[{"publication_status":"published","type":"dissertation","publist_id":"5805","_id":"1402","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.","lang":"eng"}],"citation":{"chicago":"Marhavá, Petra. “Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2014.","ista":"Marhavá P. 2014. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Marhavá P. Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana. 2014.","apa":"Marhavá, P. (2014). <i>Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana</i>. Institute of Science and Technology Austria.","ieee":"P. Marhavá, “Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2014.","short":"P. Marhavá, Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2014.","mla":"Marhavá, Petra. <i>Molecular Mechanisms of Patterning and Subcellular Trafficking in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2014."},"day":"01","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"year":"2014","oa_version":"None","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:51:49Z","OA_place":"publisher","title":"Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana","date_published":"2014-12-01T00:00:00Z","degree_awarded":"PhD","department":[{"_id":"JiFr"}],"month":"12","author":[{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","full_name":"Marhavá, Petra","last_name":"Marhavá"}],"date_updated":"2026-04-09T14:27:28Z","status":"public","page":"90","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","corr_author":"1"},{"_id":"1404","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Cremer, Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","orcid":"0000-0002-2193-3868"}],"abstract":[{"lang":"eng","text":"The co-evolution of hosts and pathogens is characterized by continuous adaptations of both parties. Pathogens of social insects need to adapt towards disease defences at two levels: 1) individual immunity of each colony member consisting of behavioural defence strategies as well as humoral and cellular immune responses and 2) social immunity that is collectively performed by all group members comprising behavioural, physiological and organisational defence strategies.\r\n\r\nTo disentangle the selection pressure on pathogens by the collective versus individual level of disease defence in social insects, we performed an evolution experiment using the Argentine Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution over 10 serial host passages to two different evolution host treatments: (1) only individual host immunity in a single host treatment, and (2) simultaneously acting individual and social immunity in a social host treatment, in which an exposed ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen evolution experiment, the 6 Metarhizium spp. strains were characterised concerning conidiospore size killing rates in singly and socially reared ants, their competitiveness under coinfecting conditions and their influence on ant behaviour. We analysed how the ancestral atrain mixture changed in conidiospere size, killing rate and strain composition dependent on host treatment (single or social hosts) during 10 passages and found that killing rate and conidiospere size of the pathogen increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting the evolved strain mixtures that evolved under either the single or social host treatment under both single and social current rearing conditions in a full factorial design experiment revealed that the additional collective defences in insect societies add new selection pressure for their coevolving pathogens that compromise their ability to adapt to its host at the group level. To our knowledge, this is the first study directly measuring the influence of social immunity on pathogen evolution."}],"type":"dissertation","publist_id":"5803","publication_status":"published","citation":{"apa":"Stock, M. (2014). <i>Evolution of a fungal pathogen towards individual versus social immunity in ants</i>. IST Austria.","short":"M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants, IST Austria, 2014.","ieee":"M. Stock, “Evolution of a fungal pathogen towards individual versus social immunity in ants,” IST Austria, 2014.","mla":"Stock, Miriam. <i>Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants</i>. IST Austria, 2014.","chicago":"Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants.” IST Austria, 2014.","ista":"Stock M. 2014. Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria.","ama":"Stock M. Evolution of a fungal pathogen towards individual versus social immunity in ants. 2014."},"day":"01","year":"2014","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2014-04-01T00:00:00Z","title":"Evolution of a fungal pathogen towards individual versus social immunity in ants","alternative_title":["IST Austria Thesis"],"date_created":"2018-12-11T11:51:49Z","OA_place":"publisher","oa_version":"None","acknowledgement":"This work was funded by the DFG and the ERC.","date_updated":"2026-04-09T14:33:27Z","author":[{"first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","full_name":"Stock, Miriam","last_name":"Stock"}],"department":[{"_id":"SyCr"}],"month":"04","corr_author":"1","article_processing_charge":"No","publisher":"IST Austria","status":"public","page":"101"},{"doi":"10.1109/ICST.2014.50","oa":1,"author":[{"full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Willibald","full_name":"Krenn, Willibald","last_name":"Krenn"},{"first_name":"Dejan","full_name":"Nickovic, Dejan","last_name":"Nickovic"}],"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"month":"03","department":[{"_id":"ToHe"}],"article_processing_charge":"No","publisher":"IEEE","related_material":{"record":[{"status":"public","id":"5411","relation":"earlier_version"},{"id":"1155","status":"public","relation":"dissertation_contains"}]},"publist_id":"4817","conference":{"location":"Cleveland, USA","end_date":"2014-04-04","start_date":"2014-03-31","name":"ICST: International Conference on Software Testing, Verification and Validation"},"publication_status":"published","arxiv":1,"publication_identifier":{"isbn":["978-1-4799-2255-0"],"issn":["2159-4848"]},"date_created":"2018-12-11T11:56:06Z","title":"Compositional specifications for IOCO testing","oa_version":"Preprint","date_updated":"2026-04-15T10:02:12Z","publication":"IEEE 7th International Conference on Software Testing, Verification and Validation","isi":1,"status":"public","ec_funded":1,"scopus_import":"1","_id":"2167","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing. In this paper, we study compositional properties of the ioco-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the ioco conformance relation, the resulting methodology can be applied to a broader class of systems."}],"external_id":{"arxiv":["1904.07083"],"isi":["000355985000040"]},"type":"conference","quality_controlled":"1","citation":{"chicago":"Daca, Przemyslaw, Thomas A Henzinger, Willibald Krenn, and Dejan Nickovic. “Compositional Specifications for IOCO Testing.” In <i>IEEE 7th International Conference on Software Testing, Verification and Validation</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/ICST.2014.50\">https://doi.org/10.1109/ICST.2014.50</a>.","ista":"Daca P, Henzinger TA, Krenn W, Nickovic D. 2014. Compositional specifications for IOCO testing. IEEE 7th International Conference on Software Testing, Verification and Validation. ICST: International Conference on Software Testing, Verification and Validation, 6823899.","ama":"Daca P, Henzinger TA, Krenn W, Nickovic D. Compositional specifications for IOCO testing. In: <i>IEEE 7th International Conference on Software Testing, Verification and Validation</i>. IEEE; 2014. doi:<a href=\"https://doi.org/10.1109/ICST.2014.50\">10.1109/ICST.2014.50</a>","apa":"Daca, P., Henzinger, T. A., Krenn, W., &#38; Nickovic, D. (2014). Compositional specifications for IOCO testing. In <i>IEEE 7th International Conference on Software Testing, Verification and Validation</i>. Cleveland, USA: IEEE. <a href=\"https://doi.org/10.1109/ICST.2014.50\">https://doi.org/10.1109/ICST.2014.50</a>","short":"P. Daca, T.A. Henzinger, W. Krenn, D. Nickovic, in:, IEEE 7th International Conference on Software Testing, Verification and Validation, IEEE, 2014.","ieee":"P. Daca, T. A. Henzinger, W. Krenn, and D. Nickovic, “Compositional specifications for IOCO testing,” in <i>IEEE 7th International Conference on Software Testing, Verification and Validation</i>, Cleveland, USA, 2014.","mla":"Daca, Przemyslaw, et al. “Compositional Specifications for IOCO Testing.” <i>IEEE 7th International Conference on Software Testing, Verification and Validation</i>, 6823899, IEEE, 2014, doi:<a href=\"https://doi.org/10.1109/ICST.2014.50\">10.1109/ICST.2014.50</a>."},"day":"01","article_number":"6823899","year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2014-03-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.07083"}]},{"doi":"10.1007/978-3-319-08867-9_31","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"month":"07","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"last_name":"Daca","full_name":"Daca, Przemyslaw","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"}],"volume":8559,"publisher":"Springer","corr_author":"1","related_material":{"record":[{"status":"public","id":"5412","relation":"earlier_version"},{"relation":"earlier_version","id":"5413","status":"public"},{"relation":"earlier_version","status":"public","id":"5414"},{"id":"1155","status":"public","relation":"dissertation_contains"}]},"publist_id":"4978","publication_status":"published","conference":{"location":"Vienna, Austria","end_date":"2014-07-22","start_date":"2014-07-18","name":"CAV: Computer Aided Verification"},"oa_version":"None","date_created":"2018-12-11T11:55:30Z","alternative_title":["LNCS"],"title":"CEGAR for qualitative analysis of probabilistic systems","date_updated":"2026-04-15T10:02:12Z","status":"public","page":"473 - 490","scopus_import":"1","ec_funded":1,"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"_id":"2063","abstract":[{"text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems.We focus on qualitative properties forMDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation ofMDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.We present an automated technique for assume-guarantee style reasoning for compositional analysis ofMDPs with qualitative properties by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements.","lang":"eng"}],"day":"01","citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">https://doi.org/10.1007/978-3-319-08867-9_31</a>.","ista":"Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic systems. In: Vol 8559. Springer; 2014:473-490. doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">10.1007/978-3-319-08867-9_31</a>","apa":"Chatterjee, K., Chmelik, M., &#38; Daca, P. (2014). CEGAR for qualitative analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">https://doi.org/10.1007/978-3-319-08867-9_31</a>","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 473–490.","short":"K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490.","mla":"Chatterjee, Krishnendu, et al. <i>CEGAR for Qualitative Analysis of Probabilistic Systems</i>. Vol. 8559, Springer, 2014, pp. 473–90, doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">10.1007/978-3-319-08867-9_31</a>."},"year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      8559","date_published":"2014-07-01T00:00:00Z"},{"date_published":"2014-01-30T00:00:00Z","OA_place":"repository","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1311.3238"}],"intvolume":"      8318","year":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"K. Chatterjee, L. Doyen, E. Filiot, J.-F. Raskin, in:, VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 78–97.","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J.-F. Raskin, “Doomsday equilibria for omega-regular games,” in <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>, San Diego, CA, United States, 2014, vol. 8318, pp. 78–97.","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>, vol. 8318, Springer Nature, 2014, pp. 78–97, doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">10.1007/978-3-642-54013-4_5</a>.","apa":"Chatterjee, K., Doyen, L., Filiot, E., &#38; Raskin, J.-F. (2014). Doomsday equilibria for omega-regular games. In <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i> (Vol. 8318, pp. 78–97). San Diego, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">https://doi.org/10.1007/978-3-642-54013-4_5</a>","ista":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. 2014. Doomsday equilibria for omega-regular games. VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 78–97.","ama":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. Doomsday equilibria for omega-regular games. In: <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>. Vol 8318. Springer Nature; 2014:78-97. doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">10.1007/978-3-642-54013-4_5</a>","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean-François Raskin. “Doomsday Equilibria for Omega-Regular Games.” In <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>, 8318:78–97. Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">https://doi.org/10.1007/978-3-642-54013-4_5</a>."},"day":"30","_id":"10885","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information games.\r\nIn this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile such that all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players objective, then the objective of every player is violated.\r\nWe present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games.We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games."}],"external_id":{"arxiv":["1311.3238"]},"type":"conference","quality_controlled":"1","ec_funded":1,"scopus_import":"1","status":"public","page":"78-97","date_updated":"2026-04-16T10:00:03Z","publication":"VMCAI 2014: Verification, Model Checking, and Abstract Interpretation","date_created":"2022-03-18T13:03:15Z","alternative_title":["LNCS"],"title":"Doomsday equilibria for omega-regular games","oa_version":"Preprint","OA_type":"green","publication_identifier":{"eisbn":["9783642540134"],"isbn":["9783642540127"],"eissn":["1611-3349"],"issn":["0302-9743"]},"arxiv":1,"conference":{"name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","start_date":"2014-01-19","end_date":"2014-01-21","location":"San Diego, CA, United States"},"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"681"}]},"article_processing_charge":"No","publisher":"Springer Nature","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"last_name":"Filiot","full_name":"Filiot, Emmanuel","first_name":"Emmanuel"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean-François"}],"volume":8318,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrCh"}],"month":"01","acknowledgement":" Supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No\r\nS11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","doi":"10.1007/978-3-642-54013-4_5","oa":1},{"pubrep_id":"422","doi":"10.1016/j.neuron.2013.09.046","oa":1,"project":[{"call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"},{"name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24"}],"department":[{"_id":"PeJo"}],"month":"01","volume":81,"author":[{"full_name":"Pernia-Andrade, Alejandro","last_name":"Pernia-Andrade","id":"36963E98-F248-11E8-B48F-1D18A9856A87","first_name":"Alejandro"},{"full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"publisher":"Elsevier","corr_author":"1","article_processing_charge":"No","publist_id":"4692","publication_status":"published","file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:09:48Z","file_size":4373072,"access_level":"open_access","creator":"system","relation":"main_file","date_updated":"2020-07-14T12:45:35Z","file_id":"4773","checksum":"438547cfcd9045a22f065f2019f07849","file_name":"IST-2016-422-v1+1_1-s2.0-S0896627313009227-main.pdf"}],"publication_identifier":{"issn":["0896-6273"]},"oa_version":"Published Version","date_created":"2018-12-11T11:56:35Z","title":"Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations","file_date_updated":"2020-07-14T12:45:35Z","isi":1,"date_updated":"2026-04-16T10:08:53Z","publication":"Neuron","status":"public","page":"140 - 152","scopus_import":"1","issue":"1","ec_funded":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"_id":"2254","abstract":[{"text":"Theta-gamma network oscillations are thought to represent key reference signals for information processing in neuronal ensembles, but the underlying synaptic mechanisms remain unclear. To address this question, we performed whole-cell (WC) patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials at low frequency, consistent with sparse coding in the dentate gyrus. GCs were exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs), primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents (IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence with the field potential predominantly in the theta frequency band, whereas IPSCs showed coherence primarily in the gamma range. Action potentials in GCs were phase locked to network oscillations. Thus, theta-gamma-modulated synaptic currents may provide a framework for sparse temporal coding of information in the dentate gyrus.","lang":"eng"}],"external_id":{"isi":["000329559000015"]},"has_accepted_license":"1","day":"08","citation":{"ieee":"A. Pernia-Andrade and P. M. Jonas, “Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations,” <i>Neuron</i>, vol. 81, no. 1. Elsevier, pp. 140–152, 2014.","short":"A. Pernia-Andrade, P.M. Jonas, Neuron 81 (2014) 140–152.","mla":"Pernia-Andrade, Alejandro, and Peter M. Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” <i>Neuron</i>, vol. 81, no. 1, Elsevier, 2014, pp. 140–52, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">10.1016/j.neuron.2013.09.046</a>.","apa":"Pernia-Andrade, A., &#38; Jonas, P. M. (2014). Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">https://doi.org/10.1016/j.neuron.2013.09.046</a>","ista":"Pernia-Andrade A, Jonas PM. 2014. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. 81(1), 140–152.","ama":"Pernia-Andrade A, Jonas PM. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. <i>Neuron</i>. 2014;81(1):140-152. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">10.1016/j.neuron.2013.09.046</a>","chicago":"Pernia-Andrade, Alejandro, and Peter M Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">https://doi.org/10.1016/j.neuron.2013.09.046</a>."},"year":"2014","ddc":["570"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","intvolume":"        81","date_published":"2014-01-08T00:00:00Z"},{"type":"journal_article","quality_controlled":"1","_id":"2253","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation."}],"external_id":{"isi":["000328661300009"]},"day":"01","citation":{"ista":"Bailly A, Wang B, Zwiewka M, Pollmann S, Schenck D, Lüthen H, Schulz A, Friml J, Geisler M. 2014. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. 77(1), 108–118.","ama":"Bailly A, Wang B, Zwiewka M, et al. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. <i>Plant Journal</i>. 2014;77(1):108-118. doi:<a href=\"https://doi.org/10.1111/tpj.12369\">10.1111/tpj.12369</a>","chicago":"Bailly, Aurélien, Bangjun Wang, Marta Zwiewka, Stephan Pollmann, Daniel Schenck, Hartwig Lüthen, Alexander Schulz, Jiří Friml, and Markus Geisler. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” <i>Plant Journal</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/tpj.12369\">https://doi.org/10.1111/tpj.12369</a>.","ieee":"A. Bailly <i>et al.</i>, “Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth,” <i>Plant Journal</i>, vol. 77, no. 1. Wiley-Blackwell, pp. 108–118, 2014.","short":"A. Bailly, B. Wang, M. Zwiewka, S. Pollmann, D. Schenck, H. Lüthen, A. Schulz, J. Friml, M. Geisler, Plant Journal 77 (2014) 108–118.","mla":"Bailly, Aurélien, et al. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” <i>Plant Journal</i>, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 108–18, doi:<a href=\"https://doi.org/10.1111/tpj.12369\">10.1111/tpj.12369</a>.","apa":"Bailly, A., Wang, B., Zwiewka, M., Pollmann, S., Schenck, D., Lüthen, H., … Geisler, M. (2014). Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12369\">https://doi.org/10.1111/tpj.12369</a>"},"year":"2014","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","intvolume":"        77","main_file_link":[{"url":"https://doi.org/10.1111/tpj.12369","open_access":"1"}],"date_published":"2014-01-01T00:00:00Z","isi":1,"publication":"Plant Journal","date_updated":"2026-04-16T10:08:41Z","status":"public","page":"108 - 118","scopus_import":"1","issue":"1","publist_id":"4694","publication_status":"published","publication_identifier":{"issn":["0960-7412"]},"oa_version":"Published Version","date_created":"2018-12-11T11:56:35Z","title":"Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth","oa":1,"doi":"10.1111/tpj.12369","project":[{"_id":"256BDAB0-B435-11E9-9278-68D0E5697425","name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur"}],"article_type":"original","department":[{"_id":"JiFr"}],"month":"01","author":[{"first_name":"Aurélien","full_name":"Bailly, Aurélien","last_name":"Bailly"},{"first_name":"Bangjun","full_name":"Wang, Bangjun","last_name":"Wang"},{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Pollmann, Stephan","last_name":"Pollmann","first_name":"Stephan"},{"first_name":"Daniel","last_name":"Schenck","full_name":"Schenck, Daniel"},{"last_name":"Lüthen","full_name":"Lüthen, Hartwig","first_name":"Hartwig"},{"first_name":"Alexander","last_name":"Schulz","full_name":"Schulz, Alexander"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí"},{"last_name":"Geisler","full_name":"Geisler, Markus","first_name":"Markus"}],"volume":77,"publisher":"Wiley-Blackwell","article_processing_charge":"No"},{"publication_status":"published","publist_id":"4740","publication_identifier":{"issn":["0169-5983"]},"oa_version":"None","date_created":"2018-12-11T11:56:25Z","title":"On secondary instabilities generating footbridges between spiral vortex flow","doi":"10.1088/0169-5983/46/2/025503","department":[{"_id":"BjHo"}],"month":"04","author":[{"last_name":"Altmeyer","full_name":"Altmeyer, Sebastian","orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"}],"volume":46,"publisher":"IOP Publishing","article_processing_charge":"No","corr_author":"1","quality_controlled":"1","type":"journal_article","external_id":{"isi":["000334075800003"]},"abstract":[{"text":"This work investigates the transition between different traveling helical waves (spirals, SPIs) in the setup of differentially independent rotating cylinders. We use direct numerical simulations to consider an infinite long and periodic Taylor-Couette apparatus with fixed axial periodicity length. We find so-called mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs, to establish stable footbridges connecting SPI states. While bridging the bifurcation branches of SPIs, the corresponding contributions within the MCS vary continuously with the control parameters. Here discussed MCSs presenting footbridge solutions start and end in different SPI branches. Therefore they differ significantly from the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010 New J. Phys. 12 113035). The latter start and end in the same SPI branch, while they always bifurcate out of those SPI branches with the larger mode amplitude. Meanwhile, these only appear within the coexisting region of both SPIs. In contrast, the footbridge solutions can also bifurcate out of the minor SPI contribution. We also find they exist in regions where only one of the SPIs contributions exists. In addition, MCS as footbridge solution can appear either stable or unstable. The latter detected transient solutions offer similar spatio-temporal characteristics to the flow establishing stable footbridges. Such transition processes are interesting for pattern-forming systems in general because they accomplish transitions between traveling waves of different azimuthal wave numbers and have not been described in the literature yet.","lang":"eng"}],"_id":"2224","language":[{"iso":"eng"}],"day":"01","citation":{"chicago":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” <i>Fluid Dynamics Research</i>. IOP Publishing, 2014. <a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">https://doi.org/10.1088/0169-5983/46/2/025503</a>.","ista":"Altmeyer S. 2014. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 46(2), 025503.","ama":"Altmeyer S. On secondary instabilities generating footbridges between spiral vortex flow. <i>Fluid Dynamics Research</i>. 2014;46(2). doi:<a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">10.1088/0169-5983/46/2/025503</a>","apa":"Altmeyer, S. (2014). On secondary instabilities generating footbridges between spiral vortex flow. <i>Fluid Dynamics Research</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">https://doi.org/10.1088/0169-5983/46/2/025503</a>","ieee":"S. Altmeyer, “On secondary instabilities generating footbridges between spiral vortex flow,” <i>Fluid Dynamics Research</i>, vol. 46, no. 2. IOP Publishing, 2014.","short":"S. Altmeyer, Fluid Dynamics Research 46 (2014).","mla":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” <i>Fluid Dynamics Research</i>, vol. 46, no. 2, 025503, IOP Publishing, 2014, doi:<a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">10.1088/0169-5983/46/2/025503</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2014","intvolume":"        46","article_number":"025503","date_published":"2014-04-01T00:00:00Z","isi":1,"date_updated":"2026-04-16T10:07:46Z","publication":"Fluid Dynamics Research","status":"public","scopus_import":"1","issue":"2"},{"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981873/"}],"date_published":"2014-01-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2014","intvolume":"        77","day":"01","citation":{"apa":"Chen, Y., Aung, K., Rolčík, J., Walicki, K., Friml, J., &#38; Brandizzí, F. (2014). Inter-regulation of the unfolded protein response and auxin signaling. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12373\">https://doi.org/10.1111/tpj.12373</a>","short":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, F. Brandizzí, Plant Journal 77 (2014) 97–107.","ieee":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, and F. Brandizzí, “Inter-regulation of the unfolded protein response and auxin signaling,” <i>Plant Journal</i>, vol. 77, no. 1. Wiley-Blackwell, pp. 97–107, 2014.","mla":"Chen, Yani, et al. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” <i>Plant Journal</i>, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 97–107, doi:<a href=\"https://doi.org/10.1111/tpj.12373\">10.1111/tpj.12373</a>.","chicago":"Chen, Yani, Kyaw Aung, Jakub Rolčík, Kathryn Walicki, Jiří Friml, and Federica Brandizzí. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” <i>Plant Journal</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/tpj.12373\">https://doi.org/10.1111/tpj.12373</a>.","ista":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. 2014. Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. 77(1), 97–107.","ama":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. Inter-regulation of the unfolded protein response and auxin signaling. <i>Plant Journal</i>. 2014;77(1):97-107. doi:<a href=\"https://doi.org/10.1111/tpj.12373\">10.1111/tpj.12373</a>"},"quality_controlled":"1","type":"journal_article","external_id":{"isi":["000328661300008"]},"abstract":[{"text":"The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes.","lang":"eng"}],"_id":"2249","language":[{"iso":"eng"}],"scopus_import":"1","issue":"1","page":"97 - 107","status":"public","isi":1,"publication":"Plant Journal","date_updated":"2026-04-16T10:08:30Z","oa_version":"Submitted Version","date_created":"2018-12-11T11:56:34Z","title":"Inter-regulation of the unfolded protein response and auxin signaling","publication_identifier":{"issn":["0960-7412"]},"publication_status":"published","publist_id":"4699","publisher":"Wiley-Blackwell","article_processing_charge":"No","department":[{"_id":"JiFr"}],"month":"01","author":[{"last_name":"Chen","full_name":"Chen, Yani","first_name":"Yani"},{"first_name":"Kyaw","full_name":"Aung, Kyaw","last_name":"Aung"},{"full_name":"Rolčík, Jakub","last_name":"Rolčík","first_name":"Jakub"},{"first_name":"Kathryn","full_name":"Walicki, Kathryn","last_name":"Walicki"},{"last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Federica","full_name":"Brandizzí, Federica","last_name":"Brandizzí"}],"volume":77,"oa":1,"doi":"10.1111/tpj.12373"},{"month":"02","department":[{"_id":"KrCh"}],"volume":521,"author":[{"last_name":"Grinshpun","full_name":"Grinshpun, Andrey","first_name":"Andrey"},{"last_name":"Phalitnonkiat","full_name":"Phalitnonkiat, Pakawat","first_name":"Pakawat"},{"last_name":"Rubin","full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha"},{"last_name":"Tarfulea","full_name":"Tarfulea, Andrei","first_name":"Andrei"}],"doi":"10.1016/j.tcs.2013.11.032","oa":1,"publisher":"Elsevier","corr_author":"1","article_processing_charge":"No","publist_id":"4703","publication_status":"published","oa_version":"Submitted Version","title":"Alternating traps in Muller and parity games","date_created":"2018-12-11T11:56:33Z","publication_identifier":{"issn":["0304-3975"]},"arxiv":1,"isi":1,"date_updated":"2026-04-16T10:08:15Z","publication":"Theoretical Computer Science","scopus_import":"1","status":"public","page":"73 - 91","day":"13","citation":{"ista":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. 2014. Alternating traps in Muller and parity games. Theoretical Computer Science. 521, 73–91.","ama":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. Alternating traps in Muller and parity games. <i>Theoretical Computer Science</i>. 2014;521:73-91. doi:<a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">10.1016/j.tcs.2013.11.032</a>","chicago":"Grinshpun, Andrey, Pakawat Phalitnonkiat, Sasha Rubin, and Andrei Tarfulea. “Alternating Traps in Muller and Parity Games.” <i>Theoretical Computer Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">https://doi.org/10.1016/j.tcs.2013.11.032</a>.","ieee":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, and A. Tarfulea, “Alternating traps in Muller and parity games,” <i>Theoretical Computer Science</i>, vol. 521. Elsevier, pp. 73–91, 2014.","short":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, A. Tarfulea, Theoretical Computer Science 521 (2014) 73–91.","mla":"Grinshpun, Andrey, et al. “Alternating Traps in Muller and Parity Games.” <i>Theoretical Computer Science</i>, vol. 521, Elsevier, 2014, pp. 73–91, doi:<a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">10.1016/j.tcs.2013.11.032</a>.","apa":"Grinshpun, A., Phalitnonkiat, P., Rubin, S., &#38; Tarfulea, A. (2014). Alternating traps in Muller and parity games. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">https://doi.org/10.1016/j.tcs.2013.11.032</a>"},"type":"journal_article","quality_controlled":"1","_id":"2246","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Muller games are played by two players moving a token along a graph; the winner is determined by the set of vertices that occur infinitely often. The central algorithmic problem is to compute the winning regions for the players. Different classes and representations of Muller games lead to problems of varying computational complexity. One such class are parity games; these are of particular significance in computational complexity, as they remain one of the few combinatorial problems known to be in NP ∩ co-NP but not known to be in P. We show that winning regions for a Muller game can be determined from the alternating structure of its traps. To every Muller game we then associate a natural number that we call its trap depth; this parameter measures how complicated the trap structure is. We present algorithms for parity games that run in polynomial time for graphs of bounded trap depth, and in general run in time exponential in the trap depth. "}],"external_id":{"arxiv":["1303.3777"],"isi":["000331433100007"]},"main_file_link":[{"url":"http://arxiv.org/abs/1303.3777","open_access":"1"}],"date_published":"2014-02-13T00:00:00Z","year":"2014","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","intvolume":"       521"},{"publist_id":"4715","publication_status":"published","publication_identifier":{"issn":["0896-6273"]},"oa_version":"None","date_created":"2018-12-11T11:56:31Z","title":"Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage","doi":"10.1016/j.neuron.2013.11.011","month":"01","department":[{"_id":"RySh"}],"volume":81,"author":[{"last_name":"Beppu","full_name":"Beppu, Kaoru","first_name":"Kaoru"},{"first_name":"Takuya","last_name":"Sasaki","full_name":"Sasaki, Takuya"},{"last_name":"Tanaka","full_name":"Tanaka, Kenji","first_name":"Kenji"},{"first_name":"Akihiro","full_name":"Yamanaka, Akihiro","last_name":"Yamanaka"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"first_name":"Ko","last_name":"Matsui","full_name":"Matsui, Ko"}],"publisher":"Elsevier","article_processing_charge":"No","type":"journal_article","quality_controlled":"1","_id":"2241","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The brain demands high-energy supply and obstruction of blood flow causes rapid deterioration of the healthiness of brain cells. Two major events occur upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity. However, cellular source of glutamate and its release mechanism upon ischemia remained unknown. Here we show a causal relationship between glial acidosis and neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2 (ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular acidification. Optical activation of ChR2 expressed in glial cells led to glial acidification and to release of glutamate. On the other hand, glial alkalization via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation of glutamate release and to the relief of ischemic brain damage in vivo. Our results suggest that controlling glial pH may be an effective therapeutic strategy for intervention of ischemic brain damage."}],"external_id":{"isi":["000330420700010"]},"day":"22","citation":{"short":"K. Beppu, T. Sasaki, K. Tanaka, A. Yamanaka, Y. Fukazawa, R. Shigemoto, K. Matsui, Neuron 81 (2014) 314–320.","ieee":"K. Beppu <i>et al.</i>, “Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage,” <i>Neuron</i>, vol. 81, no. 2. Elsevier, pp. 314–320, 2014.","mla":"Beppu, Kaoru, et al. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” <i>Neuron</i>, vol. 81, no. 2, Elsevier, 2014, pp. 314–20, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">10.1016/j.neuron.2013.11.011</a>.","apa":"Beppu, K., Sasaki, T., Tanaka, K., Yamanaka, A., Fukazawa, Y., Shigemoto, R., &#38; Matsui, K. (2014). Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">https://doi.org/10.1016/j.neuron.2013.11.011</a>","ista":"Beppu K, Sasaki T, Tanaka K, Yamanaka A, Fukazawa Y, Shigemoto R, Matsui K. 2014. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. 81(2), 314–320.","ama":"Beppu K, Sasaki T, Tanaka K, et al. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. <i>Neuron</i>. 2014;81(2):314-320. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">10.1016/j.neuron.2013.11.011</a>","chicago":"Beppu, Kaoru, Takuya Sasaki, Kenji Tanaka, Akihiro Yamanaka, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">https://doi.org/10.1016/j.neuron.2013.11.011</a>."},"year":"2014","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","intvolume":"        81","date_published":"2014-01-22T00:00:00Z","isi":1,"publication":"Neuron","date_updated":"2026-04-16T10:07:56Z","status":"public","page":"314 - 320","scopus_import":"1","issue":"2"},{"has_accepted_license":"1","day":"01","citation":{"chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” <i>Journal of Mathematical Imaging and Vision</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s10851-013-0468-x\">https://doi.org/10.1007/s10851-013-0468-x</a>.","ista":"Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 50(1), 164–177.","ama":"Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. <i>Journal of Mathematical Imaging and Vision</i>. 2014;50(1):164-177. doi:<a href=\"https://doi.org/10.1007/s10851-013-0468-x\">10.1007/s10851-013-0468-x</a>","apa":"Edelsbrunner, H., &#38; Pausinger, F. (2014). Stable length estimates of tube-like shapes. <i>Journal of Mathematical Imaging and Vision</i>. Springer. <a href=\"https://doi.org/10.1007/s10851-013-0468-x\">https://doi.org/10.1007/s10851-013-0468-x</a>","short":"H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision 50 (2014) 164–177.","ieee":"H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50, no. 1. Springer, pp. 164–177, 2014.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50, no. 1, Springer, 2014, pp. 164–77, doi:<a href=\"https://doi.org/10.1007/s10851-013-0468-x\">10.1007/s10851-013-0468-x</a>."},"type":"journal_article","quality_controlled":"1","_id":"2255","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm."}],"external_id":{"isi":["000339823000012"]},"date_published":"2014-09-01T00:00:00Z","year":"2014","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["000"],"intvolume":"        50","isi":1,"date_updated":"2026-04-16T10:09:04Z","publication":"Journal of Mathematical Imaging and Vision","file_date_updated":"2020-07-14T12:45:35Z","scopus_import":"1","issue":"1","ec_funded":1,"status":"public","page":"164 - 177","file":[{"access_level":"open_access","file_size":3941391,"date_created":"2018-12-12T10:16:18Z","content_type":"application/pdf","file_name":"IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf","checksum":"2f93f3e63a38a85cd4404d7953913b14","file_id":"5204","date_updated":"2020-07-14T12:45:35Z","relation":"main_file","creator":"system"}],"publist_id":"4691","publication_status":"published","oa_version":"Submitted Version","title":"Stable length estimates of tube-like shapes","date_created":"2018-12-11T11:56:36Z","publication_identifier":{"issn":["0924-9907"]},"project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"month":"09","department":[{"_id":"HeEd"}],"volume":50,"author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"full_name":"Pausinger, Florian","last_name":"Pausinger","first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8379-3768"}],"pubrep_id":"549","oa":1,"doi":"10.1007/s10851-013-0468-x","related_material":{"record":[{"id":"2843","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"1399"}]},"publisher":"Springer","corr_author":"1","article_processing_charge":"No"},{"publisher":"Springer","article_processing_charge":"No","corr_author":"1","pmid":1,"series_title":"MIMB","doi":"10.1007/978-1-4939-1164-6_15","department":[{"_id":"CaHe"}],"month":"08","volume":1189,"author":[{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","last_name":"Smutny"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Behrndt","full_name":"Behrndt, Martin"},{"first_name":"Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","last_name":"Campinho","full_name":"Campinho, Pedro"},{"full_name":"Ruprecht, Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","orcid":"0000-0003-4088-8633"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781493911646"],"isbn":["9781493911639"]},"place":"New York","oa_version":"None","date_created":"2019-03-26T08:55:59Z","alternative_title":["Methods in Molecular Biology"],"title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","publication_status":"published","page":"219-235","status":"public","editor":[{"first_name":"Celeste","full_name":"Nelson, Celeste","last_name":"Nelson"}],"publication":"Tissue Morphogenesis","date_updated":"2026-04-16T10:31:19Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2014","intvolume":"      1189","date_published":"2014-08-22T00:00:00Z","quality_controlled":"1","type":"book_chapter","external_id":{"pmid":["25245697"]},"_id":"6178","language":[{"iso":"eng"}],"abstract":[{"text":"Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo.","lang":"eng"}],"day":"22","citation":{"ama":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Nelson C, ed. <i>Tissue Morphogenesis</i>. Vol 1189. MIMB. New York: Springer; 2014:219-235. doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>","ista":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Tissue Morphogenesis. Methods in Molecular Biology, vol. 1189, 219–235.","chicago":"Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, 1189:219–35. MIMB. New York: Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>.","mla":"Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>.","short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, 2014, pp. 219–235.","ieee":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg, “UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo,” in <i>Tissue Morphogenesis</i>, vol. 1189, C. Nelson, Ed. New York: Springer, 2014, pp. 219–235.","apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., &#38; Heisenberg, C.-P. J. (2014). UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), <i>Tissue Morphogenesis</i> (Vol. 1189, pp. 219–235). New York: Springer. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>"}},{"publication":"Current Opinion in Insect Science","date_updated":"2026-04-27T22:30:44Z","isi":1,"page":"1 - 15","status":"public","issue":"1","ec_funded":1,"scopus_import":"1","external_id":{"isi":["000209578900002"]},"_id":"1999","language":[{"iso":"eng"}],"abstract":[{"text":"Selection for disease control is believed to have contributed to shape the organisation of insect societies — leading to interaction patterns that mitigate disease transmission risk within colonies, conferring them ‘organisational immunity’. Recent studies combining epidemiological models with social network analysis have identified general properties of interaction networks that may hinder propagation of infection within groups. These can be prophylactic and/or induced upon pathogen exposure. Here we review empirical evidence for these two types of organisational immunity in social insects and describe the individual-level behaviours that underlie it. We highlight areas requiring further investigation, and emphasise the need for tighter links between theory and empirical research and between individual-level and collective-level analyses.","lang":"eng"}],"quality_controlled":"1","type":"journal_article","day":"01","citation":{"chicago":"Stroeymeyt, Nathalie, Barbara E Casillas Perez, and Sylvia Cremer. “Organisational Immunity in Social Insects.” <i>Current Opinion in Insect Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">https://doi.org/10.1016/j.cois.2014.09.001</a>.","ista":"Stroeymeyt N, Casillas Perez BE, Cremer S. 2014. Organisational immunity in social insects. Current Opinion in Insect Science. 5(1), 1–15.","ama":"Stroeymeyt N, Casillas Perez BE, Cremer S. Organisational immunity in social insects. <i>Current Opinion in Insect Science</i>. 2014;5(1):1-15. doi:<a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">10.1016/j.cois.2014.09.001</a>","apa":"Stroeymeyt, N., Casillas Perez, B. E., &#38; Cremer, S. (2014). Organisational immunity in social insects. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">https://doi.org/10.1016/j.cois.2014.09.001</a>","ieee":"N. Stroeymeyt, B. E. Casillas Perez, and S. Cremer, “Organisational immunity in social insects,” <i>Current Opinion in Insect Science</i>, vol. 5, no. 1. Elsevier, pp. 1–15, 2014.","short":"N. Stroeymeyt, B.E. Casillas Perez, S. Cremer, Current Opinion in Insect Science 5 (2014) 1–15.","mla":"Stroeymeyt, Nathalie, et al. “Organisational Immunity in Social Insects.” <i>Current Opinion in Insect Science</i>, vol. 5, no. 1, Elsevier, 2014, pp. 1–15, doi:<a href=\"https://doi.org/10.1016/j.cois.2014.09.001\">10.1016/j.cois.2014.09.001</a>."},"intvolume":"         5","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2014","date_published":"2014-11-01T00:00:00Z","doi":"10.1016/j.cois.2014.09.001","volume":5,"author":[{"full_name":"Stroeymeyt, Nathalie","last_name":"Stroeymeyt","first_name":"Nathalie"},{"last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"month":"11","department":[{"_id":"SyCr"}],"project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","corr_author":"1","publisher":"Elsevier","related_material":{"record":[{"relation":"dissertation_contains","id":"6383"},{"relation":"dissertation_contains","id":"6435","status":"public"}]},"publication_status":"published","publist_id":"5080","title":"Organisational immunity in social insects","date_created":"2018-12-11T11:55:08Z","oa_version":"None"}]