JiFr"}],"external_id":{"isi":["000334679500008"],"pmid":["24369434"]},"date_created":"2018-12-11T11:56:25Z","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Correct positioning of membrane proteins is an essential process in eukaryotic organisms. The plant hormone auxin is distributed through intercellular transport and triggers various cellular responses. Auxin transporters of the PIN-FORMED (PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA), inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes 19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization have been genetically poorly defined. Using a fluorescence imaging-based forward genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent protein (GFP) as well as development is hypersensitive to BFA. We found that in bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent with the developmental importance of PIN proteins, functional interference with ARF1 resulted in an impaired auxin response gradient and various developmental defects including embryonic patterning defects and growth arrest. Our results show that ARF1A1C is essential for recycling of PIN auxin transporters and for various auxin-dependent developmental processes."}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":55,"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"737 - 749","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"},{"name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur","_id":"256BDAB0-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","date_published":"2014-04-01T00:00:00Z","oa_version":"Published Version","year":"2014","date_updated":"2025-09-29T11:27:52Z","type":"journal_article","day":"01","publisher":"Oxford University Press","issue":"4","status":"public","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"publist_id":"4741","doi":"10.1093/pcp/pct196","ddc":["570"],"pubrep_id":"431","article_processing_charge":"No","citation":{"chicago":"Tanaka, Hirokazu, Tomasz Nodzyński, Saeko Kitakura, Mugurel Feraru, Michiko Sasabe, Tomomi Ishikawa, Jürgen Kleine Vehn, Tatsuo Kakimoto, and Jiří Friml. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/pcp/pct196\">https://doi.org/10.1093/pcp/pct196</a>.","ista":"Tanaka H, Nodzyński T, Kitakura S, Feraru M, Sasabe M, Ishikawa T, Kleine Vehn J, Kakimoto T, Friml J. 2014. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. Plant and Cell Physiology. 55(4), 737–749.","ama":"Tanaka H, Nodzyński T, Kitakura S, et al. BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. <i>Plant and Cell Physiology</i>. 2014;55(4):737-749. doi:<a href=\"https://doi.org/10.1093/pcp/pct196\">10.1093/pcp/pct196</a>","apa":"Tanaka, H., Nodzyński, T., Kitakura, S., Feraru, M., Sasabe, M., Ishikawa, T., … Friml, J. (2014). BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pct196\">https://doi.org/10.1093/pcp/pct196</a>","ieee":"H. Tanaka <i>et al.</i>, “BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis,” <i>Plant and Cell Physiology</i>, vol. 55, no. 4. Oxford University Press, pp. 737–749, 2014.","mla":"Tanaka, Hirokazu, et al. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” <i>Plant and Cell Physiology</i>, vol. 55, no. 4, Oxford University Press, 2014, pp. 737–49, doi:<a href=\"https://doi.org/10.1093/pcp/pct196\">10.1093/pcp/pct196</a>.","short":"H. Tanaka, T. Nodzyński, S. Kitakura, M. Feraru, M. Sasabe, T. Ishikawa, J. Kleine Vehn, T. Kakimoto, J. Friml, Plant and Cell Physiology 55 (2014) 737–749."},"_id":"2223","title":"BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis","month":"04"},{"author":[{"full_name":"Bloemendal, Alex","last_name":"Bloemendal","first_name":"Alex"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"scopus_import":"1","publication":"Electronic Journal of Probability","file_date_updated":"2020-07-14T12:45:34Z","intvolume":"        19","isi":1,"ec_funded":1,"file":[{"content_type":"application/pdf","checksum":"7eb297ff367a2ee73b21b6dd1e1948e4","date_updated":"2020-07-14T12:45:34Z","file_id":"5055","date_created":"2018-12-12T10:14:06Z","file_name":"IST-2016-427-v1+1_3054-16624-4-PB.pdf","creator":"system","file_size":810150,"relation":"main_file","access_level":"open_access"}],"publication_identifier":{"issn":["1083-6489"]},"oa":1,"publication_status":"published","date_created":"2018-12-11T11:56:25Z","external_id":{"isi":["000340998500001"]},"department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"volume":19,"quality_controlled":"1","article_number":"33","abstract":[{"text":"We consider sample covariance matrices of the form X∗X, where X is an M×N matrix with independent random entries.  We prove the isotropic local Marchenko-Pastur law, i.e. we prove that the resolvent (X∗X−z)−1 converges to a multiple of the identity in the sense of quadratic forms. More precisely, we establish sharp high-probability bounds on the quantity ⟨v,(X∗X−z)−1w⟩−⟨v,w⟩m(z), where m is the Stieltjes transform of the Marchenko-Pastur law and v,w∈CN. We require the logarithms of the dimensions M and N to be comparable. Our result holds down to scales Iz≥N−1+ε and throughout the entire spectrum away from 0. We also prove analogous results for generalized Wigner matrices.\r\n","lang":"eng"}],"date_published":"2014-03-15T00:00:00Z","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","date_updated":"2025-09-29T11:26:42Z","year":"2014","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"15","publisher":"Institute of Mathematical Statistics","type":"journal_article","ddc":["510"],"pubrep_id":"427","publist_id":"4739","doi":"10.1214/EJP.v19-3054","_id":"2225","month":"03","title":"Isotropic local laws for sample covariance and generalized Wigner matrices","article_processing_charge":"No","citation":{"mla":"Bloemendal, Alex, et al. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” <i>Electronic Journal of Probability</i>, vol. 19, 33, Institute of Mathematical Statistics, 2014, doi:<a href=\"https://doi.org/10.1214/EJP.v19-3054\">10.1214/EJP.v19-3054</a>.","short":"A. Bloemendal, L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 19 (2014).","ieee":"A. Bloemendal, L. Erdös, A. Knowles, H. Yau, and J. Yin, “Isotropic local laws for sample covariance and generalized Wigner matrices,” <i>Electronic Journal of Probability</i>, vol. 19. Institute of Mathematical Statistics, 2014.","ama":"Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. Isotropic local laws for sample covariance and generalized Wigner matrices. <i>Electronic Journal of Probability</i>. 2014;19. doi:<a href=\"https://doi.org/10.1214/EJP.v19-3054\">10.1214/EJP.v19-3054</a>","apa":"Bloemendal, A., Erdös, L., Knowles, A., Yau, H., &#38; Yin, J. (2014). Isotropic local laws for sample covariance and generalized Wigner matrices. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/EJP.v19-3054\">https://doi.org/10.1214/EJP.v19-3054</a>","chicago":"Bloemendal, Alex, László Erdös, Antti Knowles, Horng Yau, and Jun Yin. “Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2014. <a href=\"https://doi.org/10.1214/EJP.v19-3054\">https://doi.org/10.1214/EJP.v19-3054</a>.","ista":"Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. 2014. Isotropic local laws for sample covariance and generalized Wigner matrices. Electronic Journal of Probability. 19, 33."}},{"department":[{"_id":"BjHo"}],"external_id":{"isi":["000332155800013"],"arxiv":["1312.5095"]},"date_created":"2018-12-11T11:56:26Z","language":[{"iso":"eng"}],"corr_author":"1","publication_status":"published","abstract":[{"text":"Coriolis force effects on shear flows are important in geophysical and astrophysical contexts. We report a study on the linear stability and the transient energy growth of the plane Couette flow with system rotation perpendicular to the shear direction. External rotation causes linear instability. At small rotation rates, the onset of linear instability scales inversely with the rotation rate and the optimal transient growth in the linearly stable region is slightly enhanced ∼Re2. The corresponding optimal initial perturbations are characterized by roll structures inclined in the streamwise direction and are twisted under external rotation. At large rotation rates, the transient growth is significantly inhibited and hence linear stability analysis is a reliable indicator for instability.","lang":"eng"}],"article_number":"013001","volume":89,"quality_controlled":"1","author":[{"first_name":"Liang","last_name":"Shi","full_name":"Shi, Liang"},{"full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754"},{"first_name":"Andreas","last_name":"Tilgner","full_name":"Tilgner, Andreas"}],"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","scopus_import":"1","intvolume":"        89","isi":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1312.5095"}],"publication_identifier":{"issn":["1539-3755"]},"oa":1,"doi":"10.1103/PhysRevE.89.013001","publist_id":"4737","arxiv":1,"article_processing_charge":"No","citation":{"short":"L. Shi, B. Hof, A. Tilgner, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","mla":"Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 1, 013001, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">10.1103/PhysRevE.89.013001</a>.","ieee":"L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 1. American Institute of Physics, 2014.","ama":"Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2014;89(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">10.1103/PhysRevE.89.013001</a>","apa":"Shi, L., Hof, B., &#38; Tilgner, A. (2014). Transient growth of Ekman-Couette flow. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">https://doi.org/10.1103/PhysRevE.89.013001</a>","chicago":"Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette Flow.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1103/PhysRevE.89.013001\">https://doi.org/10.1103/PhysRevE.89.013001</a>.","ista":"Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(1), 013001."},"_id":"2226","title":"Transient growth of Ekman-Couette flow","month":"01","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2014-01-06T00:00:00Z","project":[{"name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425"}],"year":"2014","oa_version":"Submitted Version","date_updated":"2025-09-29T11:26:12Z","type":"journal_article","day":"06","publisher":"American Institute of Physics","issue":"1","status":"public"},{"doi":"10.1007/s13127-013-0150-6","publist_id":"4734","month":"03","title":"Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences","_id":"2227","citation":{"ista":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. 2014. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 14(1), 1–10.","chicago":"Cires Rodriguez, Eduardo, Matthias Baltisberger, Candela Cuesta, Pablo Vargas, and José Prieto. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” <i>Organisms Diversity and Evolution</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s13127-013-0150-6\">https://doi.org/10.1007/s13127-013-0150-6</a>.","apa":"Cires Rodriguez, E., Baltisberger, M., Cuesta, C., Vargas, P., &#38; Prieto, J. (2014). Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. <i>Organisms Diversity and Evolution</i>. Springer. <a href=\"https://doi.org/10.1007/s13127-013-0150-6\">https://doi.org/10.1007/s13127-013-0150-6</a>","ama":"Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences. <i>Organisms Diversity and Evolution</i>. 2014;14(1):1-10. doi:<a href=\"https://doi.org/10.1007/s13127-013-0150-6\">10.1007/s13127-013-0150-6</a>","ieee":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, and J. Prieto, “Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences,” <i>Organisms Diversity and Evolution</i>, vol. 14, no. 1. Springer, pp. 1–10, 2014.","mla":"Cires Rodriguez, Eduardo, et al. “Allopolyploid Origin of the Balkan Endemic Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.” <i>Organisms Diversity and Evolution</i>, vol. 14, no. 1, Springer, 2014, pp. 1–10, doi:<a href=\"https://doi.org/10.1007/s13127-013-0150-6\">10.1007/s13127-013-0150-6</a>.","short":"E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, J. Prieto, Organisms Diversity and Evolution 14 (2014) 1–10."},"article_processing_charge":"No","date_updated":"2025-09-29T11:25:37Z","oa_version":"None","year":"2014","date_published":"2014-03-01T00:00:00Z","page":"1 - 10","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","issue":"1","day":"01","type":"journal_article","publisher":"Springer","publication_status":"published","corr_author":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:56:26Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"external_id":{"isi":["000332585400001"]},"quality_controlled":"1","volume":14,"abstract":[{"lang":"eng","text":"The Balkan Peninsula, characterized by high rates of endemism, is recognised as one of the most diverse and species-rich areas of Europe. However, little is known about the origin of Balkan endemics. The present study addresses the phylogenetic position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic status and relationship with the widespread R. parnassiifolius, based on nuclear DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with the latter as the maternal parent."}],"intvolume":"        14","isi":1,"scopus_import":"1","publication":"Organisms Diversity and Evolution","author":[{"last_name":"Cires Rodriguez","full_name":"Cires Rodriguez, Eduardo","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Eduardo"},{"first_name":"Matthias","last_name":"Baltisberger","full_name":"Baltisberger, Matthias"},{"orcid":"0000-0003-1923-2410","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","last_name":"Cuesta","full_name":"Cuesta, Candela"},{"first_name":"Pablo","last_name":"Vargas","full_name":"Vargas, Pablo"},{"full_name":"Prieto, José","last_name":"Prieto","first_name":"José"}],"publication_identifier":{"issn":["1439-6092"]}},{"project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7"},{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF"}],"date_published":"2014-03-23T00:00:00Z","date_updated":"2025-09-29T11:25:07Z","year":"2014","oa_version":"Submitted Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"686-693","status":"public","issue":"5","day":"23","publisher":"Nature Publishing Group","type":"journal_article","doi":"10.1038/nn.3678","publist_id":"4733","_id":"2228","month":"03","title":"A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons","article_processing_charge":"No","citation":{"mla":"Hu, Hua, and Peter M. Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” <i>Nature Neuroscience</i>, vol. 17, no. 5, Nature Publishing Group, 2014, pp. 686–93, doi:<a href=\"https://doi.org/10.1038/nn.3678\">10.1038/nn.3678</a>.","short":"H. Hu, P.M. Jonas, Nature Neuroscience 17 (2014) 686–693.","ieee":"H. Hu and P. M. Jonas, “A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons,” <i>Nature Neuroscience</i>, vol. 17, no. 5. Nature Publishing Group, pp. 686–693, 2014.","ama":"Hu H, Jonas PM. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. <i>Nature Neuroscience</i>. 2014;17(5):686-693. doi:<a href=\"https://doi.org/10.1038/nn.3678\">10.1038/nn.3678</a>","apa":"Hu, H., &#38; Jonas, P. M. (2014). A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3678\">https://doi.org/10.1038/nn.3678</a>","chicago":"Hu, Hua, and Peter M Jonas. “A Supercritical Density of Na^+ Channels Ensures Fast Signaling in GABAergic Interneuron Axons.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nn.3678\">https://doi.org/10.1038/nn.3678</a>.","ista":"Hu H, Jonas PM. 2014. A supercritical density of Na^+ channels ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience. 17(5), 686–693."},"publication":"Nature Neuroscience","scopus_import":"1","author":[{"full_name":"Hu, Hua","last_name":"Hu","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804"}],"intvolume":"        17","isi":1,"ec_funded":1,"publication_identifier":{"issn":["1097-6256"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286295/"}],"publication_status":"published","date_created":"2018-12-11T11:56:26Z","external_id":{"isi":["000335016200012"]},"department":[{"_id":"PeJo"}],"corr_author":"1","language":[{"iso":"eng"}],"volume":17,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion of which are basket cells (BCs), have a key role in feedforward and feedback inhibition, gamma oscillations and complex information processing. For these functions, fast propagation of action potentials (APs) from the soma to the presynaptic terminals is important. However, the functional properties of interneuron axons remain elusive. We examined interneuron axons by confocally targeted subcellular patch-clamp recording in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from the soma and propagated to the distal axon with high reliability and speed. Subcellular mapping revealed a stepwise increase of Na^+ conductance density from the soma to the proximal axon, followed by a further gradual increase in the distal axon. Active cable modeling and experiments with partial channel block revealed that low axonal Na^+ conductance density was sufficient for reliability, but high Na^+ density was necessary for both speed of propagation and fast-spiking AP phenotype. Our results suggest that a supercritical density of Na^+ channels compensates for the morphological properties of interneuron axons (small segmental diameter, extensive branching and high bouton density), ensuring fast AP propagation and high-frequency repetitive firing."}]},{"abstract":[{"lang":"eng","text":"The distance between Ca^2+ channels and release sensors determines the speed and efficacy of synaptic transmission. Tight &quot;nanodomain&quot; channel-sensor coupling initiates transmitter release at synapses in the mature brain, whereas loose &quot;microdomain&quot; coupling appears restricted to early developmental stages. To probe the coupling configuration at a plastic synapse in the mature central nervous system, we performed paired recordings between mossy fiber terminals and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled the control of initial release probability by fast endogenous Ca^2+ buffers and the generation of facilitation by buffer saturation. Thus, loose coupling provides the molecular framework for presynaptic plasticity."}],"quality_controlled":"1","volume":343,"language":[{"iso":"eng"}],"corr_author":"1","external_id":{"isi":["000330724000044"]},"department":[{"_id":"PeJo"}],"date_created":"2018-12-11T11:56:27Z","publication_status":"published","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/","open_access":"1"}],"publication_identifier":{"issn":["0036-8075"]},"oa":1,"ec_funded":1,"isi":1,"intvolume":"       343","author":[{"last_name":"Vyleta","full_name":"Vyleta, Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publication":"Science","scopus_import":"1","citation":{"ieee":"N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse,” <i>Science</i>, vol. 343, no. 6171. American Association for the Advancement of Science, pp. 665–670, 2014.","short":"N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670.","mla":"Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>, vol. 343, no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70, doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>.","chicago":"Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels and Release Sensors at a Plastic Hippocampal Synapse.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>.","ista":"Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670.","ama":"Vyleta N, Jonas PM. Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. 2014;343(6171):665-670. doi:<a href=\"https://doi.org/10.1126/science.1244811\">10.1126/science.1244811</a>","apa":"Vyleta, N., &#38; Jonas, P. M. (2014). Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1244811\">https://doi.org/10.1126/science.1244811</a>"},"article_processing_charge":"No","title":"Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal synapse","month":"02","_id":"2229","doi":"10.1126/science.1244811","publist_id":"4732","day":"01","publisher":"American Association for the Advancement of Science","type":"journal_article","issue":"6171","status":"public","page":"665 - 670","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","oa_version":"Submitted Version","date_updated":"2025-09-29T11:24:38Z","project":[{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7"}],"date_published":"2014-02-01T00:00:00Z"},{"abstract":[{"text":"Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals.","lang":"eng"}],"article_number":"16","volume":8,"quality_controlled":"1","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"external_id":{"isi":["000348105900001"]},"date_created":"2018-12-11T11:56:27Z","language":[{"iso":"eng"}],"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","file_name":"IST-2016-425-v1+1_fninf-08-00016.pdf","creator":"system","date_created":"2018-12-12T10:12:17Z","file_id":"4935","file_size":2883372,"content_type":"application/pdf","checksum":"eeca00bba7232ff7d27db83321f6ea30","date_updated":"2020-07-14T12:45:34Z"}],"oa":1,"publication_identifier":{"issn":["1662-5196"]},"author":[{"orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","last_name":"Guzmán","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"last_name":"Schmidt Hieber","full_name":"Schmidt Hieber, Christoph","first_name":"Christoph"}],"file_date_updated":"2020-07-14T12:45:34Z","scopus_import":"1","publication":"Frontiers in Neuroinformatics","isi":1,"intvolume":"         8","article_processing_charge":"No","citation":{"ieee":"J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological data with Python,” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB. Frontiers Research Foundation, 2014.","short":"J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8 (2014).","mla":"Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>, vol. 8, no. FEB, 16, Frontiers Research Foundation, 2014, doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>.","ista":"Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.","chicago":"Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying Electrophysiological Data with Python.” <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation, 2014. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>.","apa":"Guzmán, J., Schlögl, A., &#38; Schmidt Hieber, C. (2014). Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fninf.2014.00016\">https://doi.org/10.3389/fninf.2014.00016</a>","ama":"Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological data with Python. <i>Frontiers in Neuroinformatics</i>. 2014;8(FEB). doi:<a href=\"https://doi.org/10.3389/fninf.2014.00016\">10.3389/fninf.2014.00016</a>"},"_id":"2230","title":"Stimfit: Quantifying electrophysiological data with Python","month":"02","publist_id":"4731","doi":"10.3389/fninf.2014.00016","ddc":["570"],"pubrep_id":"425","day":"21","publisher":"Frontiers Research Foundation","type":"journal_article","issue":"FEB","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","date_published":"2014-02-21T00:00:00Z","year":"2014","oa_version":"Published Version","date_updated":"2025-09-29T11:24:02Z"},{"publist_id":"4730","doi":"10.1016/j.bpj.2014.01.014","_id":"2231","month":"03","title":"Noise and information transmission in promoters with multiple internal states","article_processing_charge":"No","citation":{"short":"G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.","mla":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>.","ieee":"G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” <i>Biophysical Journal</i>, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.","apa":"Rieckh, G., &#38; Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>","ama":"Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. 2014;106(5):1194-1204. doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>","ista":"Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204.","chicago":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>. Biophysical Society, 2014. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>."},"date_published":"2014-03-04T00:00:00Z","date_updated":"2025-09-29T11:23:30Z","oa_version":"Submitted Version","year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"1194 - 1204","status":"public","issue":"5","publisher":"Biophysical Society","type":"journal_article","day":"04","publication_status":"published","date_created":"2018-12-11T11:56:28Z","external_id":{"isi":["000332501300022"],"pmid":["24606943"]},"department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"corr_author":"1","volume":106,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail."}],"author":[{"id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Rieckh","full_name":"Rieckh, Georg"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"publication":"Biophysical Journal","scopus_import":"1","intvolume":"       106","isi":1,"pmid":1,"publication_identifier":{"issn":["0006-3495"]},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/","open_access":"1"}]}]