[{"date_published":"2012-01-01T00:00:00Z","quality_controlled":0,"citation":{"ama":"Kolmogorov V. The Power of Linear Programming for Valued CSPs: A Constructive Characterization. Unknown; 2012.","ista":"Kolmogorov V. 2012. The power of linear programming for valued CSPs: a constructive characterization, Unknown,p.","ieee":"V. Kolmogorov, The power of linear programming for valued CSPs: a constructive characterization. Unknown, 2012.","apa":"Kolmogorov, V. (2012). The power of linear programming for valued CSPs: a constructive characterization. Unknown.","mla":"Kolmogorov, Vladimir. The Power of Linear Programming for Valued CSPs: A Constructive Characterization. Unknown, 2012.","short":"V. Kolmogorov, The Power of Linear Programming for Valued CSPs: A Constructive Characterization, Unknown, 2012.","chicago":"Kolmogorov, Vladimir. The Power of Linear Programming for Valued CSPs: A Constructive Characterization. Unknown, 2012."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.7213"}],"day":"01","month":"01","date_updated":"2019-04-26T07:22:21Z","date_created":"2018-12-11T12:00:24Z","author":[{"full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"}],"publisher":"Unknown","status":"public","publication_status":"published","title":"The power of linear programming for valued CSPs: a constructive characterization","_id":"2929","year":"2012","extern":1,"publist_id":"3807","type":"report"},{"scopus_import":1,"day":"01","month":"10","publication":"Proceedings of the 2012 ACM conference on Computer and communications security","citation":{"ieee":"J. Almeida, M. Barbosa, E. Bangerter, G. Barthe, S. Krenn, and S. Béguelin, “Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols,” in Proceedings of the 2012 ACM conference on Computer and communications security, Raleigh, NC, USA, 2012, pp. 488–500.","apa":"Almeida, J., Barbosa, M., Bangerter, E., Barthe, G., Krenn, S., & Béguelin, S. (2012). Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols. In Proceedings of the 2012 ACM conference on Computer and communications security (pp. 488–500). Raleigh, NC, USA: ACM. https://doi.org/10.1145/2382196.2382249","ista":"Almeida J, Barbosa M, Bangerter E, Barthe G, Krenn S, Béguelin S. 2012. Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols. Proceedings of the 2012 ACM conference on Computer and communications security. CCS: Computer and Communications Security, 488–500.","ama":"Almeida J, Barbosa M, Bangerter E, Barthe G, Krenn S, Béguelin S. Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols. In: Proceedings of the 2012 ACM Conference on Computer and Communications Security. ACM; 2012:488-500. doi:10.1145/2382196.2382249","chicago":"Almeida, José, Manuel Barbosa, Endre Bangerter, Gilles Barthe, Stephan Krenn, and Santiago Béguelin. “Full Proof Cryptography: Verifiable Compilation of Efficient Zero-Knowledge Protocols.” In Proceedings of the 2012 ACM Conference on Computer and Communications Security, 488–500. ACM, 2012. https://doi.org/10.1145/2382196.2382249.","short":"J. Almeida, M. Barbosa, E. Bangerter, G. Barthe, S. Krenn, S. Béguelin, in:, Proceedings of the 2012 ACM Conference on Computer and Communications Security, ACM, 2012, pp. 488–500.","mla":"Almeida, José, et al. “Full Proof Cryptography: Verifiable Compilation of Efficient Zero-Knowledge Protocols.” Proceedings of the 2012 ACM Conference on Computer and Communications Security, ACM, 2012, pp. 488–500, doi:10.1145/2382196.2382249."},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2012/258"}],"oa":1,"quality_controlled":"1","page":"488 - 500","conference":{"name":"CCS: Computer and Communications Security","start_date":"2012-10-16","location":"Raleigh, NC, USA","end_date":"2012-10-18"},"date_published":"2012-10-01T00:00:00Z","doi":"10.1145/2382196.2382249","language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"Developers building cryptography into security-sensitive applications face a daunting task. Not only must they understand the security guarantees delivered by the constructions they choose, they must also implement and combine them correctly and efficiently. Cryptographic compilers free developers from this task by turning high-level specifications of security goals into efficient implementations. Yet, trusting such tools is hard as they rely on complex mathematical machinery and claim security properties that are subtle and difficult to verify. In this paper we present ZKCrypt, an optimizing cryptographic compiler achieving an unprecedented level of assurance without sacrificing practicality for a comprehensive class of cryptographic protocols, known as Zero-Knowledge Proofs of Knowledge. The pipeline of ZKCrypt integrates purpose-built verified compilers and verifying compilers producing formal proofs in the CertiCrypt framework. By combining the guarantees delivered by each stage, ZKCrypt provides assurance that the output implementation securely realizes the abstract proof goal given as input. We report on the main characteristics of ZKCrypt, highlight new definitions and concepts at its foundations, and illustrate its applicability through a representative example of an anonymous credential system.","lang":"eng"}],"publist_id":"3798","_id":"2937","acknowledgement":"This work was partially funded by National Funds through the FCT - Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project ENI-AC/2224/2009, by ENIAC Joint Undertaking under grant agreement number 120224, European Projects FP7-256980 NESSoS and FP7-229599 AMAROUT, Spanish National project TIN2009-14599 DESAFIOS 10, and Madrid Regional project S2009TIC-1465 PROMETIDOS.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","title":"Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols","publication_status":"published","status":"public","publisher":"ACM","department":[{"_id":"KrPi"}],"author":[{"full_name":"Almeida, José","first_name":"José","last_name":"Almeida"},{"first_name":"Manuel","last_name":"Barbosa","full_name":"Barbosa, Manuel"},{"last_name":"Bangerter","first_name":"Endre","full_name":"Bangerter, Endre"},{"full_name":"Barthe, Gilles","last_name":"Barthe","first_name":"Gilles"},{"id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2835-9093","first_name":"Stephan","last_name":"Krenn","full_name":"Krenn, Stephan"},{"first_name":"Santiago","last_name":"Béguelin","full_name":"Béguelin, Santiago"}],"date_updated":"2021-01-12T07:39:53Z","date_created":"2018-12-11T12:00:26Z","oa_version":"Submitted Version"},{"doi":"10.1145/2380356.2380370","conference":{"name":"EMSOFT: Embedded Software ","start_date":"2012-10-07","location":"Tampere, Finland","end_date":"2012-10-12"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.7019"}],"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","month":"10","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}],"date_updated":"2021-01-12T07:39:53Z","date_created":"2018-12-11T12:00:26Z","acknowledgement":"This work has been financially supported in part by the European Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract # 270180 (NOPTILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008 (Modeling and control of Networked vehicle systems in persistent autonomous operations); by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start grant (279307: Graph Games); Microsoft faculty fellows award; ERC Advanced grant QUAREM; and FWF Grant No S11403-N23 (RiSE).","year":"2012","publisher":"ACM","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","ec_funded":1,"publist_id":"3799","date_published":"2012-10-01T00:00:00Z","citation":{"ista":"Chatterjee K, Henzinger TA, Prabhu V. 2012. Finite automata with time delay blocks. roceedings of the tenth ACM international conference on Embedded software. EMSOFT: Embedded Software , 43–52.","ieee":"K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Finite automata with time delay blocks,” in roceedings of the tenth ACM international conference on Embedded software, Tampere, Finland, 2012, pp. 43–52.","apa":"Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2012). Finite automata with time delay blocks. In roceedings of the tenth ACM international conference on Embedded software (pp. 43–52). Tampere, Finland: ACM. https://doi.org/10.1145/2380356.2380370","ama":"Chatterjee K, Henzinger TA, Prabhu V. Finite automata with time delay blocks. In: Roceedings of the Tenth ACM International Conference on Embedded Software. ACM; 2012:43-52. doi:10.1145/2380356.2380370","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Finite Automata with Time Delay Blocks.” In Roceedings of the Tenth ACM International Conference on Embedded Software, 43–52. ACM, 2012. https://doi.org/10.1145/2380356.2380370.","mla":"Chatterjee, Krishnendu, et al. “Finite Automata with Time Delay Blocks.” Roceedings of the Tenth ACM International Conference on Embedded Software, ACM, 2012, pp. 43–52, doi:10.1145/2380356.2380370.","short":"K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Roceedings of the Tenth ACM International Conference on Embedded Software, ACM, 2012, pp. 43–52."},"publication":"roceedings of the tenth ACM international conference on Embedded software","page":"43 - 52","day":"01","scopus_import":1,"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2936","title":"Finite automata with time delay blocks","status":"public","abstract":[{"lang":"eng","text":"The notion of delays arises naturally in many computational models, such as, in the design of circuits, control systems, and dataflow languages. In this work, we introduce automata with delay blocks (ADBs), extending finite state automata with variable time delay blocks, for deferring individual transition output symbols, in a discrete-time setting. We show that the ADB languages strictly subsume the regular languages, and are incomparable in expressive power to the context-free languages. We show that ADBs are closed under union, concatenation and Kleene star, and under intersection with regular languages, but not closed under complementation and intersection with other ADB languages. We show that the emptiness and the membership problems are decidable in polynomial time for ADBs, whereas the universality problem is undecidable. Finally we consider the linear-time model checking problem, i.e., whether the language of an ADB is contained in a regular language, and show that the model checking problem is PSPACE-complete. Copyright 2012 ACM."}],"type":"conference"},{"intvolume":" 26","publisher":"Wiley-Blackwell","department":[{"_id":"SyCr"}],"title":"Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies","publication_status":"published","status":"public","_id":"2938","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","acknowledgement":"We thank Mark Brown, Christopher Pull, Meghan L. Vyleta, Miriam Stock, Barbara Casillas-Perez and three anonymous reviewers for valuable comments on the manuscript and Eva Sixt for ant drawings. Funding was obtained from the German Science Foundation (DFG, by an Individual Research Grant to S.C.) and the European Research Council (ERC, by an ERC-Starting Grant to SC and an Individual Marie Curie EIF fellowship to L.desU.). The authors declare no conflict of interests.","volume":26,"oa_version":"None","date_updated":"2021-01-12T07:39:54Z","date_created":"2018-12-11T12:00:27Z","author":[{"full_name":"Ugelvig, Line V","last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"type":"journal_article","issue":"6","publist_id":"3797","abstract":[{"text":"Social insects have a very high potential to become invasive pest species. Here, we explore how their social lifestyle and their interaction with parasites may contribute to this invasive success. Similar to solitary species, parasite release followed by the evolution of increased competitive ability can promote establishment of introduced social insect hosts in their introduced range. Genetic bottlenecks during introduction of low numbers of founder individuals decrease the genetic diversity at three levels: the population, the colony and the individual, with the colony level being specific to social insects. Reduced genetic diversity can affect both the individual immune system and the collective colony-level disease defences (social immunity). Still, the dual immune system is likely to make social insects more robust to parasite attack. Changes in social structure from small, family-based, territorially aggressive societies in native populations towards huge networks of cooperating nests (unicoloniality) occur in some invasive social insects, for example, most invasive ants and some termites. Unicoloniality is likely to affect disease dynamics in multiple ways. The free exchange of individuals within the population leads to an increased genetic heterogeneity among individuals of a single nest, thereby decreasing disease transmission. However, the multitude of reproductively active queens per colony buffers the effect of individual diseased queens and their offspring, which may result in a higher level of vertical disease transmission in unicolonial societies. Lastly, unicoloniality provides a competitive advantage over native species, allowing them to quickly become the dominant species in the habitat, which in turn selects for parasite adaptation to this common host genotype and thus eventually a high parasite pressure. Overall, invasions by insect societies are characterized by general features applying to all introduced species, as well as idiosyncrasies that emerge from their social lifestyle. It is important to study these effects in concert to be able to develop efficient management and biocontrol strategies. © 2012 British Ecological Society.","lang":"eng"}],"page":"1300 - 1312","quality_controlled":"1","citation":{"chicago":"Ugelvig, Line V, and Sylvia Cremer. “Effects of Social Immunity and Unicoloniality on Host Parasite Interactions in Invasive Insect Societies.” Functional Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/1365-2435.12013.","mla":"Ugelvig, Line V., and Sylvia Cremer. “Effects of Social Immunity and Unicoloniality on Host Parasite Interactions in Invasive Insect Societies.” Functional Ecology, vol. 26, no. 6, Wiley-Blackwell, 2012, pp. 1300–12, doi:10.1111/1365-2435.12013.","short":"L.V. Ugelvig, S. Cremer, Functional Ecology 26 (2012) 1300–1312.","ista":"Ugelvig LV, Cremer S. 2012. Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies. Functional Ecology. 26(6), 1300–1312.","ieee":"L. V. Ugelvig and S. Cremer, “Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies,” Functional Ecology, vol. 26, no. 6. Wiley-Blackwell, pp. 1300–1312, 2012.","apa":"Ugelvig, L. V., & Cremer, S. (2012). Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12013","ama":"Ugelvig LV, Cremer S. Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies. Functional Ecology. 2012;26(6):1300-1312. doi:10.1111/1365-2435.12013"},"publication":"Functional Ecology","language":[{"iso":"eng"}],"date_published":"2012-01-01T00:00:00Z","doi":"10.1111/1365-2435.12013","scopus_import":1,"month":"01","day":"01"},{"scopus_import":1,"month":"05","day":"08","quality_controlled":"1","page":"259 - 271","project":[{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","citation":{"chicago":"Torresani, Lorenzo, Vladimir Kolmogorov, and Carsten Rother. “A Dual Decomposition Approach to Feature Correspondence.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2012. https://doi.org/10.1109/TPAMI.2012.105.","short":"L. Torresani, V. Kolmogorov, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 35 (2012) 259–271.","mla":"Torresani, Lorenzo, et al. “A Dual Decomposition Approach to Feature Correspondence.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 35, no. 2, IEEE, 2012, pp. 259–71, doi:10.1109/TPAMI.2012.105.","apa":"Torresani, L., Kolmogorov, V., & Rother, C. (2012). A dual decomposition approach to feature correspondence. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2012.105","ieee":"L. Torresani, V. Kolmogorov, and C. Rother, “A dual decomposition approach to feature correspondence,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 35, no. 2. IEEE, pp. 259–271, 2012.","ista":"Torresani L, Kolmogorov V, Rother C. 2012. A dual decomposition approach to feature correspondence. IEEE Transactions on Pattern Analysis and Machine Intelligence. 35(2), 259–271.","ama":"Torresani L, Kolmogorov V, Rother C. A dual decomposition approach to feature correspondence. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2012;35(2):259-271. doi:10.1109/TPAMI.2012.105"},"language":[{"iso":"eng"}],"doi":"10.1109/TPAMI.2012.105","date_published":"2012-05-08T00:00:00Z","type":"journal_article","abstract":[{"text":"In this paper, we present a new approach for establishing correspondences between sparse image features related by an unknown nonrigid mapping and corrupted by clutter and occlusion, such as points extracted from images of different instances of the same object category. We formulate this matching task as an energy minimization problem by defining an elaborate objective function of the appearance and the spatial arrangement of the features. Optimization of this energy is an instance of graph matching, which is in general an NP-hard problem. We describe a novel graph matching optimization technique, which we refer to as dual decomposition (DD), and demonstrate on a variety of examples that this method outperforms existing graph matching algorithms. In the majority of our examples, DD is able to find the global minimum within a minute. The ability to globally optimize the objective allows us to accurately learn the parameters of our matching model from training examples. We show on several matching tasks that our learned model yields results superior to those of state-of-the-art methods.\r\n","lang":"eng"}],"issue":"2","publist_id":"3805","status":"public","title":"A dual decomposition approach to feature correspondence","publication_status":"published","intvolume":" 35","publisher":"IEEE","department":[{"_id":"VlKo"}],"_id":"2931","acknowledgement":"This research was funded in part by Microsoft Research.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","date_updated":"2021-01-12T07:00:46Z","date_created":"2018-12-11T12:00:24Z","oa_version":"None","volume":35,"author":[{"full_name":"Torresani, Lorenzo","last_name":"Torresani","first_name":"Lorenzo"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"}]},{"ec_funded":1,"publist_id":"3791","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"year":"2012","acknowledgement":"ERC Advanced Grant QUAREM (Quantitative Reactive Modeling), FWF National Research Network RISE (Rigorous Systems Engineering)","date_updated":"2021-01-12T07:39:56Z","date_created":"2018-12-11T12:00:28Z","volume":7539,"author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"}],"month":"09","quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2012-03-21","start_date":"2012-03-19","location":"Oxford, UK","name":"Monterey Workshop 2012"},"doi":"10.1007/978-3-642-34059-8_20","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Interface theories provide a formal framework for component-based development of software and hardware which supports the incremental design of systems and the independent implementability of components. These capabilities are ensured through mathematical properties of the parallel composition operator and the refinement relation for components. More recently, a conjunction operation was added to interface theories in order to provide support for handling multiple viewpoints, requirements engineering, and component reuse. Unfortunately, the conjunction operator does not allow independent implementability in general. In this paper, we study conditions that need to be imposed on interface models in order to enforce independent implementability with respect to conjunction. We focus on multiple viewpoint specifications and propose a new compatibility criterion between two interfaces, which we call orthogonality. We show that orthogonal interfaces can be refined separately, while preserving both orthogonality and composability with other interfaces. We illustrate the independent implementability of different viewpoints with a FIFO buffer example.","lang":"eng"}],"status":"public","title":"Independent implementability of viewpoints","intvolume":" 7539","_id":"2942","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","scopus_import":1,"day":"16","page":"380 - 395","publication":" Conference proceedings Monterey Workshop 2012","citation":{"chicago":"Henzinger, Thomas A, and Dejan Nickovic. “Independent Implementability of Viewpoints.” In Conference Proceedings Monterey Workshop 2012, 7539:380–95. Springer, 2012. https://doi.org/10.1007/978-3-642-34059-8_20.","mla":"Henzinger, Thomas A., and Dejan Nickovic. “Independent Implementability of Viewpoints.” Conference Proceedings Monterey Workshop 2012, vol. 7539, Springer, 2012, pp. 380–95, doi:10.1007/978-3-642-34059-8_20.","short":"T.A. Henzinger, D. Nickovic, in:, Conference Proceedings Monterey Workshop 2012, Springer, 2012, pp. 380–395.","ista":"Henzinger TA, Nickovic D. 2012. Independent implementability of viewpoints. Conference proceedings Monterey Workshop 2012. Monterey Workshop 2012, LNCS, vol. 7539, 380–395.","ieee":"T. A. Henzinger and D. Nickovic, “Independent implementability of viewpoints,” in Conference proceedings Monterey Workshop 2012, Oxford, UK, 2012, vol. 7539, pp. 380–395.","apa":"Henzinger, T. A., & Nickovic, D. (2012). Independent implementability of viewpoints. In Conference proceedings Monterey Workshop 2012 (Vol. 7539, pp. 380–395). Oxford, UK: Springer. https://doi.org/10.1007/978-3-642-34059-8_20","ama":"Henzinger TA, Nickovic D. Independent implementability of viewpoints. In: Conference Proceedings Monterey Workshop 2012. Vol 7539. Springer; 2012:380-395. doi:10.1007/978-3-642-34059-8_20"},"date_published":"2012-09-16T00:00:00Z"},{"publist_id":"3790","acknowledgement":"We thank Professor Philippe Cluzel and Mr Lance Min for providing advice and materials. Jeannette Chau provided technical support. Work at NU was supported by NSF Grants DMR-0715099, MCB-1022117, DMR-1206868, DMR-0520513 and DMR-1121262 (NU-MRSEC), by NIH-NCI Grant U54CA143869-01 (NU-PS-OC) and by the Chicago Biomedical Consortium with support from the Searle Funds at the Chicago Community Trust. Work at UCLA was supported by NIH Grant GM038509.","year":"2012","department":[{"_id":"CaGu"}],"publisher":"Wiley-Blackwell","publication_status":"published","author":[{"first_name":"Nastaran","last_name":"Hadizadeh Yazdi","full_name":"Hadizadeh Yazdi, Nastaran"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"},{"first_name":"Reid","last_name":"Johnson","full_name":"Johnson, Reid"},{"full_name":"Marko, John","first_name":"John","last_name":"Marko"}],"volume":86,"date_updated":"2021-01-12T07:39:56Z","date_created":"2018-12-11T12:00:28Z","month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"http://europepmc.org/articles/pmc3524407"}],"quality_controlled":"1","doi":"10.1111/mmi.12071","language":[{"iso":"eng"}],"type":"journal_article","issue":"6","abstract":[{"text":"We examine whether the Escherichia coli chromosome is folded into a self-adherent nucleoprotein complex, or alternately is a confined but otherwise unconstrained self-avoiding polymer. We address this through in vivo visualization, using an inducible GFP fusion to the nucleoid-associated protein Fis to non-specifically decorate the entire chromosome. For a range of different growth conditions, the chromosome is a compact structure that does not fill the volume of the cell, and which moves from the new pole to the cell centre. During rapid growth, chromosome segregation occurs well before cell division, with daughter chromosomes coupled by a thin inter-daughter filament before complete segregation, whereas during slow growth chromosomes stay adjacent until cell division occurs. Image correlation analysis indicates that sub-nucleoid structure is stable on a 1min timescale, comparable to the timescale for redistribution time measured for GFP-Fis after photobleaching. Optical deconvolution and writhe calculation analysis indicate that the nucleoid has a large-scale coiled organization rather than being an amorphous mass. Our observations are consistent with the chromosome having a self-adherent filament organization.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2943","intvolume":" 86","title":"Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions","status":"public","oa_version":"Submitted Version","scopus_import":1,"day":"09","citation":{"mla":"Hadizadeh Yazdi, Nastaran, et al. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.” Molecular Microbiology, vol. 86, no. 6, Wiley-Blackwell, 2012, pp. 1318–33, doi:10.1111/mmi.12071.","short":"N. Hadizadeh Yazdi, C.C. Guet, R. Johnson, J. Marko, Molecular Microbiology 86 (2012) 1318–1333.","chicago":"Hadizadeh Yazdi, Nastaran, Calin C Guet, Reid Johnson, and John Marko. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.” Molecular Microbiology. Wiley-Blackwell, 2012. https://doi.org/10.1111/mmi.12071.","ama":"Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 2012;86(6):1318-1333. doi:10.1111/mmi.12071","ista":"Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. 2012. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 86(6), 1318–1333.","apa":"Hadizadeh Yazdi, N., Guet, C. C., Johnson, R., & Marko, J. (2012). Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.12071","ieee":"N. Hadizadeh Yazdi, C. C. Guet, R. Johnson, and J. Marko, “Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions,” Molecular Microbiology, vol. 86, no. 6. Wiley-Blackwell, pp. 1318–1333, 2012."},"publication":"Molecular Microbiology","page":"1318 - 1333","date_published":"2012-11-09T00:00:00Z"},{"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"chicago":"Dolbilin, Nikolai, Herbert Edelsbrunner, and Oleg Musin. “On the Optimality of Functionals over Triangulations of Delaunay Sets.” Russian Mathematical Surveys. IOP Publishing, 2012. https://doi.org/10.1070/RM2012v067n04ABEH004807.","short":"N. Dolbilin, H. Edelsbrunner, O. Musin, Russian Mathematical Surveys 67 (2012) 781–783.","mla":"Dolbilin, Nikolai, et al. “On the Optimality of Functionals over Triangulations of Delaunay Sets.” Russian Mathematical Surveys, vol. 67, no. 4, IOP Publishing, 2012, pp. 781–83, doi:10.1070/RM2012v067n04ABEH004807.","ieee":"N. Dolbilin, H. Edelsbrunner, and O. Musin, “On the optimality of functionals over triangulations of Delaunay sets,” Russian Mathematical Surveys, vol. 67, no. 4. IOP Publishing, pp. 781–783, 2012.","apa":"Dolbilin, N., Edelsbrunner, H., & Musin, O. (2012). On the optimality of functionals over triangulations of Delaunay sets. Russian Mathematical Surveys. IOP Publishing. https://doi.org/10.1070/RM2012v067n04ABEH004807","ista":"Dolbilin N, Edelsbrunner H, Musin O. 2012. On the optimality of functionals over triangulations of Delaunay sets. Russian Mathematical Surveys. 67(4), 781–783.","ama":"Dolbilin N, Edelsbrunner H, Musin O. On the optimality of functionals over triangulations of Delaunay sets. Russian Mathematical Surveys. 2012;67(4):781-783. doi:10.1070/RM2012v067n04ABEH004807"},"publication":"Russian Mathematical Surveys","page":"781 - 783","date_published":"2012-11-01T00:00:00Z","type":"journal_article","issue":"4","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2941","intvolume":" 67","status":"public","title":"On the optimality of functionals over triangulations of Delaunay sets","ddc":["510"],"pubrep_id":"132","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2013-132-v1+1_2012-J-04-Functional-E.pdf","file_size":253816,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5239","checksum":"389a5ae53d6347de36c3468034f2821d","date_updated":"2020-07-14T12:45:55Z","date_created":"2018-12-12T10:16:49Z"}],"month":"11","oa":1,"quality_controlled":"1","doi":"10.1070/RM2012v067n04ABEH004807","language":[{"iso":"eng"}],"publist_id":"3792","file_date_updated":"2020-07-14T12:45:55Z","year":"2012","publisher":"IOP Publishing","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"first_name":"Nikolai","last_name":"Dolbilin","full_name":"Dolbilin, Nikolai"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Musin, Oleg","last_name":"Musin","first_name":"Oleg"}],"volume":67,"date_updated":"2021-01-12T07:39:55Z","date_created":"2018-12-11T12:00:28Z"},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1093/nar/gks705","language":[{"iso":"eng"}],"month":"10","year":"2012","acknowledgement":"Deutsche Forschungsgemeinschaft (DFG) (SFB 960 and FOR855); European Research Council (ERC grant ‘sRNAs’); European Union (FP7 project ‘ONCOMIRs’); German Bundesministerium für Bildung und Forschung (BMBF, NGFN+, FKZ PIM-01GS0804-5); Bavarian Genome Research Network (BayGene to G.M.); The Netherlands Organization for Scientific Research (NWO, VIDI grant to E.B.). Funding for open access charge: DFG via the open access publishing program. \r\n\r\nWe thank Sigrun Ammon and Corinna Friederich for technical assistance and Sebastian Petri and Daniel Schraivogel for helpful discussions.","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Oxford University Press","author":[{"first_name":"Anne","last_name":"Dueck","full_name":"Dueck, Anne"},{"full_name":"Ziegler, Christian","last_name":"Ziegler","first_name":"Christian"},{"full_name":"Eichner, Alexander","last_name":"Eichner","first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eugène","last_name":"Berezikov","full_name":"Berezikov, Eugène"},{"last_name":"Meister","first_name":"Gunter","full_name":"Meister, Gunter"}],"date_updated":"2021-01-12T07:39:57Z","date_created":"2018-12-11T12:00:29Z","volume":40,"file_date_updated":"2020-07-14T12:45:55Z","publist_id":"3786","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication":"Nucleic Acids Research","citation":{"ama":"Dueck A, Ziegler C, Eichner A, Berezikov E, Meister G. MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research. 2012;40(19):9850-9862. doi:10.1093/nar/gks705","apa":"Dueck, A., Ziegler, C., Eichner, A., Berezikov, E., & Meister, G. (2012). MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gks705","ieee":"A. Dueck, C. Ziegler, A. Eichner, E. Berezikov, and G. Meister, “MicroRNAs associated with the different human Argonaute proteins,” Nucleic Acids Research, vol. 40, no. 19. Oxford University Press, pp. 9850–9862, 2012.","ista":"Dueck A, Ziegler C, Eichner A, Berezikov E, Meister G. 2012. MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research. 40(19), 9850–9862.","short":"A. Dueck, C. Ziegler, A. Eichner, E. Berezikov, G. Meister, Nucleic Acids Research 40 (2012) 9850–9862.","mla":"Dueck, Anne, et al. “MicroRNAs Associated with the Different Human Argonaute Proteins.” Nucleic Acids Research, vol. 40, no. 19, Oxford University Press, 2012, pp. 9850–62, doi:10.1093/nar/gks705.","chicago":"Dueck, Anne, Christian Ziegler, Alexander Eichner, Eugène Berezikov, and Gunter Meister. “MicroRNAs Associated with the Different Human Argonaute Proteins.” Nucleic Acids Research. Oxford University Press, 2012. https://doi.org/10.1093/nar/gks705."},"page":"9850 - 9862","date_published":"2012-10-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","_id":"2946","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"MicroRNAs associated with the different human Argonaute proteins","intvolume":" 40","pubrep_id":"383","file":[{"file_size":8126936,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2015-383-v1+1_Nucl._Acids_Res.-2012-Dueck-9850-62.pdf","checksum":"1bb8d1ff894014b481657a21083c941c","date_updated":"2020-07-14T12:45:55Z","date_created":"2018-12-12T10:13:12Z","relation":"main_file","file_id":"4993"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"MicroRNAs (miRNAs) are small noncoding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3′-untranslated region (3′-UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected.","lang":"eng"}],"issue":"19"},{"main_file_link":[{"url":"http://arxiv.org/abs/1202.4140","open_access":"1"}],"oa":1,"quality_controlled":"1","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":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"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"}],"conference":{"end_date":"2012-10-06","location":"Thiruvananthapuram, India","start_date":"2012-10-03","name":" ATVA: Automated Technology for Verification and Analysis"},"doi":"10.1007/978-3-642-33386-6_30","language":[{"iso":"eng"}],"month":"06","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","year":"2012","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"},{"full_name":"Majumdar, Ritankar","last_name":"Majumdar","first_name":"Ritankar"}],"date_created":"2018-12-11T12:00:29Z","date_updated":"2021-01-12T07:39:58Z","volume":7561,"publist_id":"3785","ec_funded":1,"citation":{"ama":"Chatterjee K, Chmelik M, Majumdar R. Equivalence of games with probabilistic uncertainty and partial observation games. In: Vol 7561. Springer; 2012:385-399. doi:10.1007/978-3-642-33386-6_30","ista":"Chatterjee K, Chmelik M, Majumdar R. 2012. Equivalence of games with probabilistic uncertainty and partial observation games. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 7561, 385–399.","ieee":"K. Chatterjee, M. Chmelik, and R. Majumdar, “Equivalence of games with probabilistic uncertainty and partial observation games,” presented at the ATVA: Automated Technology for Verification and Analysis, Thiruvananthapuram, India, 2012, vol. 7561, pp. 385–399.","apa":"Chatterjee, K., Chmelik, M., & Majumdar, R. (2012). Equivalence of games with probabilistic uncertainty and partial observation games (Vol. 7561, pp. 385–399). Presented at the ATVA: Automated Technology for Verification and Analysis, Thiruvananthapuram, India: Springer. https://doi.org/10.1007/978-3-642-33386-6_30","mla":"Chatterjee, Krishnendu, et al. Equivalence of Games with Probabilistic Uncertainty and Partial Observation Games. Vol. 7561, Springer, 2012, pp. 385–99, doi:10.1007/978-3-642-33386-6_30.","short":"K. Chatterjee, M. Chmelik, R. Majumdar, in:, Springer, 2012, pp. 385–399.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Ritankar Majumdar. “Equivalence of Games with Probabilistic Uncertainty and Partial Observation Games,” 7561:385–99. Springer, 2012. https://doi.org/10.1007/978-3-642-33386-6_30."},"page":"385 - 399","date_published":"2012-06-01T00:00:00Z","scopus_import":1,"day":"01","_id":"2947","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Equivalence of games with probabilistic uncertainty and partial observation games","intvolume":" 7561","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We introduce games with probabilistic uncertainty, a model for controller synthesis in which the controller observes the state through imprecise sensors that provide correct information about the current state with a fixed probability. That is, in each step, the sensors return an observed state, and given the observed state, there is a probability distribution (due to the estimation error) over the actual current state. The controller must base its decision on the observed state (rather than the actual current state, which it does not know). On the other hand, we assume that the environment can perfectly observe the current state. We show that controller synthesis for qualitative ω-regular objectives in our model can be reduced in polynomial time to standard partial-observation stochastic games, and vice-versa. As a consequence we establish the precise decidability frontier for the new class of games, and establish optimal complexity results for all the decidable problems."}]},{"author":[{"full_name":"Girard, Jean","last_name":"Girard","first_name":"Jean"},{"full_name":"Moussion, Christine","first_name":"Christine","last_name":"Moussion","id":"3356F664-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Förster, Reinhold","first_name":"Reinhold","last_name":"Förster"}],"date_created":"2018-12-11T12:00:29Z","date_updated":"2021-01-12T07:39:57Z","oa_version":"None","volume":12,"acknowledgement":"We thank M. Sixt and A. Peixoto for helpful comments on the manuscript. Work in the laboratory of J.-P.G. is supported by grants from Fondation ARC pour la Recherche sur le Cancer, Agence Nationale de la Recherche (ANR), Institut National du Cancer (INCA), Fondation RITC and Région Midi-Pyrénées. Research by R.F. is supported by Deutsche Forschungsgemeinschaft (DFG) grants SFB621-A1, SFB738-B5, SFB587-B3, SFB900-B1 and KFO 250-FO 334/2-1. We regret that, owing to space limitations, we could not always quote the work of colleagues who have contributed to the field.","_id":"2945","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","status":"public","publication_status":"published","title":"HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes","publisher":"Nature Publishing Group","intvolume":" 12","department":[{"_id":"MiSi"}],"abstract":[{"text":"In search of foreign antigens, lymphocytes recirculate from the blood, through lymph nodes, into lymphatics and back to the blood. Dendritic cells also migrate to lymph nodes for optimal interaction with lymphocytes. This continuous trafficking of immune cells into and out of lymph nodes is essential for immune surveillance of foreign invaders. In this article, we review our current understanding of the functions of high endothelial venules (HEVs), stroma and lymphatics in the entry, positioning and exit of immune cells in lymph nodes during homeostasis, and we highlight the unexpected role of dendritic cells in the control of lymphocyte homing through HEVs.","lang":"eng"}],"issue":"11","publist_id":"3787","type":"journal_article","doi":"10.1038/nri3298","date_published":"2012-11-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Nature Reviews Immunology","citation":{"mla":"Girard, Jean, et al. “HEVs, Lymphatics and Homeostatic Immune Cell Trafficking in Lymph Nodes.” Nature Reviews Immunology, vol. 12, no. 11, Nature Publishing Group, 2012, pp. 762–73, doi:10.1038/nri3298.","short":"J. Girard, C. Moussion, R. Förster, Nature Reviews Immunology 12 (2012) 762–773.","chicago":"Girard, Jean, Christine Moussion, and Reinhold Förster. “HEVs, Lymphatics and Homeostatic Immune Cell Trafficking in Lymph Nodes.” Nature Reviews Immunology. Nature Publishing Group, 2012. https://doi.org/10.1038/nri3298.","ama":"Girard J, Moussion C, Förster R. HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes. Nature Reviews Immunology. 2012;12(11):762-773. doi:10.1038/nri3298","ista":"Girard J, Moussion C, Förster R. 2012. HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes. Nature Reviews Immunology. 12(11), 762–773.","ieee":"J. Girard, C. Moussion, and R. Förster, “HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes,” Nature Reviews Immunology, vol. 12, no. 11. Nature Publishing Group, pp. 762–773, 2012.","apa":"Girard, J., Moussion, C., & Förster, R. (2012). HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes. Nature Reviews Immunology. Nature Publishing Group. https://doi.org/10.1038/nri3298"},"quality_controlled":"1","page":"762 - 773","day":"01","month":"11","scopus_import":1},{"quality_controlled":"1","page":"1471 - 1472","publication":"Nature Neuroscience","main_file_link":[{"url":"http://www.mrcbndu.ox.ac.uk/publications/medial-entorhinal-cortex-keeps"}],"citation":{"ieee":"D. Dupret and J. L. Csicsvari, “The medial entorhinal cortex keeps Up,” Nature Neuroscience, vol. 15, no. 11. Nature Publishing Group, pp. 1471–1472, 2012.","apa":"Dupret, D., & Csicsvari, J. L. (2012). The medial entorhinal cortex keeps Up. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3245","ista":"Dupret D, Csicsvari JL. 2012. The medial entorhinal cortex keeps Up. Nature Neuroscience. 15(11), 1471–1472.","ama":"Dupret D, Csicsvari JL. The medial entorhinal cortex keeps Up. Nature Neuroscience. 2012;15(11):1471-1472. doi:10.1038/nn.3245","chicago":"Dupret, David, and Jozsef L Csicsvari. “The Medial Entorhinal Cortex Keeps Up.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3245.","short":"D. Dupret, J.L. Csicsvari, Nature Neuroscience 15 (2012) 1471–1472.","mla":"Dupret, David, and Jozsef L. Csicsvari. “The Medial Entorhinal Cortex Keeps Up.” Nature Neuroscience, vol. 15, no. 11, Nature Publishing Group, 2012, pp. 1471–72, doi:10.1038/nn.3245."},"language":[{"iso":"eng"}],"date_published":"2012-11-01T00:00:00Z","doi":"10.1038/nn.3245","scopus_import":1,"day":"01","month":"11","title":"The medial entorhinal cortex keeps Up","status":"public","publication_status":"published","department":[{"_id":"JoCs"}],"intvolume":" 15","publisher":"Nature Publishing Group","year":"2012","_id":"2949","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:00:30Z","date_updated":"2021-01-12T07:39:59Z","oa_version":"None","volume":15,"author":[{"last_name":"Dupret","first_name":"David","full_name":"Dupret, David"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"type":"journal_article","issue":"11","publist_id":"3782"},{"quality_controlled":"1","project":[{"name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","grant_number":"SFB-TR3-TP10B"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471482/"}],"oa":1,"external_id":{"pmid":["23062335"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2012.08.039","month":"10","publication_status":"published","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publisher":"Biophysical","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (TR3/B10) and a European Research Council Advanced grant to P.J.\r\nWe thank H. Hu, S. J. Guzman, and C. Schmidt-Hieber for critically reading the manuscript, I. Koeva and F. Marr for technical support, and E. Kramberger for editorial assistance.\r\n","year":"2012","pmid":1,"date_updated":"2021-01-12T07:40:01Z","date_created":"2018-12-11T12:00:32Z","volume":103,"author":[{"first_name":"Alejandro","last_name":"Pernia-Andrade","id":"36963E98-F248-11E8-B48F-1D18A9856A87","full_name":"Pernia-Andrade, Alejandro"},{"full_name":"Goswami, Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","last_name":"Goswami","first_name":"Sarit"},{"full_name":"Stickler, Yvonne","id":"63B76600-E9CC-11E9-9B5F-82450873F7A1","last_name":"Stickler","first_name":"Yvonne"},{"first_name":"Ulrich","last_name":"Fröbe","full_name":"Fröbe, Ulrich"},{"full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"publist_id":"3774","page":"1429 - 1439","publication":"Biophysical Journal","citation":{"short":"A. Pernia-Andrade, S. Goswami, Y. Stickler, U. Fröbe, A. Schlögl, P.M. Jonas, Biophysical Journal 103 (2012) 1429–1439.","mla":"Pernia-Andrade, Alejandro, et al. “A Deconvolution Based Method with High Sensitivity and Temporal Resolution for Detection of Spontaneous Synaptic Currents in Vitro and in Vivo.” Biophysical Journal, vol. 103, no. 7, Biophysical, 2012, pp. 1429–39, doi:10.1016/j.bpj.2012.08.039.","chicago":"Pernia-Andrade, Alejandro, Sarit Goswami, Yvonne Stickler, Ulrich Fröbe, Alois Schlögl, and Peter M Jonas. “A Deconvolution Based Method with High Sensitivity and Temporal Resolution for Detection of Spontaneous Synaptic Currents in Vitro and in Vivo.” Biophysical Journal. Biophysical, 2012. https://doi.org/10.1016/j.bpj.2012.08.039.","ama":"Pernia-Andrade A, Goswami S, Stickler Y, Fröbe U, Schlögl A, Jonas PM. A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. 2012;103(7):1429-1439. doi:10.1016/j.bpj.2012.08.039","ieee":"A. Pernia-Andrade, S. Goswami, Y. Stickler, U. Fröbe, A. Schlögl, and P. M. Jonas, “A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo,” Biophysical Journal, vol. 103, no. 7. Biophysical, pp. 1429–1439, 2012.","apa":"Pernia-Andrade, A., Goswami, S., Stickler, Y., Fröbe, U., Schlögl, A., & Jonas, P. M. (2012). A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. Biophysical. https://doi.org/10.1016/j.bpj.2012.08.039","ista":"Pernia-Andrade A, Goswami S, Stickler Y, Fröbe U, Schlögl A, Jonas PM. 2012. A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. 103(7), 1429–1439."},"date_published":"2012-10-03T00:00:00Z","scopus_import":1,"day":"03","status":"public","title":"A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo","intvolume":" 103","_id":"2954","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Spontaneous postsynaptic currents (PSCs) provide key information about the mechanisms of synaptic transmission and the activity modes of neuronal networks. However, detecting spontaneous PSCs in vitro and in vivo has been challenging, because of the small amplitude, the variable kinetics, and the undefined time of generation of these events. Here, we describe a, to our knowledge, new method for detecting spontaneous synaptic events by deconvolution, using a template that approximates the average time course of spontaneous PSCs. A recorded PSC trace is deconvolved from the template, resulting in a series of delta-like functions. The maxima of these delta-like events are reliably detected, revealing the precise onset times of the spontaneous PSCs. Among all detection methods, the deconvolution-based method has a unique temporal resolution, allowing the detection of individual events in high-frequency bursts. Furthermore, the deconvolution-based method has a high amplitude resolution, because deconvolution can substantially increase the signal/noise ratio. When tested against previously published methods using experimental data, the deconvolution-based method was superior for spontaneous PSCs recorded in vivo. Using the high-resolution deconvolution-based detection algorithm, we show that the frequency of spontaneous excitatory postsynaptic currents in dentate gyrus granule cells is 4.5 times higher in vivo than in vitro."}],"issue":"7"},{"project":[{"grant_number":"I 930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","call_identifier":"FWF"}],"quality_controlled":"1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1126/science.1224143","month":"10","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","year":"2012","volume":338,"date_created":"2018-12-11T12:00:30Z","date_updated":"2023-02-21T17:02:44Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1403"}]},"author":[{"last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","full_name":"Behrndt, Martin"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"first_name":"Pedro","last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Felix","last_name":"Oswald","full_name":"Oswald, Felix"},{"last_name":"Roensch","first_name":"Julia","id":"4220E59C-F248-11E8-B48F-1D18A9856A87","full_name":"Roensch, Julia"},{"full_name":"Grill, Stephan","first_name":"Stephan","last_name":"Grill"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"publist_id":"3778","page":"257 - 260","citation":{"mla":"Behrndt, Martin, et al. “Forces Driving Epithelial Spreading in Zebrafish Gastrulation.” Science, vol. 338, no. 6104, American Association for the Advancement of Science, 2012, pp. 257–60, doi:10.1126/science.1224143.","short":"M. Behrndt, G. Salbreux, P. Campinho, R. Hauschild, F. Oswald, J. Roensch, S. Grill, C.-P.J. Heisenberg, Science 338 (2012) 257–260.","chicago":"Behrndt, Martin, Guillaume Salbreux, Pedro Campinho, Robert Hauschild, Felix Oswald, Julia Roensch, Stephan Grill, and Carl-Philipp J Heisenberg. “Forces Driving Epithelial Spreading in Zebrafish Gastrulation.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224143.","ama":"Behrndt M, Salbreux G, Campinho P, et al. Forces driving epithelial spreading in zebrafish gastrulation. Science. 2012;338(6104):257-260. doi:10.1126/science.1224143","ista":"Behrndt M, Salbreux G, Campinho P, Hauschild R, Oswald F, Roensch J, Grill S, Heisenberg C-PJ. 2012. Forces driving epithelial spreading in zebrafish gastrulation. Science. 338(6104), 257–260.","ieee":"M. Behrndt et al., “Forces driving epithelial spreading in zebrafish gastrulation,” Science, vol. 338, no. 6104. American Association for the Advancement of Science, pp. 257–260, 2012.","apa":"Behrndt, M., Salbreux, G., Campinho, P., Hauschild, R., Oswald, F., Roensch, J., … Heisenberg, C.-P. J. (2012). Forces driving epithelial spreading in zebrafish gastrulation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224143"},"publication":"Science","date_published":"2012-10-12T00:00:00Z","scopus_import":1,"day":"12","intvolume":" 338","status":"public","title":"Forces driving epithelial spreading in zebrafish gastrulation","_id":"2950","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","issue":"6104","abstract":[{"text":"Contractile actomyosin rings drive various fundamental morphogenetic processes ranging from cytokinesis to wound healing. Actomyosin rings are generally thought to function by circumferential contraction. Here, we show that the spreading of the enveloping cell layer (EVL) over the yolk cell during zebrafish gastrulation is driven by a contractile actomyosin ring. In contrast to previous suggestions, we find that this ring functions not only by circumferential contraction but also by a flow-friction mechanism. This generates a pulling force through resistance against retrograde actomyosin flow. EVL spreading proceeds normally in situations where circumferential contraction is unproductive, indicating that the flow-friction mechanism is sufficient. Thus, actomyosin rings can function in epithelial morphogenesis through a combination of cable-constriction and flow-friction mechanisms.","lang":"eng"}]},{"abstract":[{"text":"Differential cell adhesion and cortex tension are thought to drive cell sorting by controlling cell-cell contact formation. Here, we show that cell adhesion and cortex tension have different mechanical functions in controlling progenitor cell-cell contact formation and sorting during zebrafish gastrulation. Cortex tension controls cell-cell contact expansion by modulating interfacial tension at the contact. By contrast, adhesion has little direct function in contact expansion, but instead is needed to mechanically couple the cortices of adhering cells at their contacts, allowing cortex tension to control contact expansion. The coupling function of adhesion is mediated by E-cadherin and limited by the mechanical anchoring of E-cadherin to the cortex. Thus, cell adhesion provides the mechanical scaffold for cell cortex tension to drive cell sorting during gastrulation.","lang":"eng"}],"publist_id":"3777","issue":"6104","type":"journal_article","author":[{"full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","first_name":"Jean-Léon"},{"last_name":"Berthoumieux","first_name":"Hélène","full_name":"Berthoumieux, Hélène"},{"full_name":"Krens, Gabriel","last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"first_name":"Frank","last_name":"Julicher","full_name":"Julicher, Frank"},{"first_name":"Ewa","last_name":"Paluch","full_name":"Paluch, Ewa"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T07:40:00Z","date_created":"2018-12-11T12:00:31Z","oa_version":"None","volume":338,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2951","year":"2012","status":"public","publication_status":"published","title":"Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells","publisher":"American Association for the Advancement of Science","department":[{"_id":"CaHe"}],"intvolume":" 338","day":"12","month":"10","scopus_import":1,"doi":"10.1126/science.1225399","date_published":"2012-10-12T00:00:00Z","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"publication":"Science","citation":{"ama":"Maître J-L, Berthoumieux H, Krens G, et al. Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. 2012;338(6104):253-256. doi:10.1126/science.1225399","ista":"Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg C-PJ. 2012. Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. 338(6104), 253–256.","apa":"Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch, E., & Heisenberg, C.-P. J. (2012). Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1225399","ieee":"J.-L. Maître et al., “Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells,” Science, vol. 338, no. 6104. American Association for the Advancement of Science, pp. 253–256, 2012.","mla":"Maître, Jean-Léon, et al. “Adhesion Functions in Cell Sorting by Mechanically Coupling the Cortices of Adhering Cells.” Science, vol. 338, no. 6104, American Association for the Advancement of Science, 2012, pp. 253–56, doi:10.1126/science.1225399.","short":"J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Science 338 (2012) 253–256.","chicago":"Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux, Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Adhesion Functions in Cell Sorting by Mechanically Coupling the Cortices of Adhering Cells.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1225399."},"quality_controlled":"1","page":"253 - 256"},{"abstract":[{"text":"Body axis elongation represents a common and fundamental morphogenetic process in development. A key mechanism triggering body axis elongation without additional growth is convergent extension (CE), whereby a tissue undergoes simultaneous narrowing and extension. Both collective cell migration and cell intercalation are thought to drive CE and are used to different degrees in various species as they elongate their body axis. Here, we provide an overview of CE as a general strategy for body axis elongation and discuss conserved and divergent mechanisms underlying CE among different species.","lang":"eng"}],"issue":"21","publist_id":"3776","type":"journal_article","date_updated":"2021-01-12T07:40:00Z","date_created":"2018-12-11T12:00:31Z","oa_version":"None","volume":139,"author":[{"first_name":"Masazumi","last_name":"Tada","full_name":"Tada, Masazumi"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"publication_status":"published","status":"public","title":"Convergent extension Using collective cell migration and cell intercalation to shape embryos","department":[{"_id":"CaHe"}],"intvolume":" 139","publisher":"Company of Biologists","_id":"2952","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"M.T. is supported by the UK Medical Research Council (MRC) and Royal Society and C.-P.H. by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF), Deutsche Forschungsgemeinschaft (DFG) and Institute of Science and Technology Austria. ","year":"2012","month":"11","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2012-11-01T00:00:00Z","doi":"10.1242/dev.073007","quality_controlled":"1","page":"3897 - 3904","publication":"Development","citation":{"chicago":"Tada, Masazumi, and Carl-Philipp J Heisenberg. “Convergent Extension Using Collective Cell Migration and Cell Intercalation to Shape Embryos.” Development. Company of Biologists, 2012. https://doi.org/10.1242/dev.073007.","mla":"Tada, Masazumi, and Carl-Philipp J. Heisenberg. “Convergent Extension Using Collective Cell Migration and Cell Intercalation to Shape Embryos.” Development, vol. 139, no. 21, Company of Biologists, 2012, pp. 3897–904, doi:10.1242/dev.073007.","short":"M. Tada, C.-P.J. Heisenberg, Development 139 (2012) 3897–3904.","ista":"Tada M, Heisenberg C-PJ. 2012. Convergent extension Using collective cell migration and cell intercalation to shape embryos. Development. 139(21), 3897–3904.","apa":"Tada, M., & Heisenberg, C.-P. J. (2012). Convergent extension Using collective cell migration and cell intercalation to shape embryos. Development. Company of Biologists. https://doi.org/10.1242/dev.073007","ieee":"M. Tada and C.-P. J. Heisenberg, “Convergent extension Using collective cell migration and cell intercalation to shape embryos,” Development, vol. 139, no. 21. Company of Biologists, pp. 3897–3904, 2012.","ama":"Tada M, Heisenberg C-PJ. Convergent extension Using collective cell migration and cell intercalation to shape embryos. Development. 2012;139(21):3897-3904. doi:10.1242/dev.073007"}},{"language":[{"iso":"eng"}],"date_published":"2012-10-01T00:00:00Z","doi":"10.1016/j.ceb.2012.09.002","quality_controlled":"1","page":"559 - 561","publication":"Current Opinion in Cell Biology","citation":{"chicago":"Heisenberg, Carl-Philipp J, and Reinhard Fässler. “Cell-Cell Adhesion and Extracellular Matrix Diversity Counts.” Current Opinion in Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ceb.2012.09.002.","mla":"Heisenberg, Carl-Philipp J., and Reinhard Fässler. “Cell-Cell Adhesion and Extracellular Matrix Diversity Counts.” Current Opinion in Cell Biology, vol. 24, no. 5, Elsevier, 2012, pp. 559–61, doi:10.1016/j.ceb.2012.09.002.","short":"C.-P.J. Heisenberg, R. Fässler, Current Opinion in Cell Biology 24 (2012) 559–561.","ista":"Heisenberg C-PJ, Fässler R. 2012. Cell-cell adhesion and extracellular matrix diversity counts. Current Opinion in Cell Biology. 24(5), 559–561.","apa":"Heisenberg, C.-P. J., & Fässler, R. (2012). Cell-cell adhesion and extracellular matrix diversity counts. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2012.09.002","ieee":"C.-P. J. Heisenberg and R. Fässler, “Cell-cell adhesion and extracellular matrix diversity counts,” Current Opinion in Cell Biology, vol. 24, no. 5. Elsevier, pp. 559–561, 2012.","ama":"Heisenberg C-PJ, Fässler R. Cell-cell adhesion and extracellular matrix diversity counts. Current Opinion in Cell Biology. 2012;24(5):559-561. doi:10.1016/j.ceb.2012.09.002"},"month":"10","day":"01","scopus_import":1,"date_updated":"2021-01-12T07:40:01Z","date_created":"2018-12-11T12:00:31Z","oa_version":"None","volume":24,"author":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Fässler, Reinhard","last_name":"Fässler","first_name":"Reinhard"}],"publication_status":"published","status":"public","title":"Cell-cell adhesion and extracellular matrix diversity counts","publisher":"Elsevier","intvolume":" 24","department":[{"_id":"CaHe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2953","year":"2012","issue":"5","publist_id":"3773","type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The activity of hippocampal pyramidal cells reflects both the current position of the animal and information related to its current behavior. Here we investigated whether single hippocampal neurons can encode several independent features defining trials during a memory task. We also tested whether task-related information is represented by partial remapping of the place cell population or, instead, via firing rate modulation of spatially stable place cells. To address these two questions, the activity of hippocampal neurons was recorded in rats performing a conditional discrimination task on a modified T-maze in which the identity of a food reward guided behavior. When the rat was on the central arm of the maze, the firing rate of pyramidal cells changed depending on two independent factors: (1) the identity of the food reward given to the animal and (2) the previous location of the animal on the maze. Importantly, some pyramidal cells encoded information relative to both factors. This trial-type specific and retrospective coding did not interfere with the spatial representation of the maze: hippocampal cells had stable place fields and their theta-phase precession profiles were unaltered during the task, indicating that trial-related information was encoded via rate remapping. During error trials, encoding of both trial-related information and spatial location was impaired. Finally, we found that pyramidal cells also encode trial-related information via rate remapping during the continuous version of the rewarded alternation task without delays. These results suggest that hippocampal neurons can encode several task-related cognitive aspects via rate remapping."}],"issue":"42","title":"Hippocampal place cells can encode multiple trial-dependent features through rate remapping","status":"public","intvolume":" 32","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2958","oa_version":"Submitted Version","scopus_import":1,"day":"17","page":"14752 - 14766","publication":"Journal of Neuroscience","citation":{"ista":"Allen K, Rawlins JN, Bannerman D, Csicsvari JL. 2012. Hippocampal place cells can encode multiple trial-dependent features through rate remapping. Journal of Neuroscience. 32(42), 14752–14766.","apa":"Allen, K., Rawlins, J. N., Bannerman, D., & Csicsvari, J. L. (2012). Hippocampal place cells can encode multiple trial-dependent features through rate remapping. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.6175-11.2012","ieee":"K. Allen, J. N. Rawlins, D. Bannerman, and J. L. Csicsvari, “Hippocampal place cells can encode multiple trial-dependent features through rate remapping,” Journal of Neuroscience, vol. 32, no. 42. Society for Neuroscience, pp. 14752–14766, 2012.","ama":"Allen K, Rawlins JN, Bannerman D, Csicsvari JL. Hippocampal place cells can encode multiple trial-dependent features through rate remapping. Journal of Neuroscience. 2012;32(42):14752-14766. doi:10.1523/JNEUROSCI.6175-11.2012","chicago":"Allen, Kevin, J Nick Rawlins, David Bannerman, and Jozsef L Csicsvari. “Hippocampal Place Cells Can Encode Multiple Trial-Dependent Features through Rate Remapping.” Journal of Neuroscience. Society for Neuroscience, 2012. https://doi.org/10.1523/JNEUROSCI.6175-11.2012.","mla":"Allen, Kevin, et al. “Hippocampal Place Cells Can Encode Multiple Trial-Dependent Features through Rate Remapping.” Journal of Neuroscience, vol. 32, no. 42, Society for Neuroscience, 2012, pp. 14752–66, doi:10.1523/JNEUROSCI.6175-11.2012.","short":"K. Allen, J.N. Rawlins, D. Bannerman, J.L. Csicsvari, Journal of Neuroscience 32 (2012) 14752–14766."},"date_published":"2012-10-17T00:00:00Z","publist_id":"3768","ec_funded":1,"publication_status":"published","publisher":"Society for Neuroscience","department":[{"_id":"JoCs"}],"year":"2012","acknowledgement":"J.C. was supported by a MRC Intramural Programme Grant (U138197111) and a European Research Council Starter Grant (281511). K.A. held a Wellcome Trust PhD studentship and a Humboldt Research Fellowship for Postdoctoral Researchers. D.M.B. was supported by Wellcome Trust Senior Fellowships (074385 and 087736).","pmid":1,"date_updated":"2021-01-12T07:40:03Z","date_created":"2018-12-11T12:00:33Z","volume":32,"author":[{"last_name":"Allen","first_name":"Kevin","full_name":"Allen, Kevin"},{"full_name":"Rawlins, J Nick","last_name":"Rawlins","first_name":"J Nick"},{"full_name":"Bannerman, David","last_name":"Bannerman","first_name":"David"},{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"month":"10","quality_controlled":"1","project":[{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"}],"external_id":{"pmid":["23077060"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531717/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.6175-11.2012"},{"month":"02","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1012.2643"}],"oa":1,"quality_controlled":"1","doi":"10.1214/11-AOS957","language":[{"iso":"eng"}],"publist_id":"3767","acknowledgement":"I wish to thank Bernd Sturmfels for many helpful discus- sions and Steffen Lauritzen for introducing me to the problem of the existence of the MLE in Gaussian graphical models. I would also like to thank two referees who provided helpful comments on the original version of this paper.\r\n","year":"2012","publisher":"Institute of Mathematical Statistics","department":[{"_id":"CaUh"}],"publication_status":"published","author":[{"full_name":"Uhler, Caroline","first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216"}],"volume":40,"date_created":"2018-12-11T12:00:33Z","date_updated":"2021-01-12T07:40:04Z","scopus_import":1,"day":"01","citation":{"short":"C. Uhler, Annals of Statistics 40 (2012) 238–261.","mla":"Uhler, Caroline. “Geometry of Maximum Likelihood Estimation in Gaussian Graphical Models.” Annals of Statistics, vol. 40, no. 1, Institute of Mathematical Statistics, 2012, pp. 238–61, doi:10.1214/11-AOS957.","chicago":"Uhler, Caroline. “Geometry of Maximum Likelihood Estimation in Gaussian Graphical Models.” Annals of Statistics. Institute of Mathematical Statistics, 2012. https://doi.org/10.1214/11-AOS957.","ama":"Uhler C. Geometry of maximum likelihood estimation in Gaussian graphical models. Annals of Statistics. 2012;40(1):238-261. doi:10.1214/11-AOS957","apa":"Uhler, C. (2012). Geometry of maximum likelihood estimation in Gaussian graphical models. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/11-AOS957","ieee":"C. Uhler, “Geometry of maximum likelihood estimation in Gaussian graphical models,” Annals of Statistics, vol. 40, no. 1. Institute of Mathematical Statistics, pp. 238–261, 2012.","ista":"Uhler C. 2012. Geometry of maximum likelihood estimation in Gaussian graphical models. Annals of Statistics. 40(1), 238–261."},"publication":"Annals of Statistics","page":"238 - 261","date_published":"2012-02-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"We study maximum likelihood estimation in Gaussian graphical models from a geometric point of view. An algebraic elimination criterion allows us to find exact lower bounds on the number of observations needed to ensure that the maximum likelihood estimator (MLE) exists with probability one. This is applied to bipartite graphs, grids and colored graphs. We also study the ML degree, and we present the first instance of a graph for which the MLE exists with probability one, even when the number of observations equals the treewidth.","lang":"eng"}],"_id":"2959","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 40","title":"Geometry of maximum likelihood estimation in Gaussian graphical models","status":"public","oa_version":"Preprint"},{"scopus_import":1,"day":"15","has_accepted_license":"1","publication":"BMC Ecology","citation":{"ista":"Cremer S, Suefuji M, Schrempf A, Heinze J. 2012. The dynamics of male-male competition in Cardiocondyla obscurior ants. BMC Ecology. 12, 7.","ieee":"S. Cremer, M. Suefuji, A. Schrempf, and J. Heinze, “The dynamics of male-male competition in Cardiocondyla obscurior ants,” BMC Ecology, vol. 12. BioMed Central, 2012.","apa":"Cremer, S., Suefuji, M., Schrempf, A., & Heinze, J. (2012). The dynamics of male-male competition in Cardiocondyla obscurior ants. BMC Ecology. BioMed Central. https://doi.org/10.1186/1472-6785-12-7","ama":"Cremer S, Suefuji M, Schrempf A, Heinze J. The dynamics of male-male competition in Cardiocondyla obscurior ants. BMC Ecology. 2012;12. doi:10.1186/1472-6785-12-7","chicago":"Cremer, Sylvia, Masaki Suefuji, Alexandra Schrempf, and Jürgen Heinze. “The Dynamics of Male-Male Competition in Cardiocondyla Obscurior Ants.” BMC Ecology. BioMed Central, 2012. https://doi.org/10.1186/1472-6785-12-7.","mla":"Cremer, Sylvia, et al. “The Dynamics of Male-Male Competition in Cardiocondyla Obscurior Ants.” BMC Ecology, vol. 12, 7, BioMed Central, 2012, doi:10.1186/1472-6785-12-7.","short":"S. Cremer, M. Suefuji, A. Schrempf, J. Heinze, BMC Ecology 12 (2012)."},"date_published":"2012-06-15T00:00:00Z","type":"journal_article","abstract":[{"text":"Background: The outcome of male-male competition can be predicted from the relative fighting qualities of the opponents, which often depend on their age. In insects, freshly emerged and still sexually inactive males are morphologically indistinct from older, sexually active males. These young inactive males may thus be easy targets for older males if they cannot conceal themselves from their attacks. The ant Cardiocondyla obscurior is characterised by lethal fighting between wingless (" ergatoid" ) males. Here, we analyse for how long young males are defenceless after eclosion, and how early adult males can detect the presence of rival males.Results: We found that old ergatoid males consistently won fights against ergatoid males younger than two days. Old males did not differentiate between different types of unpigmented pupae several days before emergence, but had more frequent contact to ready-to-eclose pupae of female sexuals and winged males than of workers and ergatoid males. In rare cases, old ergatoid males displayed alleviated biting of pigmented ergatoid male pupae shortly before adult eclosion, as well as copulation attempts to dark pupae of female sexuals and winged males. Ergatoid male behaviour may be promoted by a closer similarity of the chemical profile of ready-to-eclose pupae to the profile of adults than that of young pupae several days prior to emergence.Conclusion: Young ergatoid males of C. obscurior would benefit greatly by hiding their identity from older, resident males, as they are highly vulnerable during the first two days of their adult lives. In contrast to the winged males of the same species, which are able to prevent ergatoid male attacks by chemical female mimicry, young ergatoids do not seem to be able to produce a protective chemical profile. Conflicts in male-male competition between ergatoid males of different age thus seem to be resolved in favour of the older males. This might represent selection at the colony level rather than the individual level. © 2012 Cremer et al.; licensee BioMed Central Ltd.","lang":"eng"}],"title":"The dynamics of male-male competition in Cardiocondyla obscurior ants","ddc":["570"],"status":"public","intvolume":" 12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2966","oa_version":"Published Version","file":[{"file_name":"IST-2012-94-v1+1_1472-6785-12-7.pdf","access_level":"open_access","creator":"system","file_size":489994,"content_type":"application/pdf","file_id":"4706","relation":"main_file","date_updated":"2020-07-14T12:45:57Z","date_created":"2018-12-12T10:08:44Z","checksum":"03d004bdff3724fb1627e3f5004bad80"}],"pubrep_id":"94","month":"06","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/1472-6785-12-7","article_number":"7","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:45:57Z","publist_id":"3753","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"SyCr"}],"year":"2012","date_created":"2018-12-11T12:00:35Z","date_updated":"2021-01-12T07:40:07Z","volume":12,"author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"},{"first_name":"Masaki","last_name":"Suefuji","full_name":"Suefuji, Masaki"},{"first_name":"Alexandra","last_name":"Schrempf","full_name":"Schrempf, Alexandra"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"}]},{"day":"01","scopus_import":1,"date_published":"2012-11-01T00:00:00Z","publication":"Genetics","citation":{"ista":"Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.","apa":"Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.112.143164","ieee":"S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing summary statistics in approximate Bayesian computation,” Genetics, vol. 192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.","ama":"Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047. doi:10.1534/genetics.112.143164","chicago":"Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics. Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164.","mla":"Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.","short":"S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047."},"page":"1027 - 1047","abstract":[{"lang":"eng","text":"The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates."}],"issue":"3","type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2962","title":"A novel approach for choosing summary statistics in approximate Bayesian computation","status":"public","intvolume":" 192","month":"11","doi":"10.1534/genetics.112.143164","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/","open_access":"1"}],"oa":1,"external_id":{"pmid":["22960215"]},"quality_controlled":"1","publist_id":"3763","author":[{"full_name":"Aeschbacher, Simon","last_name":"Aeschbacher","first_name":"Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Beaumont, Mark","first_name":"Mark","last_name":"Beaumont"},{"first_name":"Andreas","last_name":"Futschik","full_name":"Futschik, Andreas"}],"date_created":"2018-12-11T12:00:34Z","date_updated":"2021-01-12T07:40:05Z","volume":192,"year":"2012","pmid":1,"publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":" http://hdl.handle.net/10760/17625","open_access":"1"}],"oa":1,"language":[{"iso":"ger"}],"month":"09","publisher":"VÖB","department":[{"_id":"E-Lib"}],"publication_status":"published","year":"2012","volume":65,"date_updated":"2021-01-12T07:40:07Z","date_created":"2018-12-11T12:00:35Z","author":[{"orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","first_name":"Patrick","full_name":"Danowski, Patrick"}],"publist_id":"3754","file_date_updated":"2020-07-14T12:45:57Z","page":"200 - 212","citation":{"ista":"Danowski P. 2012. Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 65(2), 200–212.","apa":"Danowski, P. (2012). Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB.","ieee":"P. Danowski, “Kontext Open Access: Creative Commons,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 65, no. 2. VÖB, pp. 200–212, 2012.","ama":"Danowski P. Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2012;65(2):200-212.","chicago":"Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2012.","mla":"Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 65, no. 2, VÖB, 2012, pp. 200–12.","short":"P. Danowski, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 65 (2012) 200–212."},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","date_published":"2012-09-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 65","title":"Kontext Open Access: Creative Commons","status":"public","ddc":["020"],"_id":"2965","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2012-95-v1+1_sp-beitrag_danowski_kontext_open_access_creative_commons.pdf","file_size":503345,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4703","checksum":"162eea47d9d840c26b496ba6ae4d1c09","date_updated":"2020-07-14T12:45:57Z","date_created":"2018-12-12T10:08:42Z"}],"pubrep_id":"95","popular_science":"1","type":"journal_article","issue":"2","abstract":[{"text":"Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).","lang":"eng"}]},{"language":[{"iso":"eng"}],"doi":"10.1016/j.beproc.2012.09.006","date_published":"2012-11-01T00:00:00Z","page":"262 - 266","quality_controlled":"1","citation":{"mla":"Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song by Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural Processes, vol. 91, no. 3, Elsevier, 2012, pp. 262–66, doi:10.1016/j.beproc.2012.09.006.","short":"F. Jesse, K. Riebel, Behavioural Processes 91 (2012) 262–266.","chicago":"Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song by Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural Processes. Elsevier, 2012. https://doi.org/10.1016/j.beproc.2012.09.006.","ama":"Jesse F, Riebel K. Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. 2012;91(3):262-266. doi:10.1016/j.beproc.2012.09.006","ista":"Jesse F, Riebel K. 2012. Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. 91(3), 262–266.","apa":"Jesse, F., & Riebel, K. (2012). Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. Elsevier. https://doi.org/10.1016/j.beproc.2012.09.006","ieee":"F. Jesse and K. Riebel, “Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata,” Behavioural Processes, vol. 91, no. 3. Elsevier, pp. 262–266, 2012."},"publication":"Behavioural Processes","day":"01","month":"11","volume":91,"oa_version":"None","date_created":"2018-12-11T12:00:35Z","date_updated":"2021-01-12T07:40:06Z","author":[{"first_name":"Fabienne","last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","full_name":"Jesse, Fabienne"},{"full_name":"Riebel, Katharina","first_name":"Katharina","last_name":"Riebel"}],"department":[{"_id":"JoBo"}],"publisher":"Elsevier","intvolume":" 91","status":"public","title":"Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata","publication_status":"published","_id":"2963","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","publist_id":"3756","issue":"3","abstract":[{"lang":"eng","text":"Zebra finches are an ubiquitous model system for the study of vocal learning in animal communication. Their song has been well described, but its possible function(s) in social communication are only partly understood. The so-called ‘directed song’ is a high-intensity, high-performance song given during courtship in close proximity to the female, which is known to mediate mate choice and mating. However, this singing mode constitutes only a fraction of zebra finch males’ prolific song output. Potential communicative functions of their second, ‘undirected’ singing mode remain unresolved in the face of contradicting reports of both facilitating and inhibiting effects of social company on singing. We addressed this issue by experimentally manipulating social contexts in a within-subject design, comparing a solo versus male or female only company condition, each lasting for 24 hours. Males’ total song output was significantly higher when a conspecific was in audible and visible distance than when they were alone. Male and female company had an equally facilitating effect on song output. Our findings thus indicate that singing motivation is facilitated rather than inhibited by social company, suggesting that singing in zebra finches might function both in inter- and intrasexual communication. "}],"type":"journal_article"},{"month":"12","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"conference":{"start_date":"2012-12-02","location":"Beijing, China","end_date":"2012-12-06","name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"doi":"10.1007/978-3-642-34961-4_40","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:58Z","publist_id":"3730","ec_funded":1,"year":"2012","acknowledgement":"We are grateful to Petros Mol for helpful discussions on the reduction for the hardness of the xLPN problem.\r\n","publication_status":"published","editor":[{"first_name":"Xiaoyun","last_name":"Wang","full_name":"Wang, Xiaoyun"},{"full_name":"Sako, Kazue","first_name":"Kazue","last_name":"Sako"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"author":[{"full_name":"Jain, Abhishek","first_name":"Abhishek","last_name":"Jain"},{"full_name":"Krenn, Stephan","last_name":"Krenn","first_name":"Stephan","orcid":"0000-0003-2835-9093","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Tentes, Aris","first_name":"Aris","last_name":"Tentes"}],"date_updated":"2021-01-12T07:40:11Z","date_created":"2018-12-11T12:00:38Z","volume":7658,"scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"short":"A. Jain, S. Krenn, K.Z. Pietrzak, A. Tentes, in:, X. Wang, K. Sako (Eds.), Springer, 2012, pp. 663–680.","mla":"Jain, Abhishek, et al. Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise. Edited by Xiaoyun Wang and Kazue Sako, vol. 7658, Springer, 2012, pp. 663–80, doi:10.1007/978-3-642-34961-4_40.","chicago":"Jain, Abhishek, Stephan Krenn, Krzysztof Z Pietrzak, and Aris Tentes. “Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise.” edited by Xiaoyun Wang and Kazue Sako, 7658:663–80. Springer, 2012. https://doi.org/10.1007/978-3-642-34961-4_40.","ama":"Jain A, Krenn S, Pietrzak KZ, Tentes A. Commitments and efficient zero knowledge proofs from learning parity with noise. In: Wang X, Sako K, eds. Vol 7658. Springer; 2012:663-680. doi:10.1007/978-3-642-34961-4_40","apa":"Jain, A., Krenn, S., Pietrzak, K. Z., & Tentes, A. (2012). Commitments and efficient zero knowledge proofs from learning parity with noise. In X. Wang & K. Sako (Eds.) (Vol. 7658, pp. 663–680). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China: Springer. https://doi.org/10.1007/978-3-642-34961-4_40","ieee":"A. Jain, S. Krenn, K. Z. Pietrzak, and A. Tentes, “Commitments and efficient zero knowledge proofs from learning parity with noise,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China, 2012, vol. 7658, pp. 663–680.","ista":"Jain A, Krenn S, Pietrzak KZ, Tentes A. 2012. Commitments and efficient zero knowledge proofs from learning parity with noise. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 7658, 663–680."},"page":"663 - 680","date_published":"2012-12-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We construct a perfectly binding string commitment scheme whose security is based on the learning parity with noise (LPN) assumption, or equivalently, the hardness of decoding random linear codes. Our scheme not only allows for a simple and efficient zero-knowledge proof of knowledge for committed values (essentially a Σ-protocol), but also for such proofs showing any kind of relation amongst committed values, i.e. proving that messages m_0,...,m_u, are such that m_0=C(m_1,...,m_u) for any circuit C.\r\n\r\nTo get soundness which is exponentially small in a security parameter t, and when the zero-knowledge property relies on the LPN problem with secrets of length l, our 3 round protocol has communication complexity O(t|C|l log(l)) and computational complexity of O(t|C|l) bit operations. The hidden constants are small, and the computation consists mostly of computing inner products of bit-vectors."}],"_id":"2974","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Commitments and efficient zero knowledge proofs from learning parity with noise","ddc":["004","005"],"intvolume":" 7658","pubrep_id":"721","file":[{"relation":"main_file","file_id":"5048","date_created":"2018-12-12T10:14:00Z","date_updated":"2020-07-14T12:45:58Z","checksum":"ab879537385efc4cb4203e7ef0fea17b","file_name":"IST-2016-721-v1+1_513.pdf","access_level":"open_access","content_type":"application/pdf","file_size":482570,"creator":"system"}],"oa_version":"Submitted Version"},{"oa_version":"Submitted Version","_id":"2969","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","title":"Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling","status":"public","issue":"41","abstract":[{"lang":"eng","text":"The coupling between presynaptic Ca^(2+) channels and Ca^(2+) sensors of exocytosis is a key determinant of synaptic transmission. Evoked release from parvalbumin (PV)-expressing interneurons is triggered by nanodomain coupling of P/Q-type Ca^(2+) channels, whereas release from cholecystokinin (CCK)-containing interneurons is generated by microdomain coupling of N-type channels. Nanodomain coupling has several functional advantages, including speed and efficacy of transmission. One potential disadvantage is that stochastic\r\nopening of presynaptic Ca^(2+) channels may trigger spontaneous transmitter release. We addressed this possibility in rat hippocampal\r\ngranule cells, which receive converging inputs from different inhibitory sources. Both reduction of extracellular Ca^(2+) concentration and the unselective Ca^(2+) channel blocker Cd^(2+) reduced the frequency of miniature IPSCs (mIPSCs) in granule cells by ~50%, suggesting that the opening of presynaptic Ca^(2+) channels contributes to spontaneous release. Application of the selective P/Q-type Ca^(2+) channel blocker\r\nω-agatoxin IVa had no detectable effects, whereas both the N-type blocker ω-conotoxin GVIa and the L-type blocker nimodipine reduced\r\nmIPSC frequency. Furthermore, both the fast Ca^(2+) chelator BAPTA-AM and the slow chelator EGTA-AM reduced the mIPSC frequency,\r\nsuggesting that Ca^(2+)-dependent spontaneous release is triggered by microdomain rather than nanodomain coupling. The CB_(1) receptor\r\nagonist WIN 55212-2 also decreased spontaneous release; this effect was occluded by prior application of ω-conotoxin GVIa, suggesting that a major fraction of Ca^(2+)-dependent spontaneous release was generated at the terminals of CCK-expressing interneurons. Tonic inhibition generated by spontaneous opening of presynaptic N- and L-type Ca^(2+) channels may be important for hippocampal information processing.\r\n"}],"type":"journal_article","date_published":"2012-10-10T00:00:00Z","citation":{"chicago":"Goswami, Sarit, Iancu Bucurenciu, and Peter M Jonas. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” Journal of Neuroscience. Society for Neuroscience, 2012. https://doi.org/10.1523/JNEUROSCI.6104-11.2012.","mla":"Goswami, Sarit, et al. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” Journal of Neuroscience, vol. 32, no. 41, Society for Neuroscience, 2012, pp. 14294–304, doi:10.1523/JNEUROSCI.6104-11.2012.","short":"S. Goswami, I. Bucurenciu, P.M. Jonas, Journal of Neuroscience 32 (2012) 14294–14304.","ista":"Goswami S, Bucurenciu I, Jonas PM. 2012. Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. 32(41), 14294–14304.","ieee":"S. Goswami, I. Bucurenciu, and P. M. Jonas, “Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling,” Journal of Neuroscience, vol. 32, no. 41. Society for Neuroscience, pp. 14294–14304, 2012.","apa":"Goswami, S., Bucurenciu, I., & Jonas, P. M. (2012). Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.6104-11.2012","ama":"Goswami S, Bucurenciu I, Jonas PM. Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. 2012;32(41):14294-14304. doi:10.1523/JNEUROSCI.6104-11.2012"},"publication":"Journal of Neuroscience","page":"14294 - 14304","day":"10","scopus_import":1,"author":[{"id":"3A578F32-F248-11E8-B48F-1D18A9856A87","first_name":"Sarit","last_name":"Goswami","full_name":"Goswami, Sarit"},{"full_name":"Bucurenciu, Iancu","last_name":"Bucurenciu","first_name":"Iancu"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M"}],"volume":32,"date_created":"2018-12-11T12:00:36Z","date_updated":"2021-01-12T07:40:08Z","pmid":1,"year":"2012","acknowledgement":"This work was supported by grants from the Deutsche Forschungsgemeinschaft (TR 3/B10, Leibniz program, GSC-4 Spemann Graduate School) and the European Union (European Research Council Advanced Grant).","department":[{"_id":"PeJo"}],"publisher":"Society for Neuroscience","publication_status":"published","publist_id":"3744","doi":"10.1523/JNEUROSCI.6104-11.2012","language":[{"iso":"eng"}],"external_id":{"pmid":["23055500"]},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632771/","open_access":"1"}],"project":[{"name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","grant_number":"SFB-TR3-TP10B"}],"quality_controlled":"1","month":"10"},{"scopus_import":1,"month":"12","day":"01","quality_controlled":"1","page":"527 - 532","publication":"Current Opinion in Genetics & Development","citation":{"ama":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 2012;22(6):527-532. doi:10.1016/j.gde.2012.08.004","ista":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. 2012. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 22(6), 527–532.","apa":"Kicheva, A., Bollenbach, M. T., Wartlick, O., Julicher, F., & Gonzalez Gaitan, M. (2012). Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2012.08.004","ieee":"A. Kicheva, M. T. Bollenbach, O. Wartlick, F. Julicher, and M. Gonzalez Gaitan, “Investigating the principles of morphogen gradient formation: from tissues to cells,” Current Opinion in Genetics & Development, vol. 22, no. 6. Elsevier, pp. 527–532, 2012.","mla":"Kicheva, Anna, et al. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development, vol. 22, no. 6, Elsevier, 2012, pp. 527–32, doi:10.1016/j.gde.2012.08.004.","short":"A. Kicheva, M.T. Bollenbach, O. Wartlick, F. Julicher, M. Gonzalez Gaitan, Current Opinion in Genetics & Development 22 (2012) 527–532.","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ortrud Wartlick, Frank Julicher, and Marcos Gonzalez Gaitan. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.08.004."},"language":[{"iso":"eng"}],"doi":"10.1016/j.gde.2012.08.004","date_published":"2012-12-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. Theoretical descriptions have helped to explain how gradient shape is controlled by the rates of morphogen production, spreading and degradation. These effective rates have been measured using fluorescence recovery after photobleaching (FRAP) and photoactivation. To unravel which molecular events determine the effective rates, such tissue-level assays have been combined with genetic analysis, high-resolution assays, and models that take into account interactions with receptors, extracellular components and trafficking. Nevertheless, because of the natural and experimental data variability, and the underlying assumptions of transport models, it remains challenging to conclusively distinguish between cellular mechanisms.","lang":"eng"}],"publist_id":"3739","issue":"6","title":"Investigating the principles of morphogen gradient formation: from tissues to cells","status":"public","publication_status":"published","department":[{"_id":"ToBo"}],"publisher":"Elsevier","intvolume":" 22","_id":"2970","year":"2012","acknowledgement":"AK is currently supported by an MRC CDF. MGG and OW were supported by the Swiss National Science Foundation, grants from the Swiss SystemsX.ch initiative, LipidX-2008/011, an ERC advanced investigator grant and the Polish-Swiss research program.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:40:09Z","date_created":"2018-12-11T12:00:37Z","oa_version":"None","volume":22,"author":[{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"},{"full_name":"Wartlick, Ortrud","first_name":"Ortrud","last_name":"Wartlick"},{"full_name":"Julicher, Frank","last_name":"Julicher","first_name":"Frank"},{"last_name":"Gonzalez Gaitan","first_name":"Marcos","full_name":"Gonzalez Gaitan, Marcos"}]},{"_id":"2971","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","publication_status":"published","title":"Interactive labeling of image segmentation hierarchies","status":"public","department":[{"_id":"HeEd"}],"publisher":"Springer","intvolume":" 7476","author":[{"full_name":"Zankl, Georg","last_name":"Zankl","first_name":"Georg"},{"first_name":"Yll","last_name":"Haxhimusa","full_name":"Haxhimusa, Yll"},{"full_name":"Ion, Adrian","last_name":"Ion","first_name":"Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T07:40:10Z","date_created":"2018-12-11T12:00:37Z","volume":7476,"oa_version":"None","type":"conference","abstract":[{"lang":"eng","text":"We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. "}],"publist_id":"3737","citation":{"chicago":"Zankl, Georg, Yll Haxhimusa, and Adrian Ion. “Interactive Labeling of Image Segmentation Hierarchies,” 7476:11–20. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_2.","mla":"Zankl, Georg, et al. Interactive Labeling of Image Segmentation Hierarchies. Vol. 7476, Springer, 2012, pp. 11–20, doi:10.1007/978-3-642-32717-9_2.","short":"G. Zankl, Y. Haxhimusa, A. Ion, in:, Springer, 2012, pp. 11–20.","ista":"Zankl G, Haxhimusa Y, Ion A. 2012. Interactive labeling of image segmentation hierarchies. Pattern Recognition vol. 7476, 11–20.","apa":"Zankl, G., Haxhimusa, Y., & Ion, A. (2012). Interactive labeling of image segmentation hierarchies (Vol. 7476, pp. 11–20). Presented at the Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_2","ieee":"G. Zankl, Y. Haxhimusa, and A. Ion, “Interactive labeling of image segmentation hierarchies,” presented at the Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 11–20.","ama":"Zankl G, Haxhimusa Y, Ion A. Interactive labeling of image segmentation hierarchies. In: Vol 7476. Springer; 2012:11-20. doi:10.1007/978-3-642-32717-9_2"},"quality_controlled":"1","page":"11 - 20","conference":{"start_date":"2012-08-28","location":"Graz, Austria","end_date":"2012-08-31","name":"Pattern Recognition"},"date_published":"2012-01-01T00:00:00Z","doi":"10.1007/978-3-642-32717-9_2","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"01"},{"day":"13","month":"03","page":"678 - 685","quality_controlled":0,"citation":{"chicago":"Whitford, Ryan, Ana Fernandez, Ricardo Tejos, Amparo Pérez, Jürgen Kleine Vehn, Steffen Vanneste, Andrzej Drozdzecki, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2012.02.002.","mla":"Whitford, Ryan, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell, vol. 22, no. 3, Cell Press, 2012, pp. 678–85, doi:10.1016/j.devcel.2012.02.002.","short":"R. Whitford, A. Fernandez, R. Tejos, A. Pérez, J. Kleine Vehn, S. Vanneste, A. Drozdzecki, J. Leitner, L. Abas, M. Aerts, K. Hoogewijs, P. Baster, R. De Groodt, Y. Lin, V. Storme, Y. Van De Peer, T. Beeckman, A. Madder, B. Devreese, C. Luschnig, J. Friml, P. Hilson, Developmental Cell 22 (2012) 678–685.","ista":"Whitford R, Fernandez A, Tejos R, Pérez A, Kleine Vehn J, Vanneste S, Drozdzecki A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin Y, Storme V, Van De Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson P. 2012. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 22(3), 678–685.","ieee":"R. Whitford et al., “GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses,” Developmental Cell, vol. 22, no. 3. Cell Press, pp. 678–685, 2012.","apa":"Whitford, R., Fernandez, A., Tejos, R., Pérez, A., Kleine Vehn, J., Vanneste, S., … Hilson, P. (2012). GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2012.02.002","ama":"Whitford R, Fernandez A, Tejos R, et al. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 2012;22(3):678-685. doi:10.1016/j.devcel.2012.02.002"},"publication":"Developmental Cell","doi":"10.1016/j.devcel.2012.02.002","date_published":"2012-03-13T00:00:00Z","type":"journal_article","extern":1,"issue":"3","publist_id":"3594","abstract":[{"lang":"eng","text":"Growth and development are coordinated by an array of intercellular communications. Known plant signaling molecules include phytohormones and hormone peptides. Although both classes can be implicated in the same developmental processes, little is known about the interplay between phytohormone action and peptide signaling within the cellular microenvironment. We show that genes coding for small secretory peptides, designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin. The deregulation of the GLV function impairs the formation of auxin gradients and alters the reorientation of shoots and roots after a gravity stimulus. Specifically, the GLV signal modulates the trafficking dynamics of the auxin efflux carrier PIN-FORMED2 involved in root tropic responses and meristem organization. Our work links the local action of secretory peptides with phytohormone transport. Root growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients, and modulate auxin-dependent root responses to specific stimuli."}],"publisher":"Cell Press","intvolume":" 22","publication_status":"published","title":"GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses","status":"public","year":"2012","_id":"3105","volume":22,"date_created":"2018-12-11T12:01:25Z","date_updated":"2021-01-12T07:41:06Z","author":[{"last_name":"Whitford","first_name":"Ryan","full_name":"Whitford, Ryan"},{"first_name":"Ana","last_name":"Fernandez","full_name":"Fernandez, Ana"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"first_name":"Amparo","last_name":"Pérez","full_name":"Pérez, Amparo Cuéllar"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki","first_name":"Andrzej"},{"full_name":"Leitner, Johannes","last_name":"Leitner","first_name":"Johannes"},{"full_name":"Abas, Lindy","first_name":"Lindy","last_name":"Abas"},{"last_name":"Aerts","first_name":"Maarten","full_name":"Aerts, Maarten"},{"last_name":"Hoogewijs","first_name":"Kurt","full_name":"Hoogewijs, Kurt"},{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","first_name":"Pawel","full_name":"Pawel Baster"},{"first_name":"Ruth","last_name":"De Groodt","full_name":"De Groodt, Ruth"},{"full_name":"Lin, Yao-Cheng","first_name":"Yao","last_name":"Lin"},{"last_name":"Storme","first_name":"Véronique","full_name":"Storme, Véronique"},{"first_name":"Yves","last_name":"Van De Peer","full_name":"Van de Peer, Yves"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"full_name":"Madder, Annemieke","first_name":"Annemieke","last_name":"Madder"},{"full_name":"Devreese, Bart","last_name":"Devreese","first_name":"Bart"},{"full_name":"Luschnig, Christian","first_name":"Christian","last_name":"Luschnig"},{"full_name":"Jirí Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Pierre","last_name":"Hilson","full_name":"Hilson, Pierre"}]},{"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid (BR) hormone, at the cell surface and is constitutively endocytosed. However, the importance of endocytosis for BR signaling remains unclear. Here we developed a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment of endocytosis dependent on clathrin and the guanine nucleotide exchange factor for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what is to our knowledge the first visualization of receptor-ligand complexes in plants and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling from the plasma membrane."}],"issue":"6","publist_id":"3590","title":"Fluorescent castasterone reveals BRI1 signaling from the plasma membrane","status":"public","publication_status":"published","intvolume":" 8","publisher":"Nature Publishing Group","_id":"3109","year":"2012","date_updated":"2021-01-12T07:41:07Z","date_created":"2018-12-11T12:01:26Z","volume":8,"author":[{"last_name":"Irani","first_name":"Niloufer","full_name":"Irani, Niloufer G"},{"first_name":"Simone","last_name":"Di Rubbo","full_name":"Di Rubbo, Simone"},{"first_name":"Evelien","last_name":"Mylle","full_name":"Mylle, Evelien"},{"full_name":"Van Den Begin, Jos","first_name":"Jos","last_name":"Van Den Begin"},{"first_name":"Joanna","last_name":"Schneider Pizoń","full_name":"Schneider-Pizoń, Joanna"},{"first_name":"Jaroslava","last_name":"Hniliková","full_name":"Hniliková, Jaroslava"},{"full_name":"Šíša, Miroslav","first_name":"Miroslav","last_name":"Šíša"},{"last_name":"Buyst","first_name":"Dieter","full_name":"Buyst, Dieter"},{"last_name":"Vilarrasa Blasi","first_name":"Josep","full_name":"Vilarrasa-Blasi, Josep"},{"last_name":"Szatmári","first_name":"Anna","full_name":"Szatmári, Anna-Maria"},{"full_name":"Van Damme, Daniël","last_name":"Van Damme","first_name":"Daniël"},{"full_name":"Mishev, Kiril","first_name":"Kiril","last_name":"Mishev"},{"full_name":"Codreanu, Mirela-Corina","first_name":"Mirela","last_name":"Codreanu"},{"last_name":"Kohout","first_name":"Ladislav","full_name":"Kohout, Ladislav"},{"first_name":"Miroslav","last_name":"Strnad","full_name":"Strnad, Miroslav"},{"full_name":"Caño-Delgado, Ana I","first_name":"Ana","last_name":"Caño Delgado"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Madder, Annemieke","first_name":"Annemieke","last_name":"Madder"},{"full_name":"Russinova, Eugenia","last_name":"Russinova","first_name":"Eugenia"}],"month":"06","day":"01","quality_controlled":0,"page":"583 - 589","publication":"Nature Chemical Biology","citation":{"ama":"Irani N, Di Rubbo S, Mylle E, et al. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 2012;8(6):583-589. doi:10.1038/nchembio.958","ista":"Irani N, Di Rubbo S, Mylle E, Van Den Begin J, Schneider Pizoń J, Hniliková J, Šíša M, Buyst D, Vilarrasa Blasi J, Szatmári A, Van Damme D, Mishev K, Codreanu M, Kohout L, Strnad M, Caño Delgado A, Friml J, Madder A, Russinova E. 2012. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 8(6), 583–589.","ieee":"N. Irani et al., “Fluorescent castasterone reveals BRI1 signaling from the plasma membrane,” Nature Chemical Biology, vol. 8, no. 6. Nature Publishing Group, pp. 583–589, 2012.","apa":"Irani, N., Di Rubbo, S., Mylle, E., Van Den Begin, J., Schneider Pizoń, J., Hniliková, J., … Russinova, E. (2012). Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.958","mla":"Irani, Niloufer, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology, vol. 8, no. 6, Nature Publishing Group, 2012, pp. 583–89, doi:10.1038/nchembio.958.","short":"N. Irani, S. Di Rubbo, E. Mylle, J. Van Den Begin, J. Schneider Pizoń, J. Hniliková, M. Šíša, D. Buyst, J. Vilarrasa Blasi, A. Szatmári, D. Van Damme, K. Mishev, M. Codreanu, L. Kohout, M. Strnad, A. Caño Delgado, J. Friml, A. Madder, E. Russinova, Nature Chemical Biology 8 (2012) 583–589.","chicago":"Irani, Niloufer, Simone Di Rubbo, Evelien Mylle, Jos Van Den Begin, Joanna Schneider Pizoń, Jaroslava Hniliková, Miroslav Šíša, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.958."},"doi":"10.1038/nchembio.958","date_published":"2012-06-01T00:00:00Z"},{"abstract":[{"lang":"eng","text":"\nGradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis."}],"publist_id":"3595","issue":"5","extern":1,"type":"journal_article","author":[{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"},{"first_name":"Daniel","last_name":"Lewis","full_name":"Lewis, Daniel R"},{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"first_name":"Leentje","last_name":"Jansen","full_name":"Jansen, Leentje"},{"full_name":"Goeminne, Geert","first_name":"Geert","last_name":"Goeminne"},{"full_name":"Vanden Bossche, Robin","last_name":"Vanden Bossche","first_name":"Robin"},{"full_name":"Karimi, Mansour","last_name":"Karimi","first_name":"Mansour"},{"full_name":"De Rybel, Bert","last_name":"De Rybel","first_name":"Bert"},{"full_name":"Vanholme, Bartel","first_name":"Bartel","last_name":"Vanholme"},{"last_name":"Teichmann","first_name":"Thomas","full_name":"Teichmann, Thomas"},{"last_name":"Boerjan","first_name":"Wout","full_name":"Boerjan, Wout"},{"full_name":"Van Montagu, Marc C","first_name":"Marc","last_name":"Van Montagu"},{"full_name":"Gheysen, Godelieve","first_name":"Godelieve","last_name":"Gheysen"},{"first_name":"Gloria","last_name":"Muday","full_name":"Muday, Gloria K"},{"full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"}],"date_created":"2018-12-11T12:01:24Z","date_updated":"2021-01-12T07:41:05Z","volume":109,"year":"2012","_id":"3104","publication_status":"published","status":"public","title":"Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis","publisher":"National Academy of Sciences","intvolume":" 109","month":"01","day":"31","date_published":"2012-01-31T00:00:00Z","doi":"10.1073/pnas.1121134109","publication":"PNAS","citation":{"chicago":"Grunewald, Wim, Ive De Smet, Daniel Lewis, Christian Löfke, Leentje Jansen, Geert Goeminne, Robin Vanden Bossche, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1121134109.","short":"W. Grunewald, I. De Smet, D. Lewis, C. Löfke, L. Jansen, G. Goeminne, R. Vanden Bossche, M. Karimi, B. De Rybel, B. Vanholme, T. Teichmann, W. Boerjan, M. Van Montagu, G. Gheysen, G. Muday, J. Friml, T. Beeckman, PNAS 109 (2012) 1554–1559.","mla":"Grunewald, Wim, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS, vol. 109, no. 5, National Academy of Sciences, 2012, pp. 1554–59, doi:10.1073/pnas.1121134109.","apa":"Grunewald, W., De Smet, I., Lewis, D., Löfke, C., Jansen, L., Goeminne, G., … Beeckman, T. (2012). Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1121134109","ieee":"W. Grunewald et al., “Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis,” PNAS, vol. 109, no. 5. National Academy of Sciences, pp. 1554–1559, 2012.","ista":"Grunewald W, De Smet I, Lewis D, Löfke C, Jansen L, Goeminne G, Vanden Bossche R, Karimi M, De Rybel B, Vanholme B, Teichmann T, Boerjan W, Van Montagu M, Gheysen G, Muday G, Friml J, Beeckman T. 2012. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 109(5), 1554–1559.","ama":"Grunewald W, De Smet I, Lewis D, et al. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 2012;109(5):1554-1559. doi:10.1073/pnas.1121134109"},"quality_controlled":0,"page":"1554 - 1559"},{"date_published":"2012-05-03T00:00:00Z","doi":"10.1038/nature11001","quality_controlled":0,"page":"119 - 122","publication":"Nature","citation":{"ama":"Barbez E, Kubeš M, Rolčík J, et al. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 2012;485(7396):119-122. doi:10.1038/nature11001","ista":"Barbez E, Kubeš M, Rolčík J, Béziat C, Pěnčík A, Wang B, Rosquete M, Zhu J, Dobrev P, Lee Y, Zašímalová E, Petrášek J, Geisler M, Friml J, Kleine Vehn J. 2012. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 485(7396), 119–122.","ieee":"E. Barbez et al., “A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants,” Nature, vol. 485, no. 7396. Nature Publishing Group, pp. 119–122, 2012.","apa":"Barbez, E., Kubeš, M., Rolčík, J., Béziat, C., Pěnčík, A., Wang, B., … Kleine Vehn, J. (2012). A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11001","mla":"Barbez, Elke, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature, vol. 485, no. 7396, Nature Publishing Group, 2012, pp. 119–22, doi:10.1038/nature11001.","short":"E. Barbez, M. Kubeš, J. Rolčík, C. Béziat, A. Pěnčík, B. Wang, M. Rosquete, J. Zhu, P. Dobrev, Y. Lee, E. Zašímalová, J. Petrášek, M. Geisler, J. Friml, J. Kleine Vehn, Nature 485 (2012) 119–122.","chicago":"Barbez, Elke, Martin Kubeš, Jakub Rolčík, Chloe Béziat, Aleš Pěnčík, Bangjun Wang, Michel Rosquete, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11001."},"day":"03","month":"05","date_created":"2018-12-11T12:01:26Z","date_updated":"2021-01-12T07:41:07Z","volume":485,"author":[{"first_name":"Elke","last_name":"Barbez","full_name":"Barbez, Elke"},{"first_name":"Martin","last_name":"Kubeš","full_name":"Kubeš, Martin"},{"full_name":"Rolčík, Jakub","last_name":"Rolčík","first_name":"Jakub"},{"full_name":"Béziat, Chloe","first_name":"Chloe","last_name":"Béziat"},{"full_name":"Pěnčík, Aleš","first_name":"Aleš","last_name":"Pěnčík"},{"full_name":"Wang, Bangjun","last_name":"Wang","first_name":"Bangjun"},{"first_name":"Michel","last_name":"Rosquete","full_name":"Rosquete, Michel Ruiz"},{"last_name":"Zhu","first_name":"Jinsheng","full_name":"Zhu, Jinsheng"},{"first_name":"Petre","last_name":"Dobrev","full_name":"Dobrev, Petre I"},{"full_name":"Lee, Yuree","first_name":"Yuree","last_name":"Lee"},{"first_name":"Eva","last_name":"Zašímalová","full_name":"Zašímalová, Eva"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"}],"publication_status":"published","title":"A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants","status":"public","intvolume":" 485","publisher":"Nature Publishing Group","_id":"3108","year":"2012","extern":1,"abstract":[{"lang":"eng","text":"The phytohormone auxin acts as a prominent signal, providing, by its local accumulation or depletion in selected cells, a spatial and temporal reference for changes in the developmental program. The distribution of auxin depends on both auxin metabolism (biosynthesis, conjugation and degradation) and cellular auxin transport. We identified in silico a novel putative auxin transport facilitator family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required for auxin-dependent regulation of plant growth by determining the cellular sensitivity to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic reticulum and thus auxin availability for nuclear auxin signalling. PILS activity affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via intracellular accumulation and metabolism. Our findings reveal that the transport machinery to compartmentalize auxin within the cell is of an unexpected molecular complexity and demonstrate this compartmentalization to be functionally important for a number of developmental processes."}],"issue":"7396","publist_id":"3591","type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Cell polarization via asymmetrical distribution of structures or molecules is essential for diverse cellular functions and development of organisms, but how polarity is developmentally controlled has been poorly understood. In plants, the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the cellular efflux of the quintessential phytohormone auxin plays a central role in developmental patterning, morphogenesis, and differential growth. Recently we showed that auxin promotes cell interdigitation by activating the Rho family ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our findings suggest a link between the developmental auxin signal and polar PIN1 distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation of a design principle for cell polarization that is based on Rho GTPase-mediated inhibition of endocytosis."}],"publist_id":"3593","issue":"4","extern":1,"year":"2012","_id":"3106","title":"ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis","status":"public","publication_status":"published","intvolume":" 10","publisher":"Public Library of Science","author":[{"first_name":"Shingo","last_name":"Nagawa","full_name":"Nagawa, Shingo"},{"full_name":"Xu, Tongda","last_name":"Xu","first_name":"Tongda"},{"last_name":"Lin","first_name":"Deshu","full_name":"Lin, Deshu"},{"first_name":"Pankaj","last_name":"Dhonukshe","full_name":"Dhonukshe, Pankaj"},{"full_name":"Zhang, Xingxing","last_name":"Zhang","first_name":"Xingxing"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Ben","last_name":"Scheres","full_name":"Scheres, Ben"},{"full_name":"Fu, Ying","first_name":"Ying","last_name":"Fu"},{"first_name":"Zhenbiao","last_name":"Yang","full_name":"Yang, Zhenbiao"}],"date_updated":"2021-01-12T07:41:06Z","date_created":"2018-12-11T12:01:25Z","volume":10,"day":"01","month":"04","publication":"PLoS Biology","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"chicago":"Nagawa, Shingo, Tongda Xu, Deshu Lin, Pankaj Dhonukshe, Xingxing Zhang, Jiří Friml, Ben Scheres, Ying Fu, and Zhenbiao Yang. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001299.","mla":"Nagawa, Shingo, et al. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology, vol. 10, no. 4, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001299.","short":"S. Nagawa, T. Xu, D. Lin, P. Dhonukshe, X. Zhang, J. Friml, B. Scheres, Y. Fu, Z. Yang, PLoS Biology 10 (2012).","ista":"Nagawa S, Xu T, Lin D, Dhonukshe P, Zhang X, Friml J, Scheres B, Fu Y, Yang Z. 2012. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 10(4).","ieee":"S. Nagawa et al., “ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis,” PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012.","apa":"Nagawa, S., Xu, T., Lin, D., Dhonukshe, P., Zhang, X., Friml, J., … Yang, Z. (2012). ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001299","ama":"Nagawa S, Xu T, Lin D, et al. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001299"},"quality_controlled":0,"date_published":"2012-04-01T00:00:00Z","doi":"10.1371/journal.pbio.1001299"},{"quality_controlled":"1","page":"415 - 416","publication":"Nature Chemical Biology","citation":{"short":"S. Vanneste, J. Friml, Plant Signaling: Deconstructing Auxin Sensing, Nature Publishing Group, 2012.","mla":"Vanneste, Steffen, and Jiří Friml. “Plant Signaling: Deconstructing Auxin Sensing.” Nature Chemical Biology, vol. 8, no. 5, Nature Publishing Group, 2012, pp. 415–16, doi:10.1038/nchembio.943.","chicago":"Vanneste, Steffen, and Jiří Friml. Plant Signaling: Deconstructing Auxin Sensing. Nature Chemical Biology. Vol. 8. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.943.","ama":"Vanneste S, Friml J. Plant Signaling: Deconstructing Auxin Sensing. Vol 8. Nature Publishing Group; 2012:415-416. doi:10.1038/nchembio.943","ieee":"S. Vanneste and J. Friml, Plant signaling: Deconstructing auxin sensing, vol. 8, no. 5. Nature Publishing Group, 2012, pp. 415–416.","apa":"Vanneste, S., & Friml, J. (2012). Plant signaling: Deconstructing auxin sensing. Nature Chemical Biology (Vol. 8, pp. 415–416). Nature Publishing Group. https://doi.org/10.1038/nchembio.943","ista":"Vanneste S, Friml J. 2012. Plant signaling: Deconstructing auxin sensing, Nature Publishing Group,p."},"language":[{"iso":"eng"}],"doi":"10.1038/nchembio.943","date_published":"2012-05-01T00:00:00Z","month":"05","day":"01","status":"public","publication_status":"published","title":"Plant signaling: Deconstructing auxin sensing","publisher":"Nature Publishing Group","intvolume":" 8","_id":"3107","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:01:26Z","date_updated":"2021-01-12T07:41:06Z","volume":8,"oa_version":"None","author":[{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"type":"other_academic_publication","extern":"1","issue":"5","publist_id":"3592"},{"month":"07","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2012-07-29","location":"Aire-la-Ville, Switzerland","end_date":"2012-07-31"},"publist_id":"3580","file_date_updated":"2020-07-14T12:46:00Z","publisher":"ACM","department":[{"_id":"ChWo"}],"publication_status":"published","year":"2012","acknowledgement":"This work was partially funded by NSF grants CCF-0811485 and IIS-1130934. We would like to thank Scanline VFX for additional funding. We would like to thank Jie Tan as well as our anonymous reviewers for their useful suggestions and feedback.","date_created":"2018-12-11T12:01:30Z","date_updated":"2023-02-23T11:13:07Z","related_material":{"link":[{"url":"http://dl.acm.org/citation.cfm?id=2422393","relation":"table_of_contents"}]},"author":[{"last_name":"Raveendran","first_name":"Karthik","full_name":"Raveendran, Karthik"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"},{"full_name":"Turk, Greg","first_name":"Greg","last_name":"Turk"}],"scopus_import":1,"has_accepted_license":"1","day":"29","page":"255 - 264","citation":{"mla":"Raveendran, Karthik, et al. “Controlling Liquids Using Meshes.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–64.","short":"K. Raveendran, N. Thuerey, C. Wojtan, G. Turk, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–264.","chicago":"Raveendran, Karthik, Nils Thuerey, Chris Wojtan, and Greg Turk. “Controlling Liquids Using Meshes.” In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 255–64. ACM, 2012.","ama":"Raveendran K, Thuerey N, Wojtan C, Turk G. Controlling liquids using meshes. In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. ACM; 2012:255-264.","ista":"Raveendran K, Thuerey N, Wojtan C, Turk G. 2012. Controlling liquids using meshes. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 255–264.","apa":"Raveendran, K., Thuerey, N., Wojtan, C., & Turk, G. (2012). Controlling liquids using meshes. In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation (pp. 255–264). Aire-la-Ville, Switzerland: ACM.","ieee":"K. Raveendran, N. Thuerey, C. Wojtan, and G. Turk, “Controlling liquids using meshes,” in Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Aire-la-Ville, Switzerland, 2012, pp. 255–264."},"publication":"Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation","date_published":"2012-07-29T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.\r\n"}],"ddc":["000"],"status":"public","title":"Controlling liquids using meshes","_id":"3119","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","content_type":"application/pdf","file_size":4939370,"file_name":"IST-2016-600-v1+1_ControllingLiquids_Preprint.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:11:23Z","checksum":"babda64c24cf90a4d05ae86d712bed08","file_id":"4877","relation":"main_file"}],"oa_version":"Submitted Version","pubrep_id":"600"},{"month":"07","oa":1,"quality_controlled":"1","doi":"10.1145/2185520.2185549","language":[{"iso":"eng"}],"article_number":"53","publist_id":"3581","file_date_updated":"2020-07-14T12:46:00Z","acknowledgement":"This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu Ceylan for helping with the rendering, and Art Tevs for the human performance data comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. ","year":"2012","department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","author":[{"full_name":"Bojsen-Hansen, Morten","first_name":"Morten","last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224"},{"full_name":"Li, Hao","last_name":"Li","first_name":"Hao"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"volume":31,"date_created":"2018-12-11T12:01:29Z","date_updated":"2022-05-24T08:21:11Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"short":"M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012).","mla":"Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics, vol. 31, no. 4, 53, ACM, 2012, doi:10.1145/2185520.2185549.","chicago":"Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185549.","ama":"Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185549","apa":"Bojsen-Hansen, M., Li, H., & Wojtan, C. (2012). Tracking surfaces with evolving topology. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185549","ieee":"M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012.","ista":"Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 31(4), 53."},"publication":"ACM Transactions on Graphics","article_type":"original","date_published":"2012-07-01T00:00:00Z","type":"journal_article","alternative_title":["SIGGRAPH"],"issue":"4","abstract":[{"text":"We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3118","intvolume":" 31","status":"public","ddc":["000"],"title":"Tracking surfaces with evolving topology","pubrep_id":"602","file":[{"file_size":44538518,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-602-v1+1_topoReg.pdf","checksum":"1e219c5bf4e5552c1290c62eefa5cd60","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:18:37Z","relation":"main_file","file_id":"5359"}],"oa_version":"Submitted Version"},{"publication_status":"published","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","status":"public","department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","intvolume":" 21","_id":"3122","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:01:31Z","date_updated":"2021-01-12T07:41:13Z","oa_version":"None","volume":21,"author":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"first_name":"Spencer","last_name":"Barrett","full_name":"Barrett, Spencer"}],"type":"journal_article","abstract":[{"text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ","lang":"eng"}],"issue":"15","publist_id":"3577","quality_controlled":"1","page":"3640 - 3643","publication":"Molecular Ecology","citation":{"chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x.","mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.","ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","apa":"Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x","ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x"},"language":[{"iso":"eng"}],"doi":"10.1111/j.1365-294X.2012.05643.x","date_published":"2012-08-01T00:00:00Z","scopus_import":1,"day":"01","month":"08"},{"status":"public","title":"Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA","intvolume":" 15","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3121","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type.","lang":"eng"}],"issue":"9","page":"1195 - 1197","publication":"Nature Neuroscience","citation":{"chicago":"Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta, and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3162.","short":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience 15 (2012) 1195–1197.","mla":"Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience, vol. 15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:10.1038/nn.3162.","apa":"Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., & Smith, S. (2012). Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3162","ieee":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA,” Nature Neuroscience, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197, 2012.","ista":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 15(9), 1195–1197.","ama":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 2012;15(9):1195-1197. doi:10.1038/nn.3162"},"date_published":"2012-09-01T00:00:00Z","scopus_import":1,"day":"01","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"PeJo"}],"acknowledgement":"The work was supported by the US National Institutes of Health (DA027110 and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah for helpful comments. ","year":"2012","pmid":1,"date_created":"2018-12-11T12:01:30Z","date_updated":"2021-01-12T07:41:12Z","volume":15,"author":[{"last_name":"Williams","first_name":"Courtney","full_name":"Williams, Courtney"},{"full_name":"Chen, Wenyan","last_name":"Chen","first_name":"Wenyan"},{"first_name":"Chia","last_name":"Lee","full_name":"Lee, Chia"},{"full_name":"Yaeger, Daniel","last_name":"Yaeger","first_name":"Daniel"},{"last_name":"Vyleta","first_name":"Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Nicholas"},{"first_name":"Stephen","last_name":"Smith","full_name":"Smith, Stephen"}],"publist_id":"3578","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/"}],"oa":1,"external_id":{"pmid":["22842148"]},"language":[{"iso":"eng"}],"doi":"10.1038/nn.3162","month":"09"},{"publist_id":"3579","volume":148,"date_updated":"2021-01-12T07:41:12Z","date_created":"2018-12-11T12:01:30Z","author":[{"full_name":"Brown, Gavin","last_name":"Brown","first_name":"Gavin"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","first_name":"Michael"},{"full_name":"Reid, Miles","first_name":"Miles","last_name":"Reid"}],"publisher":"Cambridge University Press","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0.","year":"2012","month":"07","language":[{"iso":"eng"}],"doi":"10.1112/S0010437X11007226","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1009.4313"}],"issue":"4","abstract":[{"lang":"eng","text":"We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 148","title":"Fano 3 folds in codimension 4 Tom and Jerry Part I","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3120","day":"01","scopus_import":1,"date_published":"2012-07-01T00:00:00Z","page":"1171 - 1194","citation":{"ama":"Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 2012;148(4):1171-1194. doi:10.1112/S0010437X11007226","apa":"Brown, G., Kerber, M., & Reid, M. (2012). Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X11007226","ieee":"G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry Part I,” Compositio Mathematica, vol. 148, no. 4. Cambridge University Press, pp. 1171–1194, 2012.","ista":"Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 148(4), 1171–1194.","short":"G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194.","mla":"Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica, vol. 148, no. 4, Cambridge University Press, 2012, pp. 1171–94, doi:10.1112/S0010437X11007226.","chicago":"Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica. Cambridge University Press, 2012. https://doi.org/10.1112/S0010437X11007226."},"publication":"Compositio Mathematica"},{"abstract":[{"lang":"eng","text":"We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms."}],"publist_id":"3582","issue":"15","type":"journal_article","date_created":"2018-12-11T12:01:29Z","date_updated":"2021-01-12T07:41:11Z","volume":160,"oa_version":"Preprint","author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"title":"Minimizing a sum of submodular functions","publication_status":"published","status":"public","intvolume":" 160","department":[{"_id":"VlKo"}],"publisher":"Elsevier","_id":"3117","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","month":"10","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2012-10-01T00:00:00Z","doi":"10.1016/j.dam.2012.05.025","quality_controlled":"1","page":"2246 - 2258","publication":"Discrete Applied Mathematics","citation":{"ista":"Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 160(15), 2246–2258.","ieee":"V. Kolmogorov, “Minimizing a sum of submodular functions,” Discrete Applied Mathematics, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.","apa":"Kolmogorov, V. (2012). Minimizing a sum of submodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2012.05.025","ama":"Kolmogorov V. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 2012;160(15):2246-2258. doi:10.1016/j.dam.2012.05.025","chicago":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2012.05.025.","mla":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:10.1016/j.dam.2012.05.025.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1006.1990"}]},{"type":"journal_article","issue":"6","abstract":[{"text":"In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.","lang":"eng"}],"intvolume":" 8","ddc":["570","576"],"title":"Limits to the rate of adaptive substitution in sexual populations","status":"public","_id":"3131","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","content_type":"application/pdf","file_size":1284801,"file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:00Z","date_updated":"2020-07-14T12:46:01Z","checksum":"729a4becda7d786c4c3db8f9a1f77953","file_id":"4659","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"114","scopus_import":1,"has_accepted_license":"1","day":"07","citation":{"ama":"Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740","ieee":"D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","apa":"Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740.","short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).","mla":"Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740.","chicago":"Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740."},"publication":"PLoS Genetics","date_published":"2012-06-07T00:00:00Z","article_number":"e1002740","ec_funded":1,"publist_id":"3566","file_date_updated":"2020-07-14T12:46:01Z","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","publication_status":"published","acknowledgement":"The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions.","year":"2012","volume":8,"date_created":"2018-12-11T12:01:34Z","date_updated":"2021-01-12T07:41:17Z","author":[{"first_name":"Daniel","last_name":"Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","full_name":"Weissman, Daniel"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"month":"06","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1002740"},{"date_created":"2018-12-11T12:01:34Z","date_updated":"2021-01-12T07:41:16Z","volume":8,"author":[{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"},{"last_name":"Silander","first_name":"Olin","full_name":"Silander, Olin"}],"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","year":"2012","acknowledgement":"We thank Alex Boehm for discussions and comments.","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"3567","article_number":"e1002803","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1002803","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06","oa_version":"Published Version","file":[{"file_size":2674138,"content_type":"application/pdf","creator":"system","file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:12:52Z","checksum":"f8506fb579eda6fc5613ba9bf421b86a","relation":"main_file","file_id":"4973"}],"pubrep_id":"386","ddc":["576"],"title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","status":"public","intvolume":" 8","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3130","abstract":[{"lang":"eng","text":"Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes."}],"issue":"6","type":"journal_article","date_published":"2012-06-28T00:00:00Z","publication":"PLoS Genetics","citation":{"chicago":"Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002803.","mla":"Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002803.","short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).","ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.","ieee":"T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","apa":"Bergmiller, T., Ackermann, M., & Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002803","ama":"Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002803"},"day":"28","has_accepted_license":"1","scopus_import":1},{"citation":{"chicago":"Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,” 7358:294–309. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_24.","mla":"Guet, Calin C., et al. Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits. Vol. 7358, Springer, 2012, pp. 294–309, doi:10.1007/978-3-642-31424-7_24.","short":"C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer, 2012, pp. 294–309.","ista":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification, LNCS, vol. 7358, 294–309.","apa":"Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., & Sezgin, A. (2012). Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358, pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_24","ieee":"C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed continuous time Markov chains for genetic regulatory circuits,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309.","ama":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. Delayed continuous time Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309. doi:10.1007/978-3-642-31424-7_24"},"quality_controlled":"1","page":"294 - 309","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"conference":{"end_date":"2012-07-13","start_date":"2012-07-07","location":"Berkeley, CA, USA","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-642-31424-7_24","date_published":"2012-07-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"07","year":"2012","_id":"3136","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by the ERC Advanced Investigator grant on Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation.","status":"public","title":"Delayed continuous time Markov chains for genetic regulatory circuits","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"publisher":"Springer","author":[{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Mateescu, Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Mateescu"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali"}],"date_created":"2018-12-11T12:01:36Z","date_updated":"2021-01-12T07:41:18Z","oa_version":"None","volume":"7358 ","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Continuous-time Markov chains (CTMC) with their rich theory and efficient simulation algorithms have been successfully used in modeling stochastic processes in diverse areas such as computer science, physics, and biology. However, systems that comprise non-instantaneous events cannot be accurately and efficiently modeled with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that allows for the specification of a lower bound on the time interval between an event's initiation and its completion, and we propose an algorithm for the computation of their behavior. Our algorithm effectively decomposes the computation into two stages: a pure CTMC governs event initiations while a deterministic process guarantees lower bounds on event completion times. Furthermore, from the nature of delayed CTMCs, we obtain a parallelized version of our algorithm. We use our formalism to model genetic regulatory circuits (biological systems where delayed events are common) and report on the results of our numerical algorithm as run on a cluster. We compare performance and accuracy of our results with results obtained by using pure CTMCs. © 2012 Springer-Verlag."}],"ec_funded":1,"publist_id":"3561"},{"scopus_import":1,"day":"01","citation":{"short":"B. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, in:, Springer, 2012, pp. 23–38.","mla":"Brázdil, Brázdil, et al. Efficient Controller Synthesis for Consumption Games with Multiple Resource Types. Vol. 7358, Springer, 2012, pp. 23–38, doi:10.1007/978-3-642-31424-7_8.","chicago":"Brázdil, Brázdil, Krishnendu Chatterjee, Antonín Kučera, and Petr Novotný. “Efficient Controller Synthesis for Consumption Games with Multiple Resource Types,” 7358:23–38. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_8.","ama":"Brázdil B, Chatterjee K, Kučera A, Novotný P. Efficient controller synthesis for consumption games with multiple resource types. In: Vol 7358. Springer; 2012:23-38. doi:10.1007/978-3-642-31424-7_8","apa":"Brázdil, B., Chatterjee, K., Kučera, A., & Novotný, P. (2012). Efficient controller synthesis for consumption games with multiple resource types (Vol. 7358, pp. 23–38). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_8","ieee":"B. Brázdil, K. Chatterjee, A. Kučera, and P. Novotný, “Efficient controller synthesis for consumption games with multiple resource types,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 23–38.","ista":"Brázdil B, Chatterjee K, Kučera A, Novotný P. 2012. Efficient controller synthesis for consumption games with multiple resource types. CAV: Computer Aided Verification, LNCS, vol. 7358, 23–38."},"page":"23 - 38","date_published":"2012-07-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or ω. The ω updates model the reloading of a given resource. Each vertex belongs either to player □ or player ◇, where the aim of player □ is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors) and bounded resource updates. "}],"_id":"3135","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Efficient controller synthesis for consumption games with multiple resource types","status":"public","intvolume":" 7358","oa_version":"Preprint","month":"07","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1202.0796","open_access":"1"}],"quality_controlled":"1","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"conference":{"end_date":"2012-07-13","location":"Berkeley, CA, USA","start_date":"2012-07-07","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-642-31424-7_8","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"3562","acknowledgement":"Tomas Brazdil, Antonin Kucera, and Petr Novotny are supported by the Czech Science Foundation, grant No. P202/10/1469. Krishnendu Chatterjee is supported by the FWF (Austrian Science Fund) NFN Grant No S11407-N23 (RiSE) and ERC Start grant (279307: Graph Games).","year":"2012","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","author":[{"last_name":"Brázdil","first_name":"Brázdil","full_name":"Brázdil, Brázdil"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr"}],"date_updated":"2021-01-12T07:41:18Z","date_created":"2018-12-11T12:01:35Z","volume":7358},{"publist_id":"3564","abstract":[{"text":"This note contributes to the point calculus of persistent homology by extending Alexander duality from spaces to real-valued functions. Given a perfect Morse function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds with common boundary M, we prove elementary relationships between the persistence diagrams of f restricted to U, to V, and to M. ","lang":"eng"}],"type":"conference","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Kerber, Michael","last_name":"Kerber","first_name":"Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","date_created":"2018-12-11T12:01:35Z","date_updated":"2021-01-12T07:41:17Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3133","year":"2012","acknowledgement":"his research is partially supported by the National Science Foundation (NSF) under grant DBI-0820624, the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.\r\nThe authors thank an anonymous referee for suggesting the simplified proof of the Contravariant PE Theorem given in this paper. They also thank Frederick Cohen, Yuriy Mileyko and Amit Patel for helpful discussions.","publisher":"ACM","department":[{"_id":"HeEd"}],"title":"Alexander duality for functions: The persistent behavior of land and water and shore","status":"public","publication_status":"published","day":"20","month":"06","scopus_import":1,"doi":"10.1145/2261250.2261287","date_published":"2012-06-20T00:00:00Z","conference":{"name":"SCG: Symposium on Computational Geometry","start_date":"2012-06-17","location":"Chapel Hill, NC, USA","end_date":"2012-06-20"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.5052"}],"citation":{"chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 249–58. ACM, 2012. https://doi.org/10.1145/2261250.2261287.","short":"H. Edelsbrunner, M. Kerber, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–258.","mla":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–58, doi:10.1145/2261250.2261287.","ieee":"H. Edelsbrunner and M. Kerber, “Alexander duality for functions: The persistent behavior of land and water and shore,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 249–258.","apa":"Edelsbrunner, H., & Kerber, M. (2012). Alexander duality for functions: The persistent behavior of land and water and shore. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 249–258). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261287","ista":"Edelsbrunner H, Kerber M. 2012. Alexander duality for functions: The persistent behavior of land and water and shore. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 249–258.","ama":"Edelsbrunner H, Kerber M. Alexander duality for functions: The persistent behavior of land and water and shore. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:249-258. doi:10.1145/2261250.2261287"},"oa":1,"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","page":"249 - 258","quality_controlled":"1"},{"abstract":[{"text":"It has been an open question whether the sum of finitely many isotropic Gaussian kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes. We give a detailed analysis of this example, showing that it has exponentially many critical points and that the resilience of the extra mode grows like √n. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. ","lang":"eng"}],"publist_id":"3563","type":"conference","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"first_name":"Brittany","last_name":"Fasy","full_name":"Fasy, Brittany"},{"first_name":"Günter","last_name":"Rote","full_name":"Rote, Günter"}],"related_material":{"record":[{"id":"2815","relation":"later_version","status":"public"}]},"date_created":"2018-12-11T12:01:35Z","date_updated":"2023-02-23T10:59:27Z","oa_version":"None","acknowledgement":"This research is partially supported by the National Science Foun- dation (NSF) under grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.","_id":"3134","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","publication_status":"published","title":"Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions","status":"public","department":[{"_id":"HeEd"}],"publisher":"ACM","month":"06","day":"20","scopus_import":1,"conference":{"name":"SCG: Symposium on Computational Geometry","end_date":"2012-06-20","location":"Chapel Hill, NC, USA","start_date":"2012-06-17"},"date_published":"2012-06-20T00:00:00Z","doi":"10.1145/2261250.2261265","language":[{"iso":"eng"}],"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","citation":{"apa":"Edelsbrunner, H., Fasy, B., & Rote, G. (2012). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 91–100). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261265","ieee":"H. Edelsbrunner, B. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 91–100.","ista":"Edelsbrunner H, Fasy B, Rote G. 2012. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 91–100.","ama":"Edelsbrunner H, Fasy B, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:91-100. doi:10.1145/2261250.2261265","chicago":"Edelsbrunner, Herbert, Brittany Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 91–100. ACM, 2012. https://doi.org/10.1145/2261250.2261265.","short":"H. Edelsbrunner, B. Fasy, G. Rote, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100.","mla":"Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100, doi:10.1145/2261250.2261265."},"quality_controlled":"1","page":"91 - 100"},{"author":[{"full_name":"Konrad, Matthias","last_name":"Konrad","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pamminger, Tobias","first_name":"Tobias","last_name":"Pamminger"},{"full_name":"Foitzik, Susanne","last_name":"Foitzik","first_name":"Susanne"}],"volume":99,"oa_version":"None","date_created":"2018-12-11T12:01:34Z","date_updated":"2021-01-12T07:41:17Z","_id":"3132","acknowledgement":"We like to thank the editor and three anonymous reviewers for their time and constructive criticism and Inon Scharf, Volker Witte and Andreas Modlmeier for helpful comments on earlier versions of the manuscript. The first and second authors appear in alphabetical order and contributed equally to this paper.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","department":[{"_id":"SyCr"}],"intvolume":" 99","publisher":"Springer","title":"Two pathways ensuring social harmony","status":"public","publication_status":"published","publist_id":"3565","issue":"8","abstract":[{"lang":"eng","text":"Reproductive division of labour is a characteristic trait of social insects. The dominant reproductive individual, often the queen, uses chemical communication and/or behaviour to maintain her social status. Queens of many social insects communicate their fertility status via cuticle-bound substances. As these substances usually possess a low volatility, their range in queen–worker communication is potentially limited. Here, we investigate the range and impact of behavioural and chemical queen signals on workers of the ant Temnothorax longispinosus. We compared the behaviour and ovary development of workers subjected to three different treatments: workers with direct chemical and physical contact to the queen, those solely under the influence of volatile queen substances and those entirely separated from the queen. In addition to short-ranged queen signals preventing ovary development in workers, we discovered a novel secondary pathway influencing worker behaviour. Workers with no physical contact to the queen, but exposed to volatile substances, started to develop their ovaries, but did not change their behaviour compared to workers in direct contact to the queen. In contrast, workers in queen-separated groups showed both increased ovary development and aggressive dominance interactions. We conclude that T. longispinosus queens influence worker ovary development and behaviour via two independent signals, both ensuring social harmony within the colony."}],"type":"journal_article","doi":"10.1007/s00114-012-0943-z","date_published":"2012-08-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ieee":"M. Konrad, T. Pamminger, and S. Foitzik, “Two pathways ensuring social harmony,” Naturwissenschaften, vol. 99, no. 8. Springer, pp. 627–636, 2012.","apa":"Konrad, M., Pamminger, T., & Foitzik, S. (2012). Two pathways ensuring social harmony. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-012-0943-z","ista":"Konrad M, Pamminger T, Foitzik S. 2012. Two pathways ensuring social harmony. Naturwissenschaften. 99(8), 627–636.","ama":"Konrad M, Pamminger T, Foitzik S. Two pathways ensuring social harmony. Naturwissenschaften. 2012;99(8):627-636. doi:10.1007/s00114-012-0943-z","chicago":"Konrad, Matthias, Tobias Pamminger, and Susanne Foitzik. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften. Springer, 2012. https://doi.org/10.1007/s00114-012-0943-z.","short":"M. Konrad, T. Pamminger, S. Foitzik, Naturwissenschaften 99 (2012) 627–636.","mla":"Konrad, Matthias, et al. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften, vol. 99, no. 8, Springer, 2012, pp. 627–36, doi:10.1007/s00114-012-0943-z."},"publication":"Naturwissenschaften","page":"627 - 636","quality_controlled":"1","day":"01","month":"08","scopus_import":1},{"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Public Library of Science","year":"2012","acknowledgement":"Supported by National Institutes of Health grants GM071338 (ML) and AI059355 (BM).\r\nWe acknowledge the expertise of Dr. Martina Ralle in Department of Biochemistry and Molecular Biology at OHSU for measurements of potassium using inductively coupled plasma mass spectrometry.","date_updated":"2021-01-12T07:41:29Z","date_created":"2018-12-11T12:01:45Z","volume":7,"author":[{"full_name":"Vyleta, Meghan","last_name":"Vyleta","first_name":"Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John","last_name":"Wong","full_name":"Wong, John"},{"full_name":"Magun, Bruce","first_name":"Bruce","last_name":"Magun"}],"article_number":"e36044","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"3526","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0036044","month":"05","title":"Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome","ddc":["610"],"status":"public","intvolume":" 7","_id":"3161","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":2984012,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2012-97-v1+1_journal.pone.0036044.pdf","checksum":"30cef37e27eaa467f6571b3640282010","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:14:30Z","relation":"main_file","file_id":"5082"}],"oa_version":"Published Version","pubrep_id":"97","type":"journal_article","abstract":[{"text":"Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by inducing efflux of cellular potassium. Loss of cellular potassium is known to potently suppress protein synthesis, leading us to test whether the inhibition of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome. Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide, puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin, ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of IL-1ß from cells in response to these agents was detected by immunoblotting and ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition of translation by each of the tested translation inhibitors led to processing of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger efflux of intracellular potassium, the addition of high extracellular potassium suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA, which are known to activate the NLRP3 inflammasome, also substantially inhibited protein translation, supporting a close association between inhibition of translation and inflammasome activation. These data demonstrate that translational inhibition itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent inflammatory signaling and that other physical, chemical, or pathogen-associated agents that impair translation may lead to IL-1ß-dependent inflammation through activation of the NLRP3 inflammasome. For agents that inhibit translation through decreased cellular potassium, the application of high extracellular potassium restores protein translation and suppresses activation of the NLRP inflammasome. For agents that inhibit translation through mechanisms that do not involve loss of potassium, high extracellular potassium suppresses IL-1ß processing through a mechanism that remains undefined.","lang":"eng"}],"issue":"5","publication":"PLoS One","citation":{"chicago":"Vyleta, Meghan, John Wong, and Bruce Magun. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036044.","short":"M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012).","mla":"Vyleta, Meghan, et al. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One, vol. 7, no. 5, e36044, Public Library of Science, 2012, doi:10.1371/journal.pone.0036044.","ieee":"M. Vyleta, J. Wong, and B. Magun, “Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome,” PLoS One, vol. 7, no. 5. Public Library of Science, 2012.","apa":"Vyleta, M., Wong, J., & Magun, B. (2012). Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036044","ista":"Vyleta M, Wong J, Magun B. 2012. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 7(5), e36044.","ama":"Vyleta M, Wong J, Magun B. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 2012;7(5). doi:10.1371/journal.pone.0036044"},"date_published":"2012-05-14T00:00:00Z","scopus_import":1,"day":"14","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-29860-8_12","conference":{"name":"RV: Runtime Verification","location":"San Francisco, CA, United States","start_date":"2011-09-27","end_date":"2011-09-30"},"quality_controlled":"1","oa":1,"month":"01","volume":7186,"date_updated":"2021-01-12T07:41:29Z","date_created":"2018-12-11T12:01:45Z","author":[{"full_name":"Asarin, Eugene","first_name":"Eugene","last_name":"Asarin"},{"full_name":"Donzé, Alexandre","first_name":"Alexandre","last_name":"Donzé"},{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"},{"full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2012","publist_id":"3525","file_date_updated":"2020-07-14T12:46:01Z","date_published":"2012-01-01T00:00:00Z","page":"147 - 160","citation":{"ama":"Asarin E, Donzé A, Maler O, Nickovic D. Parametric identification of temporal properties. In: Vol 7186. Springer; 2012:147-160. doi:10.1007/978-3-642-29860-8_12","apa":"Asarin, E., Donzé, A., Maler, O., & Nickovic, D. (2012). Parametric identification of temporal properties (Vol. 7186, pp. 147–160). Presented at the RV: Runtime Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-642-29860-8_12","ieee":"E. Asarin, A. Donzé, O. Maler, and D. Nickovic, “Parametric identification of temporal properties,” presented at the RV: Runtime Verification, San Francisco, CA, United States, 2012, vol. 7186, pp. 147–160.","ista":"Asarin E, Donzé A, Maler O, Nickovic D. 2012. Parametric identification of temporal properties. RV: Runtime Verification, LNCS, vol. 7186, 147–160.","short":"E. Asarin, A. Donzé, O. Maler, D. Nickovic, in:, Springer, 2012, pp. 147–160.","mla":"Asarin, Eugene, et al. Parametric Identification of Temporal Properties. Vol. 7186, Springer, 2012, pp. 147–60, doi:10.1007/978-3-642-29860-8_12.","chicago":"Asarin, Eugene, Alexandre Donzé, Oded Maler, and Dejan Nickovic. “Parametric Identification of Temporal Properties,” 7186:147–60. Springer, 2012. https://doi.org/10.1007/978-3-642-29860-8_12."},"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":1,"file":[{"file_name":"2012_RV_Asarin.pdf","access_level":"open_access","content_type":"application/pdf","file_size":374726,"creator":"dernst","relation":"main_file","file_id":"7862","date_created":"2020-05-15T12:50:15Z","date_updated":"2020-07-14T12:46:01Z","checksum":"ba4a75287008fc64b8fbf78a7476ec32"}],"oa_version":"Submitted Version","intvolume":" 7186","ddc":["000"],"title":"Parametric identification of temporal properties","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3162","abstract":[{"text":"Given a dense-time real-valued signal and a parameterized temporal logic formula with both magnitude and timing parameters, we compute the subset of the parameter space that renders the formula satisfied by the trace. We provide two preliminary implementations, one which follows the exact semantics and attempts to compute the validity domain by quantifier elimination in linear arithmetics and one which conducts adaptive search in the parameter space.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference"},{"abstract":[{"text":"There is a long-running controversy about how early cell fate decisions are made in the developing mammalian embryo. 1,2 In particular, it is controversial when the first events that can predict the establishment of the pluripotent and extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur. It has long been proposed that the position and polarity of cells at the 16- to 32-cell stage embryo influence their decision to either give rise to the pluripotent cell lineage that eventually contributes to the inner cell mass (ICM), comprising the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm (TE) surrounding the blastocoel. The positioning of cells in the embryo at this developmental stage could largely be the result of random events, making this a stochastic model of cell lineage allocation. Contrary to such a stochastic model, some studies have detected putative differences in the lineage potential of individual blastomeres before compaction, indicating that the first cell fate decisions may occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a key transcription factor (TF) controlling pre-implantation development in the mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications of such molecular heterogeneities in early development and offer potential avenues toward a mechanistic understanding of these observations, contributing to the resolution of the controversy of developmental cell lineage allocation.","lang":"eng"}],"publist_id":"3531","issue":"11","type":"journal_article","date_updated":"2021-01-12T07:41:28Z","date_created":"2018-12-11T12:01:44Z","volume":11,"oa_version":"None","author":[{"first_name":"Periklis","last_name":"Pantazis","full_name":"Pantazis, Periklis"},{"full_name":"Bollenbach, Tobias","first_name":"Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"publication_status":"published","status":"public","title":"Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo","publisher":"Taylor and Francis","department":[{"_id":"ToBo"}],"intvolume":" 11","_id":"3160","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","day":"01","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2012-06-01T00:00:00Z","doi":"10.4161/cc.20118","quality_controlled":"1","page":"2055 - 2058","publication":"Cell Cycle","citation":{"short":"P. Pantazis, M.T. Bollenbach, Cell Cycle 11 (2012) 2055–2058.","mla":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle, vol. 11, no. 11, Taylor and Francis, 2012, pp. 2055–58, doi:10.4161/cc.20118.","chicago":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle. Taylor and Francis, 2012. https://doi.org/10.4161/cc.20118.","ama":"Pantazis P, Bollenbach MT. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 2012;11(11):2055-2058. doi:10.4161/cc.20118","ieee":"P. Pantazis and M. T. Bollenbach, “Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo,” Cell Cycle, vol. 11, no. 11. Taylor and Francis, pp. 2055–2058, 2012.","apa":"Pantazis, P., & Bollenbach, M. T. (2012). Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. Taylor and Francis. https://doi.org/10.4161/cc.20118","ista":"Pantazis P, Bollenbach MT. 2012. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 11(11), 2055–2058."}},{"issue":"3","publist_id":"3521","abstract":[{"text":"Overview of the Special Issue on structured prediction and inference.","lang":"eng"}],"type":"journal_article","volume":99,"oa_version":"None","date_created":"2018-12-11T12:01:46Z","date_updated":"2021-01-12T07:41:30Z","author":[{"full_name":"Blaschko, Matthew","first_name":"Matthew","last_name":"Blaschko"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"department":[{"_id":"ChLa"}],"intvolume":" 99","publisher":"Springer","title":"Guest editorial: Special issue on structured prediction and inference","publication_status":"published","status":"public","_id":"3164","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","day":"01","month":"09","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2012-09-01T00:00:00Z","doi":"10.1007/s11263-012-0530-y","page":"257 - 258","quality_controlled":"1","citation":{"ista":"Blaschko M, Lampert C. 2012. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 99(3), 257–258.","apa":"Blaschko, M., & Lampert, C. (2012). Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. Springer. https://doi.org/10.1007/s11263-012-0530-y","ieee":"M. Blaschko and C. Lampert, “Guest editorial: Special issue on structured prediction and inference,” International Journal of Computer Vision, vol. 99, no. 3. Springer, pp. 257–258, 2012.","ama":"Blaschko M, Lampert C. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 2012;99(3):257-258. doi:10.1007/s11263-012-0530-y","chicago":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision. Springer, 2012. https://doi.org/10.1007/s11263-012-0530-y.","mla":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision, vol. 99, no. 3, Springer, 2012, pp. 257–58, doi:10.1007/s11263-012-0530-y.","short":"M. Blaschko, C. Lampert, International Journal of Computer Vision 99 (2012) 257–258."},"publication":"International Journal of Computer Vision"},{"article_number":"6","ec_funded":1,"publist_id":"3518","file_date_updated":"2020-07-14T12:46:02Z","acknowledgement":"The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ","year":"2012","publisher":"BioMed Central","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"Vladar","full_name":"Vladar, Harold"}],"volume":7,"date_updated":"2021-01-12T07:41:31Z","date_created":"2018-12-11T12:01:46Z","month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1186/1745-6150-7-6","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3166","intvolume":" 7","ddc":["570","576"],"status":"public","title":"Amino acid fermentation at the origin of the genetic code","pubrep_id":"99","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:15:44Z","date_updated":"2020-07-14T12:46:02Z","checksum":"e511e401e239ef608a7fd79b21a06d78","relation":"main_file","file_id":"5166","file_size":4099536,"content_type":"application/pdf","creator":"system","file_name":"IST-2012-99-v1+1_1745-6150-7-6.pdf","access_level":"open_access"}],"has_accepted_license":"1","day":"10","citation":{"ista":"de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6.","ieee":"H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” Biology Direct, vol. 7. BioMed Central, 2012.","apa":"de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6","ama":"de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-6","chicago":"Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6.","mla":"de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6.","short":"H. de Vladar, Biology Direct 7 (2012)."},"publication":"Biology Direct","date_published":"2012-02-10T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1126/science.336.6077.32","date_published":"2012-04-06T00:00:00Z","article_type":"letter_note","page":"32-34","publication":"Science","external_id":{"pmid":["22491839"]},"citation":{"short":"M. Weber, Science 336 (2012) 32–34.","mla":"Weber, Michele. “NextGen Speaks 13 .” Science, vol. 336, no. 6077, American Association for the Advancement of Science, 2012, pp. 32–34, doi:10.1126/science.336.6077.32.","chicago":"Weber, Michele. “NextGen Speaks 13 .” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.336.6077.32.","ama":"Weber M. NextGen speaks 13 . Science. 2012;336(6077):32-34. doi:10.1126/science.336.6077.32","ieee":"M. Weber, “NextGen speaks 13 ,” Science, vol. 336, no. 6077. American Association for the Advancement of Science, pp. 32–34, 2012.","apa":"Weber, M. (2012). NextGen speaks 13 . Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.336.6077.32","ista":"Weber M. 2012. NextGen speaks 13 . Science. 336(6077), 32–34."},"month":"04","day":"06","date_updated":"2021-01-12T07:41:32Z","date_created":"2018-12-11T12:01:47Z","volume":336,"oa_version":"None","author":[{"full_name":"Weber, Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","last_name":"Weber","first_name":"Michele"}],"popular_science":"1","title":"NextGen speaks 13 ","status":"public","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"American Association for the Advancement of Science","intvolume":" 336","_id":"3167","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publist_id":"3516","issue":"6077","type":"journal_article"},{"intvolume":" 25","publisher":"Springer","publication_status":"published","title":"Parallel repetition of computationally sound protocols revisited","status":"public","_id":"3241","year":"2012","volume":25,"date_created":"2018-12-11T12:02:12Z","date_updated":"2021-01-12T07:42:03Z","author":[{"full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"last_name":"Wikström","first_name":"Douglas","full_name":"Wikström, Douglas"}],"type":"journal_article","extern":1,"issue":"1","publist_id":"3439","abstract":[{"lang":"eng","text":"We prove a negative result concerning error reduction by parallel repetition for computationally sound protocols, e.g., interactive arguments. Our main result is a complete and computationally sound eight round interactive argument for which k-fold parallel repetition does not reduce the error below a constant for any polynomial k. The starting point for our construction is the work of Bellare, Impagliazzo and Naor (FOCS'97). For any fixed k, they construct a four round protocol for which k-fold parallel repetition does not lower the soundness error. The communication complexity of this protocol is linear in k. By using universal arguments due to Barak and Goldreich (CCC 2002), we turn this protocol into an eight-round protocol whose complexity is basically independent of k. "}],"page":"116 - 135","quality_controlled":0,"citation":{"ieee":"K. Z. Pietrzak and D. Wikström, “Parallel repetition of computationally sound protocols revisited,” Journal of Cryptology, vol. 25, no. 1. Springer, pp. 116–135, 2012.","apa":"Pietrzak, K. Z., & Wikström, D. (2012). Parallel repetition of computationally sound protocols revisited. 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Wikström, Journal of Cryptology 25 (2012) 116–135.","mla":"Pietrzak, Krzysztof Z., and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited.” Journal of Cryptology, vol. 25, no. 1, Springer, 2012, pp. 116–35, doi:10.1007/s00145-010-9090-x."},"publication":"Journal of Cryptology","date_published":"2012-11-01T00:00:00Z","doi":"10.1007/s00145-010-9090-x","month":"11","day":"01"},{"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 (Modern Graph Algorithmic Techniques in Formal Verification), FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.\r\nThe authors would like to thank Avik Chaudhuri for his invaluable help and feedback.","year":"2012","volume":7148,"date_updated":"2021-01-12T07:42:08Z","date_created":"2018-12-11T12:02:16Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Vishwanath","last_name":"Raman","full_name":"Raman, Vishwanath"}],"publist_id":"3405","ec_funded":1,"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.2697"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-27940-9_11","conference":{"start_date":"2012-01-22","location":"Philadelphia, PA, USA","end_date":"2012-01-24","name":"VMCAI: Verification, Model Checking and Abstract Interpretation"},"month":"01","intvolume":" 7148","status":"public","title":"Synthesizing protocols for digital contract signing","_id":"3252","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents, the trusted third party (TTP) and the protocols as path formulas in Linear Temporal Logic (LTL) and prove that the satisfaction of the objectives of the agents and the TTP imply satisfaction of the protocol objectives. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail in synthesizing these protocols, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of assume-guarantee synthesis as follows: (a) any solution of assume-guarantee synthesis is attack-free; no subset of participants can violate the objectives of the other participants without violating their own objectives; (b) the Asokan-Shoup-Waidner (ASW) certified mail protocol that has known vulnerabilities is not a solution of AGS; and (c) the Kremer-Markowitch (KM) non-repudiation protocol is a solution of AGS. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can generate correct protocols and automatically discover vulnerabilities. The solution to assume-guarantee synthesis can be computed efficiently as the secure equilibrium solution of three-player graph games. © 2012 Springer-Verlag.","lang":"eng"}],"page":"152 - 168","citation":{"ieee":"K. Chatterjee and V. Raman, “Synthesizing protocols for digital contract signing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 152–168.","apa":"Chatterjee, K., & Raman, V. (2012). Synthesizing protocols for digital contract signing (Vol. 7148, pp. 152–168). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_11","ista":"Chatterjee K, Raman V. 2012. Synthesizing protocols for digital contract signing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 152–168.","ama":"Chatterjee K, Raman V. Synthesizing protocols for digital contract signing. In: Vol 7148. Springer; 2012:152-168. doi:10.1007/978-3-642-27940-9_11","chicago":"Chatterjee, Krishnendu, and Vishwanath Raman. “Synthesizing Protocols for Digital Contract Signing,” 7148:152–68. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_11.","short":"K. Chatterjee, V. Raman, in:, Springer, 2012, pp. 152–168.","mla":"Chatterjee, Krishnendu, and Vishwanath Raman. Synthesizing Protocols for Digital Contract Signing. Vol. 7148, Springer, 2012, pp. 152–68, doi:10.1007/978-3-642-27940-9_11."},"date_published":"2012-01-20T00:00:00Z","scopus_import":1,"day":"20"},{"scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"37 - 46","citation":{"ieee":"K. Chatterjee and L. Doyen, “Games and Markov decision processes with mean payoff parity and energy parity objectives,” presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic, 2012, vol. 7119, pp. 37–46.","apa":"Chatterjee, K., & Doyen, L. (2012). Games and Markov decision processes with mean payoff parity and energy parity objectives (Vol. 7119, pp. 37–46). Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-25929-6_3","ista":"Chatterjee K, Doyen L. 2012. Games and Markov decision processes with mean payoff parity and energy parity objectives. MEMICS: Mathematical and Engineering Methods in Computer Science, LNCS, vol. 7119, 37–46.","ama":"Chatterjee K, Doyen L. Games and Markov decision processes with mean payoff parity and energy parity objectives. In: Vol 7119. Springer; 2012:37-46. doi:10.1007/978-3-642-25929-6_3","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives,” 7119:37–46. Springer, 2012. https://doi.org/10.1007/978-3-642-25929-6_3.","short":"K. Chatterjee, L. Doyen, in:, Springer, 2012, pp. 37–46.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives. Vol. 7119, Springer, 2012, pp. 37–46, doi:10.1007/978-3-642-25929-6_3."},"date_published":"2012-01-01T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"In this paper we survey results of two-player games on graphs and Markov decision processes with parity, mean-payoff and energy objectives, and the combination of mean-payoff and energy objectives with parity objectives. These problems have applications in verification and synthesis of reactive systems in resource-constrained environments.","lang":"eng"}],"intvolume":" 7119","ddc":["000"],"title":"Games and Markov decision processes with mean payoff parity and energy parity objectives","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3255","oa_version":"Submitted Version","file":[{"file_id":"7863","relation":"main_file","date_created":"2020-05-15T12:53:12Z","date_updated":"2020-07-14T12:46:05Z","checksum":"eed2cc1e76b160418c977e76e8899a60","file_name":"2012_MEMICS_Chatterjee.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":114060}],"month":"01","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-25929-6_3","conference":{"name":"MEMICS: Mathematical and Engineering Methods in Computer Science","start_date":"2011-10-14","location":"Lednice, Czech Republic","end_date":"2011-10-16"},"publist_id":"3400","file_date_updated":"2020-07-14T12:46:05Z","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","acknowledgement":"This work was partially supported by FWF NFN Grant S11407-N23 (RiSE) and a Microsoft faculty fellowship.","year":"2012","volume":7119,"date_updated":"2021-01-12T07:42:10Z","date_created":"2018-12-11T12:02:17Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3250","year":"2012","title":"Cryptography from learning parity with noise","status":"public","publication_status":"published","intvolume":" 7147","publisher":"Springer","department":[{"_id":"KrPi"}],"author":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"date_created":"2018-12-11T12:02:15Z","date_updated":"2021-01-12T07:42:07Z","oa_version":"None","volume":7147,"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"The Learning Parity with Noise (LPN) problem has recently found many applications in cryptography as the hardness assumption underlying the constructions of "provably secure" cryptographic schemes like encryption or authentication protocols. Being provably secure means that the scheme comes with a proof showing that the existence of an efficient adversary against the scheme implies that the underlying hardness assumption is wrong. LPN based schemes are appealing for theoretical and practical reasons. On the theoretical side, LPN based schemes offer a very strong security guarantee. The LPN problem is equivalent to the problem of decoding random linear codes, a problem that has been extensively studied in the last half century. The fastest known algorithms run in exponential time and unlike most number-theoretic problems used in cryptography, the LPN problem does not succumb to known quantum algorithms. On the practical side, LPN based schemes are often extremely simple and efficient in terms of code-size as well as time and space requirements. This makes them prime candidates for light-weight devices like RFID tags, which are too weak to implement standard cryptographic primitives like the AES block-cipher. This talk will be a gentle introduction to provable security using simple LPN based schemes as examples. Starting from pseudorandom generators and symmetric key encryption, over secret-key authentication protocols, and, if time admits, touching on recent constructions of public-key identification, commitments and zero-knowledge proofs.","lang":"eng"}],"publist_id":"3407","citation":{"chicago":"Pietrzak, Krzysztof Z. “Cryptography from Learning Parity with Noise,” 7147:99–114. Springer, 2012. https://doi.org/10.1007/978-3-642-27660-6_9.","short":"K.Z. Pietrzak, in:, Springer, 2012, pp. 99–114.","mla":"Pietrzak, Krzysztof Z. Cryptography from Learning Parity with Noise. Vol. 7147, Springer, 2012, pp. 99–114, doi:10.1007/978-3-642-27660-6_9.","apa":"Pietrzak, K. Z. (2012). Cryptography from learning parity with noise (Vol. 7147, pp. 99–114). 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Springer; 2012:99-114. doi:10.1007/978-3-642-27660-6_9"},"quality_controlled":"1","page":"99 - 114","conference":{"name":"SOFSEM: Current Trends in Theory and Practice of Computer Science","location":"Špindlerův Mlýn, Czech Republic","start_date":"2012-01-21","end_date":"2012-01-27"},"doi":"10.1007/978-3-642-27660-6_9","date_published":"2012-02-19T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"19","month":"02"},{"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00454-011-9382-4","month":"03","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer","year":"2012","acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0057 and HR0011-09-0065 as well as the National Science Foundation (NSF) under grant DBI-0820624.","date_created":"2018-12-11T12:02:17Z","date_updated":"2021-01-12T07:42:10Z","volume":47,"author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","first_name":"Michael"}],"file_date_updated":"2020-07-14T12:46:05Z","publist_id":"3398","page":"393 - 414","publication":"Discrete & Computational Geometry","citation":{"chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Dual Complexes of Cubical Subdivisions of ℝn.” Discrete & Computational Geometry. Springer, 2012. https://doi.org/10.1007/s00454-011-9382-4.","short":"H. Edelsbrunner, M. Kerber, Discrete & Computational Geometry 47 (2012) 393–414.","mla":"Edelsbrunner, Herbert, and Michael Kerber. “Dual Complexes of Cubical Subdivisions of ℝn.” Discrete & Computational Geometry, vol. 47, no. 2, Springer, 2012, pp. 393–414, doi:10.1007/s00454-011-9382-4.","ieee":"H. Edelsbrunner and M. Kerber, “Dual complexes of cubical subdivisions of ℝn,” Discrete & Computational Geometry, vol. 47, no. 2. Springer, pp. 393–414, 2012.","apa":"Edelsbrunner, H., & Kerber, M. (2012). Dual complexes of cubical subdivisions of ℝn. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-011-9382-4","ista":"Edelsbrunner H, Kerber M. 2012. Dual complexes of cubical subdivisions of ℝn. Discrete & Computational Geometry. 47(2), 393–414.","ama":"Edelsbrunner H, Kerber M. Dual complexes of cubical subdivisions of ℝn. Discrete & Computational Geometry. 2012;47(2):393-414. doi:10.1007/s00454-011-9382-4"},"date_published":"2012-03-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","ddc":["000"],"title":"Dual complexes of cubical subdivisions of ℝn","status":"public","intvolume":" 47","_id":"3256","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"IST-2016-543-v1+1_2012-J-08-HierarchyCubeComplex.pdf","creator":"system","content_type":"application/pdf","file_size":203636,"file_id":"4675","relation":"main_file","checksum":"76486f3b2c9e7fd81342f3832ca387e7","date_created":"2018-12-12T10:08:15Z","date_updated":"2020-07-14T12:46:05Z"}],"oa_version":"Submitted Version","pubrep_id":"543","type":"journal_article","abstract":[{"lang":"eng","text":"We use a distortion to define the dual complex of a cubical subdivision of ℝ n as an n-dimensional subcomplex of the nerve of the set of n-cubes. Motivated by the topological analysis of high-dimensional digital image data, we consider such subdivisions defined by generalizations of quad- and oct-trees to n dimensions. Assuming the subdivision is balanced, we show that mapping each vertex to the center of the corresponding n-cube gives a geometric realization of the dual complex in ℝ n."}],"issue":"2"},{"publist_id":"3403","ec_funded":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}],"year":"2012","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","date_created":"2018-12-11T12:02:17Z","date_updated":"2021-01-12T07:42:09Z","volume":211,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"month":"02","quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"main_file_link":[{"url":"http://arise.or.at/pubpdf/The_complexity_of_stochastic_M___u_ller_games.pdf"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.ic.2011.11.004","type":"journal_article","abstract":[{"lang":"eng","text":"The theory of graph games with ω-regular winning conditions is the foundation for modeling and synthesizing reactive processes. In the case of stochastic reactive processes, the corresponding stochastic graph games have three players, two of them (System and Environment) behaving adversarially, and the third (Uncertainty) behaving probabilistically. We consider two problems for stochastic graph games: the qualitative problem asks for the set of states from which a player can win with probability 1 (almost-sure winning); and the quantitative problem asks for the maximal probability of winning (optimal winning) from each state. We consider ω-regular winning conditions formalized as Müller winning conditions. We present optimal memory bounds for pure (deterministic) almost-sure winning and optimal winning strategies in stochastic graph games with Müller winning conditions. We also study the complexity of stochastic Müller games and show that both the qualitative and quantitative analysis problems are PSPACE-complete. Our results are relevant in synthesis of stochastic reactive processes."}],"title":"The complexity of stochastic Müller games","status":"public","intvolume":" 211","_id":"3254","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","scopus_import":1,"day":"01","page":"29 - 48","publication":"Information and Computation","citation":{"chicago":"Chatterjee, Krishnendu. “The Complexity of Stochastic Müller Games.” Information and Computation. Elsevier, 2012. https://doi.org/10.1016/j.ic.2011.11.004.","mla":"Chatterjee, Krishnendu. “The Complexity of Stochastic Müller Games.” Information and Computation, vol. 211, Elsevier, 2012, pp. 29–48, doi:10.1016/j.ic.2011.11.004.","short":"K. Chatterjee, Information and Computation 211 (2012) 29–48.","ista":"Chatterjee K. 2012. The complexity of stochastic Müller games. Information and Computation. 211, 29–48.","apa":"Chatterjee, K. (2012). The complexity of stochastic Müller games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2011.11.004","ieee":"K. Chatterjee, “The complexity of stochastic Müller games,” Information and Computation, vol. 211. Elsevier, pp. 29–48, 2012.","ama":"Chatterjee K. The complexity of stochastic Müller games. Information and Computation. 2012;211:29-48. doi:10.1016/j.ic.2011.11.004"},"date_published":"2012-02-01T00:00:00Z"},{"publist_id":"3404","abstract":[{"text":"We describe a framework for reasoning about programs with lists carrying integer numerical data. We use abstract domains to describe and manipulate complex constraints on configurations of these programs mixing constraints on the shape of the heap, sizes of the lists, on the multisets of data stored in these lists, and on the data at their different positions. Moreover, we provide powerful techniques for automatic validation of Hoare-triples and invariant checking, as well as for automatic synthesis of invariants and procedure summaries using modular inter-procedural analysis. The approach has been implemented in a tool called Celia and experimented successfully on a large benchmark of programs.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"author":[{"first_name":"Ahmed","last_name":"Bouajjani","full_name":"Bouajjani, Ahmed"},{"full_name":"Dragoi, Cezara","last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Enea, Constantin","first_name":"Constantin","last_name":"Enea"},{"last_name":"Sighireanu","first_name":"Mihaela","full_name":"Sighireanu, Mihaela"}],"oa_version":"None","volume":7148,"date_updated":"2021-01-12T07:42:09Z","date_created":"2018-12-11T12:02:17Z","_id":"3253","year":"2012","acknowledgement":"This work was partly supported by the French National Research Agency (ANR) project Veridyc (ANR-09-SEGI-016).","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 7148","publisher":"Springer","department":[{"_id":"ToHe"}],"status":"public","publication_status":"published","title":"Abstract domains for automated reasoning about list manipulating programs with infinite data","month":"02","day":"26","date_published":"2012-02-26T00:00:00Z","doi":"10.1007/978-3-642-27940-9_1","conference":{"end_date":"2012-01-24","start_date":"2012-01-22","location":"Philadelphia, PA, USA","name":"VMCAI: Verification, Model Checking and Abstract Interpretation"},"language":[{"iso":"eng"}],"citation":{"chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Abstract Domains for Automated Reasoning about List Manipulating Programs with Infinite Data,” 7148:1–22. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_1.","mla":"Bouajjani, Ahmed, et al. Abstract Domains for Automated Reasoning about List Manipulating Programs with Infinite Data. Vol. 7148, Springer, 2012, pp. 1–22, doi:10.1007/978-3-642-27940-9_1.","short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2012, pp. 1–22.","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Abstract domains for automated reasoning about list manipulating programs with infinite data. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 1–22.","apa":"Bouajjani, A., Dragoi, C., Enea, C., & Sighireanu, M. (2012). Abstract domains for automated reasoning about list manipulating programs with infinite data (Vol. 7148, pp. 1–22). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_1","ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Abstract domains for automated reasoning about list manipulating programs with infinite data,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 1–22.","ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Abstract domains for automated reasoning about list manipulating programs with infinite data. In: Vol 7148. Springer; 2012:1-22. doi:10.1007/978-3-642-27940-9_1"},"page":"1 - 22","quality_controlled":"1"},{"quality_controlled":"1","citation":{"mla":"Ion, Adrian, et al. Image Segmentation by Figure-Ground Composition into Maximal Cliques. 6126486, IEEE, 2012, doi:10.1109/ICCV.2011.6126486.","short":"A. Ion, J. Carreira, C. Sminchisescu, in:, IEEE, 2012.","chicago":"Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Image Segmentation by Figure-Ground Composition into Maximal Cliques.” IEEE, 2012. https://doi.org/10.1109/ICCV.2011.6126486.","ama":"Ion A, Carreira J, Sminchisescu C. Image segmentation by figure-ground composition into maximal cliques. In: IEEE; 2012. doi:10.1109/ICCV.2011.6126486","ista":"Ion A, Carreira J, Sminchisescu C. 2012. Image segmentation by figure-ground composition into maximal cliques. ICCV: International Conference on Computer Vision, 6126486.","apa":"Ion, A., Carreira, J., & Sminchisescu, C. (2012). Image segmentation by figure-ground composition into maximal cliques. Presented at the ICCV: International Conference on Computer Vision, Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126486","ieee":"A. Ion, J. Carreira, and C. Sminchisescu, “Image segmentation by figure-ground composition into maximal cliques,” presented at the ICCV: International Conference on Computer Vision, Barcelona, Spain, 2012."},"language":[{"iso":"eng"}],"date_published":"2012-01-12T00:00:00Z","doi":"10.1109/ICCV.2011.6126486","conference":{"name":"ICCV: International Conference on Computer Vision","end_date":"2011-11-13","start_date":"2011-11-06","location":"Barcelona, Spain"},"month":"01","day":"12","department":[{"_id":"HeEd"}],"publisher":"IEEE","publication_status":"published","title":"Image segmentation by figure-ground composition into maximal cliques","status":"public","_id":"3265","year":"2012","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_updated":"2021-01-12T07:42:15Z","date_created":"2018-12-11T12:02:21Z","author":[{"last_name":"Ion","first_name":"Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87","full_name":"Ion, Adrian"},{"last_name":"Carreira","first_name":"Joao","full_name":"Carreira, Joao"},{"full_name":"Sminchisescu, Cristian","last_name":"Sminchisescu","first_name":"Cristian"}],"type":"conference","article_number":"6126486","publist_id":"3382","abstract":[{"lang":"eng","text":"We propose a mid-level statistical model for image segmentation that composes multiple figure-ground hypotheses (FG) obtained by applying constraints at different locations and scales, into larger interpretations (tilings) of the entire image. Inference is cast as optimization over sets of maximal cliques sampled from a graph connecting all non-overlapping figure-ground segment hypotheses. Potential functions over cliques combine unary, Gestalt-based figure qualities, and pairwise compatibilities among spatially neighboring segments, constrained by T-junctions and the boundary interface statistics of real scenes. Learning the model parameters is based on maximum likelihood, alternating between sampling image tilings and optimizing their potential function parameters. State of the art results are reported on the Berkeley and Stanford segmentation datasets, as well as VOC2009, where a 28% improvement was achieved."}]},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Traditionally, symmetric-key message authentication codes (MACs) are easily built from pseudorandom functions (PRFs). In this work we propose a wide variety of other approaches to building efficient MACs, without going through a PRF first. In particular, unlike deterministic PRF-based MACs, where each message has a unique valid tag, we give a number of probabilistic MAC constructions from various other primitives/assumptions. Our main results are summarized as follows: We show several new probabilistic MAC constructions from a variety of general assumptions, including CCA-secure encryption, Hash Proof Systems and key-homomorphic weak PRFs. By instantiating these frameworks under concrete number theoretic assumptions, we get several schemes which are more efficient than just using a state-of-the-art PRF instantiation under the corresponding assumption. For probabilistic MACs, unlike deterministic ones, unforgeability against a chosen message attack (uf-cma ) alone does not imply security if the adversary can additionally make verification queries (uf-cmva ). We give an efficient generic transformation from any uf-cma secure MAC which is "message-hiding" into a uf-cmva secure MAC. This resolves the main open problem of Kiltz et al. from Eurocrypt'11; By using our transformation on their constructions, we get the first efficient MACs from the LPN assumption. While all our new MAC constructions immediately give efficient actively secure, two-round symmetric-key identification schemes, we also show a very simple, three-round actively secure identification protocol from any weak PRF. In particular, the resulting protocol is much more efficient than the trivial approach of building a regular PRF from a weak PRF. © 2012 International Association for Cryptologic Research."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3282","intvolume":" 7237","status":"public","title":"Message authentication, revisited","ddc":["000","004"],"pubrep_id":"686","file":[{"checksum":"8557c17a8c2586d06ebfe62d934f5c5f","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:14:23Z","file_id":"5074","relation":"main_file","creator":"system","file_size":372292,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-686-v1+1_059.pdf"}],"oa_version":"Submitted Version","has_accepted_license":"1","day":"10","citation":{"apa":"Dodis, Y., Pietrzak, K. Z., Kiltz, E., & Wichs, D. (2012). Message authentication, revisited (Vol. 7237, pp. 355–374). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Cambridge, UK: Springer. https://doi.org/10.1007/978-3-642-29011-4_22","ieee":"Y. Dodis, K. Z. Pietrzak, E. Kiltz, and D. Wichs, “Message authentication, revisited,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Cambridge, UK, 2012, vol. 7237, pp. 355–374.","ista":"Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. 2012. Message authentication, revisited. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 7237, 355–374.","ama":"Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. Message authentication, revisited. In: Vol 7237. Springer; 2012:355-374. doi:10.1007/978-3-642-29011-4_22","chicago":"Dodis, Yevgeniy, Krzysztof Z Pietrzak, Eike Kiltz, and Daniel Wichs. “Message Authentication, Revisited,” 7237:355–74. Springer, 2012. https://doi.org/10.1007/978-3-642-29011-4_22.","short":"Y. Dodis, K.Z. Pietrzak, E. Kiltz, D. Wichs, in:, Springer, 2012, pp. 355–374.","mla":"Dodis, Yevgeniy, et al. Message Authentication, Revisited. Vol. 7237, Springer, 2012, pp. 355–74, doi:10.1007/978-3-642-29011-4_22."},"page":"355 - 374","date_published":"2012-03-10T00:00:00Z","ec_funded":1,"publist_id":"3364","file_date_updated":"2020-07-14T12:46:06Z","acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC)","year":"2012","publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","author":[{"full_name":"Dodis, Yevgeniy","last_name":"Dodis","first_name":"Yevgeniy"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"first_name":"Eike","last_name":"Kiltz","full_name":"Kiltz, Eike"},{"first_name":"Daniel","last_name":"Wichs","full_name":"Wichs, Daniel"}],"volume":7237,"date_updated":"2021-01-12T07:42:22Z","date_created":"2018-12-11T12:02:27Z","month":"03","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/978-3-642-29011-4_22","conference":{"end_date":"2012-04-19","start_date":"2012-04-15","location":"Cambridge, UK","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"language":[{"iso":"eng"}]},{"volume":7194,"date_updated":"2021-01-12T07:42:21Z","date_created":"2018-12-11T12:02:26Z","author":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"KrPi"}],"publisher":"Springer","publication_status":"published","acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC).","year":"2012","publist_id":"3366","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-28914-9_31","conference":{"end_date":"2012-03-21","location":"Taormina, Sicily, Italy","start_date":"2012-03-19","name":"TCC: Theory of Cryptography Conference"},"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.iacr.org/archive/tcc2012/71940166/71940166.pdf"}],"oa":1,"month":"05","oa_version":"Submitted Version","intvolume":" 7194","status":"public","title":"Subspace LWE","_id":"3280","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The (decisional) learning with errors problem (LWE) asks to distinguish "noisy" inner products of a secret vector with random vectors from uniform. The learning parities with noise problem (LPN) is the special case where the elements of the vectors are bits. In recent years, the LWE and LPN problems have found many applications in cryptography. In this paper we introduce a (seemingly) much stronger adaptive assumption, called "subspace LWE" (SLWE), where the adversary can learn the inner product of the secret and random vectors after they were projected into an adaptively and adversarially chosen subspace. We prove that, surprisingly, the SLWE problem mapping into subspaces of dimension d is almost as hard as LWE using secrets of length d (the other direction is trivial.) This result immediately implies that several existing cryptosystems whose security is based on the hardness of the LWE/LPN problems are provably secure in a much stronger sense than anticipated. As an illustrative example we show that the standard way of using LPN for symmetric CPA secure encryption is even secure against a very powerful class of related key attacks. ","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2012-05-04T00:00:00Z","page":"548 - 563","citation":{"ista":"Pietrzak KZ. 2012. Subspace LWE. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 548–563.","apa":"Pietrzak, K. Z. (2012). Subspace LWE (Vol. 7194, pp. 548–563). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_31","ieee":"K. Z. Pietrzak, “Subspace LWE,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 548–563.","ama":"Pietrzak KZ. Subspace LWE. In: Vol 7194. Springer; 2012:548-563. doi:10.1007/978-3-642-28914-9_31","chicago":"Pietrzak, Krzysztof Z. “Subspace LWE,” 7194:548–63. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_31.","mla":"Pietrzak, Krzysztof Z. Subspace LWE. Vol. 7194, Springer, 2012, pp. 548–63, doi:10.1007/978-3-642-28914-9_31.","short":"K.Z. Pietrzak, in:, Springer, 2012, pp. 548–563."},"day":"04"},{"day":"04","month":"05","main_file_link":[{"url":"http://www.iacr.org/archive/tcc2012/tcc2012-index.html"}],"citation":{"ama":"Pietrzak KZ, Rosen A, Segev G. Lossy functions do not amplify well. In: Vol 7194. Springer; 2012:458-475. doi:10.1007/978-3-642-28914-9_26","apa":"Pietrzak, K. Z., Rosen, A., & Segev, G. (2012). Lossy functions do not amplify well (Vol. 7194, pp. 458–475). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_26","ieee":"K. Z. Pietrzak, A. Rosen, and G. Segev, “Lossy functions do not amplify well,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 458–475.","ista":"Pietrzak KZ, Rosen A, Segev G. 2012. Lossy functions do not amplify well. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 458–475.","short":"K.Z. Pietrzak, A. Rosen, G. Segev, in:, Springer, 2012, pp. 458–475.","mla":"Pietrzak, Krzysztof Z., et al. Lossy Functions Do Not Amplify Well. Vol. 7194, Springer, 2012, pp. 458–75, doi:10.1007/978-3-642-28914-9_26.","chicago":"Pietrzak, Krzysztof Z, Alon Rosen, and Gil Segev. “Lossy Functions Do Not Amplify Well,” 7194:458–75. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_26."},"quality_controlled":"1","page":"458 - 475","conference":{"end_date":"2012-03-21","start_date":"2012-03-19","location":"Taormina, Sicily, Italy","name":"TCC: Theory of Cryptography Conference"},"date_published":"2012-05-04T00:00:00Z","doi":"10.1007/978-3-642-28914-9_26","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We consider the problem of amplifying the "lossiness" of functions. We say that an oracle circuit C*: {0,1} m → {0,1}* amplifies relative lossiness from ℓ/n to L/m if for every function f:{0,1} n → {0,1} n it holds that 1 If f is injective then so is C f. 2 If f has image size of at most 2 n-ℓ, then C f has image size at most 2 m-L. The question is whether such C* exists for L/m ≫ ℓ/n. This problem arises naturally in the context of cryptographic "lossy functions," where the relative lossiness is the key parameter. We show that for every circuit C* that makes at most t queries to f, the relative lossiness of C f is at most L/m ≤ ℓ/n + O(log t)/n. In particular, no black-box method making a polynomial t = poly(n) number of queries can amplify relative lossiness by more than an O(logn)/n additive term. We show that this is tight by giving a simple construction (cascading with some randomization) that achieves such amplification.","lang":"eng"}],"publist_id":"3365","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3281","year":"2012","acknowledgement":"We would like to thank Oded Goldreich and Omer Rein- gold for discussions at an early stage of this project, and Scott Aaronson for clarifications regarding the collision problem.\r\n","title":"Lossy functions do not amplify well","publication_status":"published","status":"public","publisher":"Springer","department":[{"_id":"KrPi"}],"intvolume":" 7194","author":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rosen","first_name":"Alon","full_name":"Rosen, Alon"},{"last_name":"Segev","first_name":"Gil","full_name":"Segev, Gil"}],"date_created":"2018-12-11T12:02:26Z","date_updated":"2021-01-12T07:42:22Z","oa_version":"None","volume":7194},{"month":"01","day":"01","date_published":"2012-01-01T00:00:00Z","conference":{"name":"SODA: Symposium on Discrete Algorithms"},"page":"750 - 759","quality_controlled":0,"oa":1,"citation":{"ama":"Kolmogorov V, Živný S. The complexity of conservative valued CSPs. In: SIAM; 2012:750-759.","ista":"Kolmogorov V, Živný S. 2012. The complexity of conservative valued CSPs. SODA: Symposium on Discrete Algorithms, 750–759.","apa":"Kolmogorov, V., & Živný, S. (2012). The complexity of conservative valued CSPs (pp. 750–759). Presented at the SODA: Symposium on Discrete Algorithms, SIAM.","ieee":"V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,” presented at the SODA: Symposium on Discrete Algorithms, 2012, pp. 750–759.","mla":"Kolmogorov, Vladimir, and Stanislav Živný. The Complexity of Conservative Valued CSPs. SIAM, 2012, pp. 750–59.","short":"V. Kolmogorov, S. Živný, in:, SIAM, 2012, pp. 750–759.","chicago":"Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs,” 750–59. SIAM, 2012."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1008.1555"}],"extern":1,"publist_id":"3362","abstract":[{"lang":"eng","text":"We study the complexity of valued constraint satisfaction problems (VCSP). A problem from VCSP is characterised by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimise the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well-understood, see Raghavendra [FOCS’08]. However, there is no characterisation of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimisation perspective.\nWe consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e. relations), such languages have been called conservative and studied by Bulatov [LICS’03] and recently by Barto [LICS’11]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [AIJ’06] for languages over Boolean domains, by Deineko et al. [JACM’08] for {0,1}-valued languages (a.k.a Max-CSP), and by Takhanov [STACS’10] for {0,∞}-valued languages containing all finite- valued unary cost functions (a.k.a. Min-Cost-Hom).\nWe prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimorphisms), then any instance can be solved in polynomial time (via a new algorithm developed in this paper), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains is significantly harder than the Boolean case. The polynomial-time algorithm we present for the tractable cases is a generalisation of the submodular minimisation problem and a result of Cohen et al. [TCS’08].\nOur results generalise previous results by Takhanov [STACS’10] and (a subset of results) by Cohen et al. [AIJ’06] and Deineko et al. [JACM’08]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [JACM’08], and provide a powerful tool for proving hardness of finite-valued and general-valued languages."}],"type":"conference","date_updated":"2021-01-12T07:42:23Z","date_created":"2018-12-11T12:02:27Z","author":[{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"},{"first_name":"Stanislav","last_name":"Živný","full_name":"Živný, Stanislav"}],"publisher":"SIAM","title":"The complexity of conservative valued CSPs","status":"public","publication_status":"published","acknowledgement":"Vladimir Kolmogorov is supported by the Royal Academy of Eng ineering/EPSRC.","_id":"3284","year":"2012"},{"author":[{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"first_name":"Alex","last_name":"Carrete","full_name":"Carrete, Alex"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"date_created":"2018-12-11T11:45:51Z","date_updated":"2021-01-12T07:42:29Z","volume":134,"oa_version":"None","year":"2012","_id":"330","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor","publisher":"ACS","intvolume":" 134","abstract":[{"lang":"eng","text":"A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles with controlled composition is presented. CZTS nanoparticles were prepared through the reaction of the metals' amino complexes with elemental sulfur in a continuous-flow reactor at moderate temperatures (300-330 °C). High-resolution transmission electron microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic structure compatible with that of the kesterite. Chemical characterization of the materials showed the presence of the four elements in each individual nanocrystal. Composition control was achieved by adjusting the solution flow rate through the reactor and the proper choice of the nominal precursor concentration within the flowing solution. Single-particle analysis revealed a composition distribution within each sample, which was optimized at the highest synthesis temperatures used. "}],"issue":"3","publist_id":"7531","extern":"1","type":"journal_article","doi":"10.1021/ja209688a","date_published":"2012-01-02T00:00:00Z","language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","citation":{"ama":"Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 2012;134(3):1438-1441. doi:10.1021/ja209688a","ista":"Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. 2012. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 134(3), 1438–1441.","apa":"Shavel, A., Cadavid, D., Ibáñez, M., Carrete, A., & Cabot, A. (2012). Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja209688a","ieee":"A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, and A. Cabot, “Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor,” Journal of the American Chemical Society, vol. 134, no. 3. ACS, pp. 1438–1441, 2012.","mla":"Shavel, Alexey, et al. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society, vol. 134, no. 3, ACS, 2012, pp. 1438–41, doi:10.1021/ja209688a.","short":"A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, A. Cabot, Journal of the American Chemical Society 134 (2012) 1438–1441.","chicago":"Shavel, Alexey, Doris Cadavid, Maria Ibáñez, Alex Carrete, and Andreu Cabot. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja209688a."},"article_type":"original","quality_controlled":"1","page":"1438 - 1441","day":"02","month":"01","article_processing_charge":"No"},{"month":"01","doi":"10.1038/nrn3125","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Synaptic Mechanisms of Neuronal Network Function","_id":"25BC64A8-B435-11E9-9278-68D0E5697425","grant_number":"JO_780/A5"},{"grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen"}],"quality_controlled":"1","publist_id":"3322","file_date_updated":"2020-07-14T12:46:07Z","author":[{"full_name":"Eggermann, Emmanuel","id":"34DACA34-E9AE-11E9-849C-D35BD8ADC20C","last_name":"Eggermann","first_name":"Emmanuel"},{"full_name":"Bucurenciu, Iancu","last_name":"Bucurenciu","first_name":"Iancu","id":"4BD1D872-E9AE-11E9-9EE9-8BF4597A9E2A"},{"first_name":"Sarit","last_name":"Goswami","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","full_name":"Goswami, Sarit"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"volume":13,"date_created":"2018-12-11T12:02:38Z","date_updated":"2021-01-12T07:42:36Z","year":"2012","acknowledgement":"Work of the authors was funded by grants of the Deutsche Forschungsgemeinschaft to P.J. (grants SFB 780/A5, TR 3/B10 and the Leibniz programme), a European Research Council Advanced grant to P.J. and a Swiss National Foundation fellowship to E.E.\r\nWe thank D. Tsien and E. Neher for their comments on this Review, J. Guzmán and A. Pernía-Andrade for reading earlier versions and E. Kramberger for perfect editorial support. We apologize that owing to space constraints, not all relevant papers could be cited.\r\n","department":[{"_id":"PeJo"}],"publisher":"Nature Publishing Group","publication_status":"published","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2012-01-01T00:00:00Z","citation":{"ista":"Eggermann E, Bucurenciu I, Goswami S, Jonas PM. 2012. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. 13(1), 7–21.","ieee":"E. Eggermann, I. Bucurenciu, S. Goswami, and P. M. Jonas, “Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses,” Nature Reviews Neuroscience, vol. 13, no. 1. Nature Publishing Group, pp. 7–21, 2012.","apa":"Eggermann, E., Bucurenciu, I., Goswami, S., & Jonas, P. M. (2012). Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nrn3125","ama":"Eggermann E, Bucurenciu I, Goswami S, Jonas PM. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. 2012;13(1):7-21. doi:10.1038/nrn3125","chicago":"Eggermann, Emmanuel, Iancu Bucurenciu, Sarit Goswami, and Peter M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” Nature Reviews Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nrn3125.","mla":"Eggermann, Emmanuel, et al. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” Nature Reviews Neuroscience, vol. 13, no. 1, Nature Publishing Group, 2012, pp. 7–21, doi:10.1038/nrn3125.","short":"E. Eggermann, I. Bucurenciu, S. Goswami, P.M. Jonas, Nature Reviews Neuroscience 13 (2012) 7–21."},"publication":"Nature Reviews Neuroscience","page":"7 - 21","issue":"1","abstract":[{"text":"The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant of the signalling properties of synapses in the nervous system. Recent functional analysis indicates that in some fast central synapses, transmitter release is triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors at the nanometre scale. Molecular analysis suggests that this tight coupling is generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors and various other synaptic proteins. Nanodomain coupling has several functional advantages, as it increases the efficacy, speed and energy efficiency of synaptic transmission.","lang":"eng"}],"type":"journal_article","pubrep_id":"820","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"4931","checksum":"4c1c86b2f6e4e1562f5bb800b457ea9f","date_created":"2018-12-12T10:12:13Z","date_updated":"2020-07-14T12:46:07Z","access_level":"open_access","file_name":"IST-2017-820-v1+1_17463_3_art_file_109404_ltmxbw.pdf","file_size":314246,"content_type":"application/pdf","creator":"system"},{"relation":"main_file","file_id":"4932","checksum":"bceb2efdd49d115f4dde8486bc1be3f2","date_created":"2018-12-12T10:12:14Z","date_updated":"2020-07-14T12:46:07Z","access_level":"open_access","file_name":"IST-2017-820-v1+2_17463_3_figure_109402_ltmwlp.pdf","file_size":1840216,"content_type":"application/pdf","creator":"system"}],"_id":"3317","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","status":"public","ddc":["570"],"title":"Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses"},{"department":[{"_id":"KrCh"}],"publisher":"World Scientific Publishing","intvolume":" 23","title":"Discounting and averaging in games across time scales","status":"public","publication_status":"published","_id":"3314","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":23,"oa_version":"None","date_created":"2018-12-11T12:02:37Z","date_updated":"2021-01-12T07:42:35Z","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Majumdar","first_name":"Ritankar","full_name":"Majumdar, Ritankar"}],"type":"journal_article","issue":"3","publist_id":"3326","abstract":[{"lang":"eng","text":"We introduce two-level discounted and mean-payoff games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted or mean-payoff game and the lower level game is a (undiscounted) reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. For both discounted and mean-payoff two-level games, we show the existence of pure memoryless optimal strategies for both players and an ordered field property. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted or mean-payoff games can be decided in NP ∩ coNP. We also give an alternate strategy improvement algorithm to compute the value. © 2012 World Scientific Publishing Company."}],"page":"609 - 625","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","citation":{"ama":"Chatterjee K, Majumdar R. Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. 2012;23(3):609-625. doi:10.1142/S0129054112400308","ista":"Chatterjee K, Majumdar R. 2012. Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. 23(3), 609–625.","ieee":"K. Chatterjee and R. Majumdar, “Discounting and averaging in games across time scales,” International Journal of Foundations of Computer Science, vol. 23, no. 3. World Scientific Publishing, pp. 609–625, 2012.","apa":"Chatterjee, K., & Majumdar, R. (2012). Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054112400308","mla":"Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” International Journal of Foundations of Computer Science, vol. 23, no. 3, World Scientific Publishing, 2012, pp. 609–25, doi:10.1142/S0129054112400308.","short":"K. Chatterjee, R. Majumdar, International Journal of Foundations of Computer Science 23 (2012) 609–625.","chicago":"Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2012. https://doi.org/10.1142/S0129054112400308."},"publication":"International Journal of Foundations of Computer Science","language":[{"iso":"eng"}],"doi":"10.1142/S0129054112400308","date_published":"2012-04-01T00:00:00Z","scopus_import":1,"day":"01","month":"04"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution P; then, P's offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(nlogn)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. A variant of the algorithm, which we have implemented using the cgal library, is based on rational arithmetic and answers the same deconstruction problem up to an uncertainty parameter δ its running time additionally depends on δ. If the input shape is found to be approximable, this algorithm also computes an approximate solution for the problem. It also allows us to solve parameter-optimization problems induced by the offset-deconstruction problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution P with at most one more vertex than a vertex-minimal one."}],"issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3115","status":"public","title":"Deconstructing approximate offsets","intvolume":" 48","oa_version":"Preprint","scopus_import":1,"day":"01","publication":"Discrete & Computational Geometry","citation":{"ieee":"E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing approximate offsets,” Discrete & Computational Geometry, vol. 48, no. 4. Springer, pp. 964–989, 2012.","apa":"Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2012). Deconstructing approximate offsets. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-012-9441-5","ista":"Berberich E, Halperin D, Kerber M, Pogalnikova R. 2012. Deconstructing approximate offsets. Discrete & Computational Geometry. 48(4), 964–989.","ama":"Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate offsets. Discrete & Computational Geometry. 2012;48(4):964-989. doi:10.1007/s00454-012-9441-5","chicago":"Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry. Springer, 2012. https://doi.org/10.1007/s00454-012-9441-5.","short":"E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, Discrete & Computational Geometry 48 (2012) 964–989.","mla":"Berberich, Eric, et al. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry, vol. 48, no. 4, Springer, 2012, pp. 964–89, doi:10.1007/s00454-012-9441-5."},"page":"964 - 989","date_published":"2012-12-01T00:00:00Z","publist_id":"3584","year":"2012","acknowledgement":"We thank Eyal Flato (Plataine Ltd.) for raising the offset-deconstruction problem in connection with wood cutting. We also thank Tim Bretl (UIUC) for suggesting the digital-pen offset-deconstruction problem. This work has been supported in part by the Israel Science Foundation (grant no. 1102/11), by the German–Israeli Foundation (grant no. 969/07), by the Hermann Minkowski–Minerva Center for Geometry at Tel Aviv University, and by the EU Project under Contract No. 255827 (CGL—Computational Geometry Learning).\r\n","publication_status":"published","publisher":"Springer","department":[{"_id":"HeEd"}],"author":[{"full_name":"Berberich, Eric","first_name":"Eric","last_name":"Berberich"},{"full_name":"Halperin, Dan","first_name":"Dan","last_name":"Halperin"},{"orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael"},{"last_name":"Pogalnikova","first_name":"Roza","full_name":"Pogalnikova, Roza"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3329"}]},"date_created":"2018-12-11T12:01:28Z","date_updated":"2023-02-23T11:22:30Z","volume":48,"month":"12","external_id":{"arxiv":["1109.2158"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.2158"}],"oa":1,"quality_controlled":"1","doi":"10.1007/s00454-012-9441-5","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"doi":"10.1016/j.jsc.2011.11.001","date_published":"2012-03-01T00:00:00Z","page":"239 - 258","quality_controlled":"1","citation":{"mla":"Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” Journal of Symbolic Computation, vol. 47, no. 3, Elsevier, 2012, pp. 239–58, doi:10.1016/j.jsc.2011.11.001.","short":"M. Kerber, M. Sagraloff, Journal of Symbolic Computation 47 (2012) 239–258.","chicago":"Kerber, Michael, and Michael Sagraloff. “A Worst Case Bound for Topology Computation of Algebraic Curves.” Journal of Symbolic Computation. Elsevier, 2012. https://doi.org/10.1016/j.jsc.2011.11.001.","ama":"Kerber M, Sagraloff M. A worst case bound for topology computation of algebraic curves. Journal of Symbolic Computation. 2012;47(3):239-258. doi:10.1016/j.jsc.2011.11.001","ista":"Kerber M, Sagraloff M. 2012. A worst case bound for topology computation of algebraic curves. Journal of Symbolic Computation. 47(3), 239–258.","ieee":"M. Kerber and M. Sagraloff, “A worst case bound for topology computation of algebraic curves,” Journal of Symbolic Computation, vol. 47, no. 3. Elsevier, pp. 239–258, 2012.","apa":"Kerber, M., & Sagraloff, M. (2012). A worst case bound for topology computation of algebraic curves. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2011.11.001"},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.1510"}],"publication":" Journal of Symbolic Computation","month":"03","day":"01","scopus_import":1,"volume":47,"oa_version":"Preprint","date_created":"2018-12-11T12:02:43Z","date_updated":"2021-01-12T07:42:43Z","author":[{"id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael"},{"full_name":"Sagraloff, Michael","last_name":"Sagraloff","first_name":"Michael"}],"publisher":"Elsevier","intvolume":" 47","department":[{"_id":"HeEd"}],"status":"public","title":"A worst case bound for topology computation of algebraic curves","publication_status":"published","_id":"3331","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","publist_id":"3303","issue":"3","abstract":[{"text":"Computing the topology of an algebraic plane curve C means computing a combinatorial graph that is isotopic to C and thus represents its topology in R2. We prove that, for a polynomial of degree n with integer coefficients bounded by 2ρ, the topology of the induced curve can be computed with bit operations ( indicates that we omit logarithmic factors). Our analysis improves the previous best known complexity bounds by a factor of n2. The improvement is based on new techniques to compute and refine isolating intervals for the real roots of polynomials, and on the consequent amortized analysis of the critical fibers of the algebraic curve.","lang":"eng"}],"type":"journal_article"},{"doi":"10.1088/0022-3727/45/41/415301","date_published":"2012-10-17T00:00:00Z","language":[{"iso":"eng"}],"publication":"Journal of Physics D: Applied Physics","citation":{"chicago":"Fan, Jiandong, Reza Zamani, Cristina Fábrega, Alexey Shavel, Cristina Flox, Maria Ibáñez, Teresa Andreu, et al. “Solution-Growth and Optoelectronic Performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 Core–Shell Nanowires with Tunable Shell Thickness.” Journal of Physics D: Applied Physics. IOP Publishing Ltd., 2012. https://doi.org/10.1088/0022-3727/45/41/415301.","mla":"Fan, Jiandong, et al. “Solution-Growth and Optoelectronic Performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 Core–Shell Nanowires with Tunable Shell Thickness.” Journal of Physics D: Applied Physics, vol. 45, no. 41, IOP Publishing Ltd., 2012, doi:10.1088/0022-3727/45/41/415301.","short":"J. Fan, R. Zamani, C. Fábrega, A. Shavel, C. Flox, M. Ibáñez, T. Andreu, A. López, J. Arbiol, J. Morante, A. Cabot, Journal of Physics D: Applied Physics 45 (2012).","ista":"Fan J, Zamani R, Fábrega C, Shavel A, Flox C, Ibáñez M, Andreu T, López A, Arbiol J, Morante J, Cabot A. 2012. Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal of Physics D: Applied Physics. 45(41).","apa":"Fan, J., Zamani, R., Fábrega, C., Shavel, A., Flox, C., Ibáñez, M., … Cabot, A. (2012). Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal of Physics D: Applied Physics. IOP Publishing Ltd. https://doi.org/10.1088/0022-3727/45/41/415301","ieee":"J. Fan et al., “Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness,” Journal of Physics D: Applied Physics, vol. 45, no. 41. IOP Publishing Ltd., 2012.","ama":"Fan J, Zamani R, Fábrega C, et al. Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness. Journal of Physics D: Applied Physics. 2012;45(41). doi:10.1088/0022-3727/45/41/415301"},"quality_controlled":"1","article_type":"original","day":"17","month":"10","article_processing_charge":"No","author":[{"first_name":"Jiandong","last_name":"Fan","full_name":"Fan, Jiandong"},{"full_name":"Zamani, Reza","last_name":"Zamani","first_name":"Reza"},{"last_name":"Fábrega","first_name":"Cristina","full_name":"Fábrega, Cristina"},{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"last_name":"Flox","first_name":"Cristina","full_name":"Flox, Cristina"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"first_name":"Teresa","last_name":"Andreu","full_name":"Andreu, Teresa"},{"full_name":"López, Amtonio","first_name":"Amtonio","last_name":"López"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"first_name":"Joan","last_name":"Morante","full_name":"Morante, Joan"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"date_created":"2018-12-11T11:45:56Z","date_updated":"2021-01-12T07:43:36Z","oa_version":"None","volume":45,"_id":"346","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The research was supported by the European Regional Development Funds and the Spanish MICINN projects MAT2010-15138, MAT2010-21510 and CSD2009-00050. JF and AS thank the FI-DGR and BP grants from the Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) from the Catalan Government. MI and AC thank the Spanish MICINN for the PhD grant and the financial support through the Ramóny Cajal program.","year":"2012","publication_status":"published","status":"public","title":"Solution-growth and optoelectronic performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires with tunable shell thickness","publisher":"IOP Publishing Ltd.","intvolume":" 45","abstract":[{"lang":"eng","text":"Arrays of vertically aligned ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell nanowires (NWs) were prepared by means of the combination of two solution-growth processes. First, single-crystal ZnO NWs with controlled n-type doping were grown on conducting substrates by a low-cost, high-yield and seed-free electrochemical route. These NWs were covered by a titanium oxide shell of tunable thickness mediating successive adsorption-hydrolysis-condensation steps. Using this atomic-layer growth procedure, titania shells with controlled thickness and the anatase TiO2 phase were obtained after sintering at 450 °C. Higher sintering temperatures resulted in the formation of ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs by the interdiffusion of Zn and Ti ions at the ZnO–TiO2 interface. The performance of ZnO : Cl/TiO2 and ZnO : Cl/ZnxTiOy/TiO2 core–shell NWs towards photoelectrochemical (PEC) water splitting was investigated as a function of the titania shell thickness. Furthermore, the performance of such core–shell NWs as photoelectrodes in dye-sensitized solar cells was also characterized. The TiO2 presence at the ZnO : Cl surface promoted a two-fold increase on the produced photocurrent densities, probing their potential for PEC and optoelectronic applications. Electrochemical impedance spectroscopy was used to corroborate the lower resistance for charge transfer between the NWs and the electrolyte in the presence of the TiO2 shell."}],"publist_id":"7486","issue":"41","extern":"1","type":"journal_article"},{"scopus_import":1,"day":"04","month":"05","page":"137 - 164","quality_controlled":"1","citation":{"chicago":"Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule Based Systems.” Theoretical Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2011.12.059.","mla":"Feret, Jérôme, et al. “Lumpability Abstractions of Rule Based Systems.” Theoretical Computer Science, vol. 431, Elsevier, 2012, pp. 137–64, doi:10.1016/j.tcs.2011.12.059.","short":"J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, Theoretical Computer Science 431 (2012) 137–164.","ista":"Feret J, Henzinger TA, Koeppl H, Petrov T. 2012. Lumpability abstractions of rule based systems. Theoretical Computer Science. 431, 137–164.","apa":"Feret, J., Henzinger, T. A., Koeppl, H., & Petrov, T. (2012). Lumpability abstractions of rule based systems. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2011.12.059","ieee":"J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule based systems,” Theoretical Computer Science, vol. 431. Elsevier, pp. 137–164, 2012.","ama":"Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule based systems. Theoretical Computer Science. 2012;431:137-164. doi:10.1016/j.tcs.2011.12.059"},"publication":"Theoretical Computer Science","language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2011.12.059","date_published":"2012-05-04T00:00:00Z","type":"journal_article","publist_id":"3515","abstract":[{"lang":"eng","text":"The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a mathematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the combinatorial complexity by quotienting the reachable set of molecular species into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently, we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper, we prove that this quotienting yields a sufficient condition for weak lumpability (that is to say that the quotient system is still Markovian for a given set of initial distributions) and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system (which means that the conditional probability of being in a given state in the original system knowing that we are in its equivalence class is an invariant of the system). We illustrate the framework on a case study of the epidermal growth factor (EGF)/insulin receptor crosstalk."}],"publisher":"Elsevier","intvolume":" 431","department":[{"_id":"ToHe"}],"publication_status":"published","status":"public","title":"Lumpability abstractions of rule based systems","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3168","acknowledgement":"We would like to thank the anonymous reviewers for their comments on the different versions of the paper. We would also like to thank Ferdinanda Camporesi for her careful reading and the useful insights that she gave us about the paper.\r\nJérôme Feret’s contribution was partially supported by the AbstractCell ANR-Chair of Excellence. Heinz Koeppl’s research is supported by the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov’s research is supported by SystemsX.ch (the Swiss Initiative in Systems Biology).","year":"2012","oa_version":"None","volume":431,"date_updated":"2023-02-23T11:39:40Z","date_created":"2018-12-11T12:01:47Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3719"}]},"pubrep_id":"73","author":[{"last_name":"Feret","first_name":"Jérôme","full_name":"Feret, Jérôme"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Heinz","last_name":"Koeppl","full_name":"Koeppl, Heinz"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","first_name":"Tatjana"}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"The potential to control the composition and crystal phase at the nanometer scale enable the production of nanocrystalline materials with enhanced functionalities and new applications. In the present work, we detail a novel colloidal synthesis route to prepare nanoparticles of the ternary semiconductor Cu2GeSe3 (CGSe) with nanometer-scale control over their crystal phases. We also demonstrate the structural effect on the thermoelectric properties of bottom-up-prepared CGSe nanomaterials. By careful adjustment of the nucleation and growth temperatures, pure orthorhombic CGSe nanoparticles with cationic order or polytypic CGSe nanoparticles with disordered cation positions can be produced. In this second type of nanoparticle, a high density of twins can be created to periodically change the atomic plane stacking, forming a hexagonal wurtzite CGSe phase. The high yield of the synthetic routes reported here allows the production of single-phase and multiphase CGSe nanoparticles in the gram scale, which permits characterization of the thermoelectric properties of these materials. Reduced thermal conductivities and a related 2.5-fold increase of the thermoelectric figure of merit for multiphase nanomaterials compared to pure-phase CGSe are systematically obtained. These results are discussed in terms of the density and efficiency of phonon scattering centers in both types of materials."}],"issue":"23","publist_id":"7452","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"377","year":"2012","title":"Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials","status":"public","publication_status":"published","intvolume":" 24","publisher":"American Chemical Society","author":[{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Reza","last_name":"Zamani","full_name":"Zamani, Reza"},{"last_name":"Li","first_name":"Wenhua","full_name":"Li, Wenhua"},{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"last_name":"Gorse","first_name":"Stéphane","full_name":"Gorse, Stéphane"},{"last_name":"Katchoi","first_name":"Nebll","full_name":"Katchoi, Nebll"},{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"last_name":"López","first_name":"Antonioo","full_name":"López, Antonioo"},{"first_name":"Joan","last_name":"Morante","full_name":"Morante, Joan"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"date_updated":"2021-01-12T07:52:04Z","date_created":"2018-12-11T11:46:07Z","volume":24,"oa_version":"None","day":"14","month":"11","article_processing_charge":"No","publication":"Chemistry of Materials","citation":{"ista":"Ibáñez M, Zamani R, Li W, Cadavid D, Gorse S, Katchoi N, Shavel A, López A, Morante J, Arbiol J, Cabot A. 2012. Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of Materials. 24(23), 4615–4622.","ieee":"M. Ibáñez et al., “Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials,” Chemistry of Materials, vol. 24, no. 23. American Chemical Society, pp. 4615–4622, 2012.","apa":"Ibáñez, M., Zamani, R., Li, W., Cadavid, D., Gorse, S., Katchoi, N., … Cabot, A. (2012). Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/cm303252q","ama":"Ibáñez M, Zamani R, Li W, et al. Crystallographic control at the nanoscale to enhance functionality: Polytypic Cu2GeSe3 nanoparticles as thermoelectric materials. Chemistry of Materials. 2012;24(23):4615-4622. doi:10.1021/cm303252q","chicago":"Ibáñez, Maria, Reza Zamani, Wenhua Li, Doris Cadavid, Stéphane Gorse, Nebll Katchoi, Alexey Shavel, et al. “Crystallographic Control at the Nanoscale to Enhance Functionality: Polytypic Cu2GeSe3 Nanoparticles as Thermoelectric Materials.” Chemistry of Materials. American Chemical Society, 2012. https://doi.org/10.1021/cm303252q.","mla":"Ibáñez, Maria, et al. “Crystallographic Control at the Nanoscale to Enhance Functionality: Polytypic Cu2GeSe3 Nanoparticles as Thermoelectric Materials.” Chemistry of Materials, vol. 24, no. 23, American Chemical Society, 2012, pp. 4615–22, doi:10.1021/cm303252q.","short":"M. Ibáñez, R. Zamani, W. Li, D. Cadavid, S. Gorse, N. Katchoi, A. Shavel, A. López, J. Morante, J. Arbiol, A. Cabot, Chemistry of Materials 24 (2012) 4615–4622."},"page":"4615 - 4622","doi":"10.1021/cm303252q","date_published":"2012-11-14T00:00:00Z","language":[{"iso":"eng"}]},{"doi":"10.1016/j.jcss.2011.05.002","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jcss.2011.05.002"}],"oa":1,"quality_controlled":"1","month":"03","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"date_created":"2018-12-11T12:05:29Z","date_updated":"2022-05-24T08:00:54Z","volume":78,"year":"2012","acknowledgement":"This research was supported in part by the ONR grant N00014-02-1-0671, by the AFOSR MURI grant F49620-00-1-0327, and by the NSF grants CCR-9988172, CCR-0085949, and CCR-0225610.","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:17Z","publist_id":"2341","date_published":"2012-03-02T00:00:00Z","publication":"Journal of Computer and System Sciences","citation":{"short":"K. Chatterjee, T.A. Henzinger, Journal of Computer and System Sciences 78 (2012) 394–413.","mla":"Chatterjee, Krishnendu, and Thomas A. Henzinger. “A Survey of Stochastic ω Regular Games.” Journal of Computer and System Sciences, vol. 78, no. 2, Elsevier, 2012, pp. 394–413, doi:10.1016/j.jcss.2011.05.002.","chicago":"Chatterjee, Krishnendu, and Thomas A Henzinger. “A Survey of Stochastic ω Regular Games.” Journal of Computer and System Sciences. Elsevier, 2012. https://doi.org/10.1016/j.jcss.2011.05.002.","ama":"Chatterjee K, Henzinger TA. A survey of stochastic ω regular games. Journal of Computer and System Sciences. 2012;78(2):394-413. doi:10.1016/j.jcss.2011.05.002","ieee":"K. Chatterjee and T. A. Henzinger, “A survey of stochastic ω regular games,” Journal of Computer and System Sciences, vol. 78, no. 2. Elsevier, pp. 394–413, 2012.","apa":"Chatterjee, K., & Henzinger, T. A. (2012). A survey of stochastic ω regular games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2011.05.002","ista":"Chatterjee K, Henzinger TA. 2012. A survey of stochastic ω regular games. Journal of Computer and System Sciences. 78(2), 394–413."},"article_type":"original","page":"394 - 413","day":"02","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"file_name":"a_survey_of_stochastic_omega-regular_games.pdf","access_level":"open_access","content_type":"application/pdf","file_size":336450,"creator":"kschuh","relation":"main_file","file_id":"5897","date_updated":"2020-07-14T12:46:17Z","date_created":"2019-01-29T10:54:28Z","checksum":"241b939deb4517cdd4426d49c67e3fa2"}],"oa_version":"Submitted Version","_id":"3846","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A survey of stochastic ω regular games","status":"public","ddc":["000"],"intvolume":" 78","abstract":[{"text":"We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications.","lang":"eng"}],"issue":"2","type":"journal_article"},{"publication":"Physical Review Letters","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1108.0022","open_access":"1"}],"citation":{"ama":"Alpichshev Z, Biswas R, Balatsky A, et al. STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters. 2012;108(20). doi:10.1103/PhysRevLett.108.206402","ieee":"Z. Alpichshev et al., “STM imaging of impurity resonances on Bi 2Se 3,” Physical Review Letters, vol. 108, no. 20. American Physical Society, 2012.","apa":"Alpichshev, Z., Biswas, R., Balatsky, A., Analytis, J., Chu, J., Fisher, I., & Kapitulnik, A. (2012). STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.108.206402","ista":"Alpichshev Z, Biswas R, Balatsky A, Analytis J, Chu J, Fisher I, Kapitulnik A. 2012. STM imaging of impurity resonances on Bi 2Se 3. Physical Review Letters. 108(20).","short":"Z. Alpichshev, R. Biswas, A. Balatsky, J. Analytis, J. Chu, I. Fisher, A. Kapitulnik, Physical Review Letters 108 (2012).","mla":"Alpichshev, Zhanybek, et al. “STM Imaging of Impurity Resonances on Bi 2Se 3.” Physical Review Letters, vol. 108, no. 20, American Physical Society, 2012, doi:10.1103/PhysRevLett.108.206402.","chicago":"Alpichshev, Zhanybek, Rudro Biswas, Alexander Balatsky, James Analytis, Jiunhaw Chu, Ian Fisher, and Aharon Kapitulnik. “STM Imaging of Impurity Resonances on Bi 2Se 3.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.108.206402."},"doi":"10.1103/PhysRevLett.108.206402","date_published":"2012-01-01T00:00:00Z","language":[{"iso":"eng"}],"month":"01","day":"01","_id":"387","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","status":"public","title":"STM imaging of impurity resonances on Bi 2Se 3","publication_status":"published","intvolume":" 108","publisher":"American Physical Society","author":[{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","first_name":"Zhanybek","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek"},{"last_name":"Biswas","first_name":"Rudro","full_name":"Biswas, Rudro"},{"last_name":"Balatsky","first_name":"Alexander","full_name":"Balatsky, Alexander"},{"first_name":"James","last_name":"Analytis","full_name":"Analytis, James"},{"full_name":"Chu, Jiunhaw","last_name":"Chu","first_name":"Jiunhaw"},{"full_name":"Fisher, Ian","last_name":"Fisher","first_name":"Ian"},{"full_name":"Kapitulnik, Aharon","last_name":"Kapitulnik","first_name":"Aharon"}],"date_updated":"2021-01-12T07:52:49Z","date_created":"2018-12-11T11:46:11Z","volume":108,"oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"In this Letter we present detailed study of the density of states near defects in Bi 2Se 3. In particular, we present data on the commonly found triangular defects in this system. While we do not find any measurable quasiparticle scattering interference effects, we do find localized resonances, which can be well fitted by theory once the potential is taken to be extended to properly account for the observed defects. The data together with the fits confirm that while the local density of states around the Dirac point of the electronic spectrum at the surface is significantly disrupted near the impurity by the creation of low-energy resonance state, the Dirac point is not locally destroyed. We discuss our results in terms of the expected protected surface state of topological insulators. © 2012 American Physical Society."}],"publist_id":"7442","issue":"20","extern":"1"},{"month":"06","day":"01","quality_controlled":0,"page":"2497 - 2514","publication":"Plant Cell","citation":{"short":"M. Dai, C. Zhang, U. Kania, F. Chen, Q. Xue, T. Mccray, G. Li, G. Qin, M. Wakeley, W. Terzaghi, J. Wan, Y. Zhao, J. Xu, J. Friml, X. Deng, H. Wang, Plant Cell 24 (2012) 2497–2514.","mla":"Dai, Mingqiu, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell, vol. 24, no. 6, American Society of Plant Biologists, 2012, pp. 2497–514, doi:10.1105/tpc.112.098905.","chicago":"Dai, Mingqiu, Chen Zhang, Urszula Kania, Fang Chen, Qin Xue, Tyra Mccray, Gang Li, et al. “A PP6 Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.098905.","ama":"Dai M, Zhang C, Kania U, et al. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. 2012;24(6):2497-2514. doi:10.1105/tpc.112.098905","ieee":"M. Dai et al., “A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis,” Plant Cell, vol. 24, no. 6. American Society of Plant Biologists, pp. 2497–2514, 2012.","apa":"Dai, M., Zhang, C., Kania, U., Chen, F., Xue, Q., Mccray, T., … Wang, H. (2012). A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.098905","ista":"Dai M, Zhang C, Kania U, Chen F, Xue Q, Mccray T, Li G, Qin G, Wakeley M, Terzaghi W, Wan J, Zhao Y, Xu J, Friml J, Deng X, Wang H. 2012. A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell. 24(6), 2497–2514."},"date_published":"2012-06-01T00:00:00Z","doi":"10.1105/tpc.112.098905","type":"journal_article","extern":1,"abstract":[{"text":"The directional transport of the phytohormone auxin depends on the phosphorylation status and polar localization of PIN-FORMED (PIN) auxin efflux proteins. While PINIOD (PID) kinase is directly involved in the phosphorylation of PIN proteins, the phosphatase holoenzyme complexes that dephosphorylate PIN proteins remain elusive. Here, we demonstrate that mutations simultaneously disrupting the function of Arabidopsis thaliana FyPP1 (for Phytochrome-associated serine/threonine protein phosphatase1) and FyPP3, two homologous genes encoding the catalytic subunits of protein phosphatase6 (PP6), cause elevated accumulation of phosphorylated PIN proteins, correlating with a basal-to-apical shift in subcellular PIN localization. The changes in PIN polarity result in increased root basipetal auxin transport and severe defects, including shorter roots, fewer lateral roots, defective columella cells, root meristem collapse, abnormal cotyledons (small, cup-shaped, or fused cotyledons), and altered leaf venation. Our molecular, biochemical, and genetic data support the notion that FyPP1/3, SAL (for SAPS DOMAIN-LIKE), and PP2AA proteins (RCN1 [for ROOTS CURL IN NAPHTHYLPHTHALAMIC ACID1] or PP2AA1, PP2AA2, and PP2AA3) physically interact to form a novel PP6-type heterotrimeric holoenzyme complex. We also show that FyPP1/3, SAL, and PP2AA interact with a subset of PIN proteins and that for SAL the strength of the interaction depends on the PIN phosphorylation status. Thus, an Arabidopsis PP6-type phosphatase holoenzyme acts antagonistically with PID to direct auxin transport polarity and plant development by directly regulating PIN phosphorylation. ","lang":"eng"}],"issue":"6","publist_id":"3589","status":"public","publication_status":"published","title":"A PP6 type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis","publisher":"American Society of Plant Biologists","intvolume":" 24","_id":"3110","year":"2012","date_updated":"2021-01-12T07:41:08Z","date_created":"2018-12-11T12:01:27Z","volume":24,"author":[{"first_name":"Mingqiu","last_name":"Dai","full_name":"Dai, Mingqiu"},{"full_name":"Zhang, Chen","last_name":"Zhang","first_name":"Chen"},{"full_name":"Urszula Kania","last_name":"Kania","first_name":"Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chen, Fang","last_name":"Chen","first_name":"Fang"},{"last_name":"Xue","first_name":"Qin","full_name":"Xue, Qin"},{"full_name":"McCray, Tyra","last_name":"Mccray","first_name":"Tyra"},{"full_name":"Li, Gang","last_name":"Li","first_name":"Gang"},{"full_name":"Qin, Genji","first_name":"Genji","last_name":"Qin"},{"first_name":"Michelle","last_name":"Wakeley","full_name":"Wakeley, Michelle"},{"first_name":"William","last_name":"Terzaghi","full_name":"Terzaghi, William"},{"last_name":"Wan","first_name":"Jianmin","full_name":"Wan, Jianmin"},{"first_name":"Yunde","last_name":"Zhao","full_name":"Zhao, Yunde"},{"last_name":"Xu","first_name":"Jian","full_name":"Xu, Jian"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml"},{"first_name":"Xing","last_name":"Deng","full_name":"Deng, Xing W"},{"last_name":"Wang","first_name":"Haiyang","full_name":"Wang, Haiyang"}]},{"day":"31","month":"07","publication":"PNAS","citation":{"chicago":"Martinière, Alexandre, Irene Lavagi, Gayathri Nageswaran, Daniel Rolfe, Lilly Maneta Peyret, Doan Luu, Stanley Botchway, et al. “Cell Wall Constrains Lateral Diffusion of Plant Plasma Membrane Proteins.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1202040109.","short":"A. Martinière, I. Lavagi, G. Nageswaran, D. Rolfe, L. Maneta Peyret, D. Luu, S. Botchway, S. Webb, S. Mongrand, C. Maurel, M. Martin Fernandez, J. Kleine Vehn, J. Friml, P. Moreau, J. Runions, PNAS 109 (2012) 12805–12810.","mla":"Martinière, Alexandre, et al. “Cell Wall Constrains Lateral Diffusion of Plant Plasma Membrane Proteins.” PNAS, vol. 109, no. 31, National Academy of Sciences, 2012, pp. 12805–10, doi:10.1073/pnas.1202040109.","apa":"Martinière, A., Lavagi, I., Nageswaran, G., Rolfe, D., Maneta Peyret, L., Luu, D., … Runions, J. (2012). Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1202040109","ieee":"A. Martinière et al., “Cell wall constrains lateral diffusion of plant plasma membrane proteins,” PNAS, vol. 109, no. 31. National Academy of Sciences, pp. 12805–12810, 2012.","ista":"Martinière A, Lavagi I, Nageswaran G, Rolfe D, Maneta Peyret L, Luu D, Botchway S, Webb S, Mongrand S, Maurel C, Martin Fernandez M, Kleine Vehn J, Friml J, Moreau P, Runions J. 2012. Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. 109(31), 12805–12810.","ama":"Martinière A, Lavagi I, Nageswaran G, et al. Cell wall constrains lateral diffusion of plant plasma membrane proteins. PNAS. 2012;109(31):12805-12810. doi:10.1073/pnas.1202040109"},"quality_controlled":0,"page":"12805 - 12810","date_published":"2012-07-31T00:00:00Z","doi":"10.1073/pnas.1202040109","type":"journal_article","abstract":[{"lang":"eng","text":"A cell membrane can be considered a liquid-phase plane in which lipids and proteins theoretically are free to diffuse. Numerous reports,however, describe retarded diffusion ofmembrane proteins in animal cells. This anomalous diffusion results from a combination of structuring factors including protein-protein interactions, cytoskeleton corralling, and lipid organization into microdomains. In plant cells, plasma-membrane (PM) proteins have been described as relatively immobile, but the control mechanisms that structure the PM have not been studied. Here, we use fluorescence recovery after photobleaching to estimate mobility of a set of minimal PM proteins. These proteins consist only of a PM-anchoring domain fused to a fluorescent protein, but their mobilities remained limited, as is the case for many full-length proteins. Neither the cytoskeleton nor membrane microdomain structure was involved in constraining the diffusion of these proteins. The cell wall, however, was shown to have a crucial role in immobilizing PM proteins. In addition, by single-molecule fluorescence imaging we confirmed that the pattern of cellulose deposition in the cell wall affects the trajectory and speed ofPMprotein diffusion. Regulation ofPMprotein dynamics by the plant cell wall can be interpreted as a mechanism for regulating protein interactions in processes such as trafficking and signal transduction."}],"publist_id":"3586","issue":"31","extern":1,"_id":"3113","year":"2012","title":"Cell wall constrains lateral diffusion of plant plasma membrane proteins","status":"public","publication_status":"published","intvolume":" 109","publisher":"National Academy of Sciences","author":[{"full_name":"Martinière, Alexandre","last_name":"Martinière","first_name":"Alexandre"},{"first_name":"Irene","last_name":"Lavagi","full_name":"Lavagi, Irene"},{"full_name":"Nageswaran, Gayathri","first_name":"Gayathri","last_name":"Nageswaran"},{"first_name":"Daniel","last_name":"Rolfe","full_name":"Rolfe, Daniel J"},{"full_name":"Maneta-Peyret, Lilly","first_name":"Lilly","last_name":"Maneta Peyret"},{"full_name":"Luu, Doan-Trung","first_name":"Doan","last_name":"Luu"},{"first_name":"Stanley","last_name":"Botchway","full_name":"Botchway, Stanley W"},{"full_name":"Webb, Stephen E","last_name":"Webb","first_name":"Stephen"},{"full_name":"Mongrand, Sebastien","first_name":"Sebastien","last_name":"Mongrand"},{"last_name":"Maurel","first_name":"Christophe","full_name":"Maurel, Christophe"},{"last_name":"Martin Fernandez","first_name":"Marisa","full_name":"Martin-Fernandez, Marisa L"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Jirí Friml"},{"full_name":"Moreau, Patrick","last_name":"Moreau","first_name":"Patrick"},{"first_name":"John","last_name":"Runions","full_name":"Runions, John"}],"date_updated":"2021-01-12T07:41:09Z","date_created":"2018-12-11T12:01:28Z","volume":109},{"title":"ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis","publication_status":"published","status":"public","intvolume":" 3","publisher":"Nature Publishing Group","_id":"3114","year":"2012","date_created":"2018-12-11T12:01:28Z","date_updated":"2021-01-12T07:41:09Z","volume":3,"author":[{"last_name":"Ding","first_name":"Zhaojun","full_name":"Ding, Zhaojun"},{"full_name":"Wang, Bangjun","last_name":"Wang","first_name":"Bangjun"},{"full_name":"Moreno, Ignacio","first_name":"Ignacio","last_name":"Moreno"},{"last_name":"Dupláková","first_name":"Nikoleta","full_name":"Dupláková, Nikoleta"},{"full_name":"Sibu Simon","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","first_name":"Sibu"},{"full_name":"Carraro, Nicola","first_name":"Nicola","last_name":"Carraro"},{"full_name":"Reemmer, Jesica","first_name":"Jesica","last_name":"Reemmer"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Xu Chen"},{"full_name":"Tejos, Ricardo I","first_name":"Ricardo","last_name":"Tejos"},{"last_name":"Skůpa","first_name":"Petr","full_name":"Skůpa, Petr"},{"full_name":"Pollmann, Stephan","first_name":"Stephan","last_name":"Pollmann"},{"first_name":"Jozef","last_name":"Mravec","full_name":"Mravec, Jozef"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"full_name":"Honys, David","last_name":"Honys","first_name":"David"},{"last_name":"Rolčík","first_name":"Jakub","full_name":"Rolčík, Jakub"},{"first_name":"Angus","last_name":"Murphy","full_name":"Murphy, Angus S"},{"last_name":"Orellana","first_name":"Ariel","full_name":"Orellana, Ariel"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml"}],"type":"journal_article","extern":1,"abstract":[{"text":"Auxin is a key coordinative signal required for many aspects of plant development and its levels are controlled by auxin metabolism and intercellular auxin transport. Here we find that a member of PIN auxin transporter family, PIN8 is expressed in male gametophyte of Arabidopsis thaliana and has a crucial role in pollen development and functionality. Ectopic expression in sporophytic tissues establishes a role of PIN8 in regulating auxin homoeostasis and metabolism. PIN8 co-localizes with PIN5 to the endoplasmic reticulum (ER) where it acts as an auxin transporter. Genetic analyses reveal an antagonistic action of PIN5 and PIN8 in the regulation of intracellular auxin homoeostasis and gametophyte as well as sporophyte development. Our results reveal a role of the auxin transport in male gametophyte development in which the distinct actions of ER-localized PIN transporters regulate cellular auxin homoeostasis and maintain the auxin levels optimal for pollen development and pollen tube growth.","lang":"eng"}],"issue":"AN 941","publist_id":"3585","quality_controlled":0,"publication":"Nature Communications","citation":{"mla":"Ding, Zhaojun, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature Communications, vol. 3, no. AN 941, Nature Publishing Group, 2012, doi:10.1038/ncomms1941.","short":"Z. Ding, B. Wang, I. Moreno, N. Dupláková, S. Simon, N. Carraro, J. Reemmer, A. Pěnčík, X. Chen, R. Tejos, P. Skůpa, S. Pollmann, J. Mravec, J. Petrášek, E. Zažímalová, D. Honys, J. Rolčík, A. Murphy, A. Orellana, M. Geisler, J. Friml, Nature Communications 3 (2012).","chicago":"Ding, Zhaojun, Bangjun Wang, Ignacio Moreno, Nikoleta Dupláková, Sibu Simon, Nicola Carraro, Jesica Reemmer, et al. “ER-Localized Auxin Transporter PIN8 Regulates Auxin Homeostasis and Male Gametophyte Development in Arabidopsis.” Nature Communications. Nature Publishing Group, 2012. https://doi.org/10.1038/ncomms1941.","ama":"Ding Z, Wang B, Moreno I, et al. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. 2012;3(AN 941). doi:10.1038/ncomms1941","ista":"Ding Z, Wang B, Moreno I, Dupláková N, Simon S, Carraro N, Reemmer J, Pěnčík A, Chen X, Tejos R, Skůpa P, Pollmann S, Mravec J, Petrášek J, Zažímalová E, Honys D, Rolčík J, Murphy A, Orellana A, Geisler M, Friml J. 2012. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. 3(AN 941).","apa":"Ding, Z., Wang, B., Moreno, I., Dupláková, N., Simon, S., Carraro, N., … Friml, J. (2012). ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms1941","ieee":"Z. Ding et al., “ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis,” Nature Communications, vol. 3, no. AN 941. Nature Publishing Group, 2012."},"doi":"10.1038/ncomms1941","date_published":"2012-07-03T00:00:00Z","day":"03","month":"07"},{"type":"journal_article","abstract":[{"lang":"eng","text":"PIN-FORMED (PIN) protein-mediated auxin polar transport is critically important for development, pattern formation, and morphogenesis in plants. Auxin has been implicated in the regulation of polar auxin transport by inhibiting PIN endocytosis [1, 2], but how auxin regulates this process is poorly understood. Our genetic screen identified the Arabidopsis SPIKE1 (SPK1) gene whose loss-of-function mutations increased lateral root density and retarded gravitropic responses, as do pin2 knockout mutations [3]. SPK1 belongs to the conserved DHR2-Dock family of Rho guanine nucleotide exchange factors [4-6]. The spk1 mutations induced PIN2 internalization that was not suppressed by auxin, as did the loss-of-function mutations for Rho-like GTPase from Plants 6 (ROP6)-GTPase or its effector RIC1. Furthermore, SPK1 was required for auxin induction of ROP6 activation. Our results have established a Rho GTPase-based auxin signaling pathway that maintains PIN2 polar distribution to the plasma membrane via inhibition of its internalization in Arabidopsis roots. Our findings provide new insights into signaling mechanisms that underlie the regulation of the dynamic trafficking of PINs required for long-distance auxin transport and that link auxin signaling to PIN-mediated pattern formation and morphogenesis."}],"issue":"14","publist_id":"3588","extern":1,"_id":"3111","year":"2012","status":"public","title":"A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots","publication_status":"published","publisher":"Cell Press","intvolume":" 22","author":[{"full_name":"Lin, Deshu","first_name":"Deshu","last_name":"Lin"},{"full_name":"Nagawa, Shingo","first_name":"Shingo","last_name":"Nagawa"},{"first_name":"Jisheng","last_name":"Chen","full_name":"Chen, Jisheng"},{"last_name":"Cao","first_name":"Lingyan","full_name":"Cao, Lingyan"},{"last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Xu Chen"},{"full_name":"Xu, Tongda","first_name":"Tongda","last_name":"Xu"},{"full_name":"Hongjiang Li","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","first_name":"Hongjiang","last_name":"Li"},{"full_name":"Dhonukshe, Pankaj","first_name":"Pankaj","last_name":"Dhonukshe"},{"full_name":"Yamamuro, Chizuko","first_name":"Chizuko","last_name":"Yamamuro"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"full_name":"Scheres, Ben","last_name":"Scheres","first_name":"Ben"},{"last_name":"Fu","first_name":"Ying","full_name":"Fu, Ying"},{"first_name":"Zhenbiao","last_name":"Yang","full_name":"Yang, Zhenbiao"}],"date_created":"2018-12-11T12:01:27Z","date_updated":"2021-01-12T07:41:08Z","volume":22,"month":"07","day":"24","publication":"Current Biology","citation":{"mla":"Lin, Deshu, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology, vol. 22, no. 14, Cell Press, 2012, pp. 1319–25, doi:10.1016/j.cub.2012.05.019.","short":"D. Lin, S. Nagawa, J. Chen, L. Cao, X. Chen, T. Xu, H. Li, P. Dhonukshe, C. Yamamuro, J. Friml, B. Scheres, Y. Fu, Z. Yang, Current Biology 22 (2012) 1319–1325.","chicago":"Lin, Deshu, Shingo Nagawa, Jisheng Chen, Lingyan Cao, Xu Chen, Tongda Xu, Hongjiang Li, et al. “A ROP GTPase Dependent Auxin Signaling Pathway Regulates the Subcellular Distribution of PIN2 in Arabidopsis Roots.” Current Biology. Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.019.","ama":"Lin D, Nagawa S, Chen J, et al. A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. 2012;22(14):1319-1325. doi:10.1016/j.cub.2012.05.019","ista":"Lin D, Nagawa S, Chen J, Cao L, Chen X, Xu T, Li H, Dhonukshe P, Yamamuro C, Friml J, Scheres B, Fu Y, Yang Z. 2012. A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. 22(14), 1319–1325.","ieee":"D. Lin et al., “A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots,” Current Biology, vol. 22, no. 14. Cell Press, pp. 1319–1325, 2012.","apa":"Lin, D., Nagawa, S., Chen, J., Cao, L., Chen, X., Xu, T., … Yang, Z. (2012). A ROP GTPase dependent auxin signaling pathway regulates the subcellular distribution of PIN2 in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.019"},"quality_controlled":0,"page":"1319 - 1325","doi":"10.1016/j.cub.2012.05.019","date_published":"2012-07-24T00:00:00Z"},{"month":"07","day":"24","date_published":"2012-07-24T00:00:00Z","doi":"10.1016/j.cub.2012.05.020","citation":{"ista":"Chen X, Naramoto S, Robert S, Tejos R, Löfke C, Lin D, Yang Z, Friml J. 2012. ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. 22(14), 1326–1332.","apa":"Chen, X., Naramoto, S., Robert, S., Tejos, R., Löfke, C., Lin, D., … Friml, J. (2012). ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.05.020","ieee":"X. Chen et al., “ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots,” Current Biology, vol. 22, no. 14. Cell Press, pp. 1326–1332, 2012.","ama":"Chen X, Naramoto S, Robert S, et al. ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots. Current Biology. 2012;22(14):1326-1332. doi:10.1016/j.cub.2012.05.020","chicago":"Chen, Xu, Satoshi Naramoto, Stéphanie Robert, Ricardo Tejos, Christian Löfke, Deshu Lin, Zhenbiao Yang, and Jiří Friml. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” Current Biology. Cell Press, 2012. https://doi.org/10.1016/j.cub.2012.05.020.","mla":"Chen, Xu, et al. “ABP1 and ROP6 GTPase Signaling Regulate Clathrin Mediated Endocytosis in Arabidopsis Roots.” Current Biology, vol. 22, no. 14, Cell Press, 2012, pp. 1326–32, doi:10.1016/j.cub.2012.05.020.","short":"X. Chen, S. Naramoto, S. Robert, R. Tejos, C. Löfke, D. Lin, Z. Yang, J. Friml, Current Biology 22 (2012) 1326–1332."},"publication":"Current Biology","page":"1326 - 1332","quality_controlled":0,"publist_id":"3587","issue":"14","abstract":[{"text":"The dynamic spatial and temporal distribution of the crucial plant signaling molecule auxin is achieved by feedback coordination of auxin signaling and intercellular auxin transport pathways [1, 2]. Developmental roles of auxin have been attributed predominantly to its effect on transcription; however, an alternative pathway involving AUXIN BINDING PROTEIN1 (ABP1) has been proposed to regulate clathrin-mediated endocytosis in roots and Rho-like GTPase (ROP)-dependent pavement cell interdigitation in leaves [3, 4]. In this study, we show that ROP6 and its downstream effector RIC1 regulate clathrin association with the plasma membrane for clathrin-mediated endocytosis, as well as for its feedback regulation by auxin. Genetic analysis revealed that ROP6/RIC1 acts downstream of ABP1 to regulate endocytosis. This signaling circuit is also involved in the feedback regulation of PIN-FORMED 1 (PIN1) and PIN2 auxin transporters activity (via its constitutive endocytosis) and corresponding auxin transport-mediated processes, including root gravitropism and leave vascular tissue patterning. Our findings suggest that the signaling module auxin-ABP1-ROP6/RIC1-clathrin-PIN1/PIN2 is a shared component of the feedback regulation of auxin transport during both root and aerial development.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"full_name":"Xu Chen","first_name":"Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Naramoto, Satoshi","first_name":"Satoshi","last_name":"Naramoto"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"full_name":"Lin, Deshu","first_name":"Deshu","last_name":"Lin"},{"full_name":"Yang, Zhenbiao","first_name":"Zhenbiao","last_name":"Yang"},{"full_name":"Jirí Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"volume":22,"date_updated":"2021-01-12T07:41:08Z","date_created":"2018-12-11T12:01:27Z","year":"2012","_id":"3112","publisher":"Cell Press","intvolume":" 22","status":"public","title":"ABP1 and ROP6 GTPase signaling regulate clathrin mediated endocytosis in Arabidopsis roots","publication_status":"published"},{"month":"10","oa":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","doi":"10.1007/s10703-012-0164-2","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"3570","file_date_updated":"2020-07-14T12:46:00Z","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, FWF NFN Grant No. S11407-N23(RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, ERC Advanced grant QUAREM, and FWF Grant No. S11403-N23 (RiSE).","year":"2012","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"volume":43,"date_created":"2018-12-11T12:01:33Z","date_updated":"2021-01-12T07:41:15Z","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"ama":"Chatterjee K, Doyen L, Henzinger TA. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 2012;43(2):268-284. doi:10.1007/s10703-012-0164-2","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2012). A survey of partial-observation stochastic parity games. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0164-2","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of partial-observation stochastic parity games,” Formal Methods in System Design, vol. 43, no. 2. Springer, pp. 268–284, 2012.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2012. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 43(2), 268–284.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design 43 (2012) 268–284.","mla":"Chatterjee, Krishnendu, et al. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design, vol. 43, no. 2, Springer, 2012, pp. 268–84, doi:10.1007/s10703-012-0164-2.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design. Springer, 2012. https://doi.org/10.1007/s10703-012-0164-2."},"publication":"Formal Methods in System Design","page":"268 - 284","date_published":"2012-10-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We consider two-player zero-sum stochastic games on graphs with ω-regular winning conditions specified as parity objectives. These games have applications in the design and control of reactive systems. We survey the complexity results for the problem of deciding the winner in such games, and in classes of interest obtained as special cases, based on the information and the power of randomization available to the players, on the class of objectives and on the winning mode. On the basis of information, these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have complete view of the game). The one-sided partial-observation games have two important subclasses: the one-player games, known as partial-observation Markov decision processes (POMDPs), and the blind one-player games, known as probabilistic automata. 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. Finally, various classes of games are obtained by restricting the parity objective to a reachability, safety, Büchi, or coBüchi condition. We also consider several winning modes, such as sure-winning (i.e., all outcomes of a strategy have to satisfy the winning condition), almost-sure winning (i.e., winning with probability 1), limit-sure winning (i.e., winning with probability arbitrarily close to 1), and value-threshold winning (i.e., winning with probability at least ν, where ν is a given rational). "}],"_id":"3128","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 43","title":"A survey of partial-observation stochastic parity games","status":"public","ddc":["005"],"pubrep_id":"303","file":[{"date_created":"2018-12-12T10:11:27Z","date_updated":"2020-07-14T12:46:00Z","checksum":"dd3d590f383bb2ac6cfda1489ac1c42a","relation":"main_file","file_id":"4882","content_type":"application/pdf","file_size":163983,"creator":"system","file_name":"IST-2014-303-v1+1_Survey_Partial-Observation_Stochastic_Parity_Games.pdf","access_level":"open_access"}],"oa_version":"Submitted Version"},{"oa":1,"quality_controlled":"1","conference":{"end_date":"2012-10-13","location":"Florence, Italy","start_date":"2012-10-07","name":"ECCV: European Conference on Computer Vision"},"doi":"10.1007/978-3-642-33715-4_18","language":[{"iso":"eng"}],"month":"10","year":"2012","publication_status":"published","publisher":"Springer","department":[{"_id":"ChLa"}],"author":[{"last_name":"Sharmanska","first_name":"Viktoriia","orcid":"0000-0003-0192-9308","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","full_name":"Sharmanska, Viktoriia"},{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T12:01:32Z","date_updated":"2023-02-23T11:13:25Z","volume":7576,"file_date_updated":"2020-07-14T12:46:00Z","publist_id":"3574","citation":{"chicago":"Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Augmented Attribute Representations,” 7576:242–55. Springer, 2012. https://doi.org/10.1007/978-3-642-33715-4_18.","mla":"Sharmanska, Viktoriia, et al. Augmented Attribute Representations. Vol. 7576, no. PART 5, Springer, 2012, pp. 242–55, doi:10.1007/978-3-642-33715-4_18.","short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, Springer, 2012, pp. 242–255.","ista":"Sharmanska V, Quadrianto N, Lampert C. 2012. Augmented attribute representations. ECCV: European Conference on Computer Vision, LNCS, vol. 7576, 242–255.","ieee":"V. Sharmanska, N. Quadrianto, and C. Lampert, “Augmented attribute representations,” presented at the ECCV: European Conference on Computer Vision, Florence, Italy, 2012, vol. 7576, no. PART 5, pp. 242–255.","apa":"Sharmanska, V., Quadrianto, N., & Lampert, C. (2012). Augmented attribute representations (Vol. 7576, pp. 242–255). Presented at the ECCV: European Conference on Computer Vision, Florence, Italy: Springer. https://doi.org/10.1007/978-3-642-33715-4_18","ama":"Sharmanska V, Quadrianto N, Lampert C. Augmented attribute representations. In: Vol 7576. Springer; 2012:242-255. doi:10.1007/978-3-642-33715-4_18"},"page":"242 - 255","date_published":"2012-10-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3125","status":"public","title":"Augmented attribute representations","ddc":["000"],"intvolume":" 7576","oa_version":"Submitted Version","file":[{"file_name":"2012_ECCV_Sharmanska.pdf","access_level":"open_access","creator":"dernst","file_size":6073897,"content_type":"application/pdf","file_id":"7861","relation":"main_file","date_created":"2020-05-15T12:29:04Z","date_updated":"2020-07-14T12:46:00Z","checksum":"bccdbe0663780d25a1e0524002b2d896"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We propose a new learning method to infer a mid-level feature representation that combines the advantage of semantic attribute representations with the higher expressive power of non-semantic features. The idea lies in augmenting an existing attribute-based representation with additional dimensions for which an autoencoder model is coupled with a large-margin principle. This construction allows a smooth transition between the zero-shot regime with no training example, the unsupervised regime with training examples but without class labels, and the supervised regime with training examples and with class labels. The resulting optimization problem can be solved efficiently, because several of the necessity steps have closed-form solutions. Through extensive experiments we show that the augmented representation achieves better results in terms of object categorization accuracy than the semantic representation alone.","lang":"eng"}],"issue":"PART 5"},{"publist_id":"3569","year":"2012","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","author":[{"last_name":"Busaryev","first_name":"Oleksiy","full_name":"Busaryev, Oleksiy"},{"last_name":"Cabello","first_name":"Sergio","full_name":"Cabello, Sergio"},{"first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"full_name":"Dey, Tamal","last_name":"Dey","first_name":"Tamal"},{"last_name":"Wang","first_name":"Yusu","full_name":"Wang, Yusu"}],"volume":7357,"date_created":"2018-12-11T12:01:33Z","date_updated":"2021-01-12T07:41:15Z","month":"06","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1107.3793"}],"external_id":{"arxiv":["1107.3793"]},"quality_controlled":"1","doi":"10.1007/978-3-642-31155-0_17","conference":{"end_date":"2012-07-06","location":"Helsinki, Finland","start_date":"2012-07-04","name":"SWAT: Symposium and Workshops on Algorithm Theory"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Let K be a simplicial complex and g the rank of its p-th homology group Hp(K) defined with ℤ2 coefficients. We show that we can compute a basis H of Hp(K) and annotate each p-simplex of K with a binary vector of length g with the following property: the annotations, summed over all p-simplices in any p-cycle z, provide the coordinate vector of the homology class [z] in the basis H. The basis and the annotations for all simplices can be computed in O(n ω ) time, where n is the size of K and ω < 2.376 is a quantity so that two n×n matrices can be multiplied in O(n ω ) time. The precomputed annotations permit answering queries about the independence or the triviality of p-cycles efficiently.\r\n\r\nUsing annotations of edges in 2-complexes, we derive better algorithms for computing optimal basis and optimal homologous cycles in 1 - dimensional homology. Specifically, for computing an optimal basis of H1(K) , we improve the previously known time complexity from O(n 4) to O(n ω + n 2 g ω − 1). Here n denotes the size of the 2-skeleton of K and g the rank of H1(K) . Computing an optimal cycle homologous to a given 1-cycle is NP-hard even for surfaces and an algorithm taking 2 O(g) nlogn time is known for surfaces. We extend this algorithm to work with arbitrary 2-complexes in O(n ω ) + 2 O(g) n 2logn time using annotations.\r\n"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3129","intvolume":" 7357","title":"Annotating simplices with a homology basis and its applications","status":"public","oa_version":"Preprint","scopus_import":1,"day":"19","citation":{"short":"O. Busaryev, S. Cabello, C. Chen, T. Dey, Y. Wang, in:, Springer, 2012, pp. 189–200.","mla":"Busaryev, Oleksiy, et al. Annotating Simplices with a Homology Basis and Its Applications. Vol. 7357, Springer, 2012, pp. 189–200, doi:10.1007/978-3-642-31155-0_17.","chicago":"Busaryev, Oleksiy, Sergio Cabello, Chao Chen, Tamal Dey, and Yusu Wang. “Annotating Simplices with a Homology Basis and Its Applications,” 7357:189–200. Springer, 2012. https://doi.org/10.1007/978-3-642-31155-0_17.","ama":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. Annotating simplices with a homology basis and its applications. In: Vol 7357. Springer; 2012:189-200. doi:10.1007/978-3-642-31155-0_17","apa":"Busaryev, O., Cabello, S., Chen, C., Dey, T., & Wang, Y. (2012). Annotating simplices with a homology basis and its applications (Vol. 7357, pp. 189–200). Presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-642-31155-0_17","ieee":"O. Busaryev, S. Cabello, C. Chen, T. Dey, and Y. Wang, “Annotating simplices with a homology basis and its applications,” presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland, 2012, vol. 7357, pp. 189–200.","ista":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. 2012. Annotating simplices with a homology basis and its applications. SWAT: Symposium and Workshops on Algorithm Theory, LNCS, vol. 7357, 189–200."},"page":"189 - 200","date_published":"2012-06-19T00:00:00Z"},{"citation":{"mla":"Müller, Andreas, et al. Information Theoretic Clustering Using Minimal Spanning Trees. Vol. 7476, Springer, 2012, pp. 205–15, doi:10.1007/978-3-642-32717-9_21.","short":"A. Müller, S. Nowozin, C. Lampert, in:, Springer, 2012, pp. 205–215.","chicago":"Müller, Andreas, Sebastian Nowozin, and Christoph Lampert. “Information Theoretic Clustering Using Minimal Spanning Trees,” 7476:205–15. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_21.","ama":"Müller A, Nowozin S, Lampert C. Information theoretic clustering using minimal spanning trees. In: Vol 7476. Springer; 2012:205-215. doi:10.1007/978-3-642-32717-9_21","ista":"Müller A, Nowozin S, Lampert C. 2012. Information theoretic clustering using minimal spanning trees. DAGM: German Association For Pattern Recognition, LNCS, vol. 7476, 205–215.","apa":"Müller, A., Nowozin, S., & Lampert, C. (2012). Information theoretic clustering using minimal spanning trees (Vol. 7476, pp. 205–215). Presented at the DAGM: German Association For Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_21","ieee":"A. Müller, S. Nowozin, and C. Lampert, “Information theoretic clustering using minimal spanning trees,” presented at the DAGM: German Association For Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 205–215."},"page":"205 - 215","quality_controlled":"1","date_published":"2012-08-14T00:00:00Z","doi":"10.1007/978-3-642-32717-9_21","conference":{"location":"Graz, Austria","start_date":"2012-08-28","end_date":"2012-08-31","name":"DAGM: German Association For Pattern Recognition"},"language":[{"iso":"eng"}],"scopus_import":1,"month":"08","day":"14","_id":"3126","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","intvolume":" 7476","publisher":"Springer","department":[{"_id":"ChLa"}],"publication_status":"published","status":"public","title":"Information theoretic clustering using minimal spanning trees","author":[{"full_name":"Müller, Andreas","first_name":"Andreas","last_name":"Müller"},{"full_name":"Nowozin, Sebastian","first_name":"Sebastian","last_name":"Nowozin"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"volume":7476,"oa_version":"None","date_created":"2018-12-11T12:01:32Z","date_updated":"2021-01-12T07:41:14Z","type":"conference","alternative_title":["LNCS"],"publist_id":"3573","abstract":[{"lang":"eng","text":"In this work we propose a new information-theoretic clustering algorithm that infers cluster memberships by direct optimization of a non-parametric mutual information estimate between data distribution and cluster assignment. Although the optimization objective has a solid theoretical foundation it is hard to optimize. We propose an approximate optimization formulation that leads to an efficient algorithm with low runtime complexity. The algorithm has a single free parameter, the number of clusters to find. We demonstrate superior performance on several synthetic and real datasets.\r\n"}]},{"date_published":"2012-06-01T00:00:00Z","page":"203 - 218","citation":{"ama":"Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. Synchronous interface theories and time triggered scheduling. In: Vol 7273. Springer; 2012:203-218. doi:10.1007/978-3-642-30793-5_13","ieee":"B. Delahaye, U. Fahrenberg, T. A. Henzinger, A. Legay, and D. Nickovic, “Synchronous interface theories and time triggered scheduling,” presented at the FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden, 2012, vol. 7273, pp. 203–218.","apa":"Delahaye, B., Fahrenberg, U., Henzinger, T. A., Legay, A., & Nickovic, D. (2012). Synchronous interface theories and time triggered scheduling (Vol. 7273, pp. 203–218). Presented at the FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems , Stockholm, Sweden: Springer. https://doi.org/10.1007/978-3-642-30793-5_13","ista":"Delahaye B, Fahrenberg U, Henzinger TA, Legay A, Nickovic D. 2012. Synchronous interface theories and time triggered scheduling. FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems , LNCS, vol. 7273, 203–218.","short":"B. Delahaye, U. Fahrenberg, T.A. Henzinger, A. Legay, D. Nickovic, in:, Springer, 2012, pp. 203–218.","mla":"Delahaye, Benoît, et al. Synchronous Interface Theories and Time Triggered Scheduling. Vol. 7273, Springer, 2012, pp. 203–18, doi:10.1007/978-3-642-30793-5_13.","chicago":"Delahaye, Benoît, Uli Fahrenberg, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Synchronous Interface Theories and Time Triggered Scheduling,” 7273:203–18. Springer, 2012. https://doi.org/10.1007/978-3-642-30793-5_13."},"has_accepted_license":"1","day":"01","scopus_import":1,"file":[{"access_level":"open_access","file_name":"IST-2012-88-v1+1_Synchronous_interface_theories_and_time_triggered_scheduling.pdf","file_size":493198,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4879","checksum":"feae2e07f2d9a59843f8ddabf25d179f","date_created":"2018-12-12T10:11:25Z","date_updated":"2020-07-14T12:46:01Z"}],"oa_version":"Submitted Version","pubrep_id":"88","intvolume":" 7273","title":"Synchronous interface theories and time triggered scheduling","status":"public","ddc":["004"],"_id":"3155","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We propose synchronous interfaces, a new interface theory for discrete-time systems. We use an application to time-triggered scheduling to drive the design choices for our formalism; in particular, additionally to deriving useful mathematical properties, we focus on providing a syntax which is adapted to natural high-level system modeling. As a result, we develop an interface model that relies on a guarded-command based language and is equipped with shared variables and explicit discrete-time clocks. We define all standard interface operations: compatibility checking, composition, refinement, and shared refinement. Apart from the synchronous interface model, the contribution of this paper is the establishment of a formal relation between interface theories and real-time scheduling, where we demonstrate a fully automatic framework for the incremental computation of time-triggered schedules."}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-30793-5_13","conference":{"name":"FORTE: Formal Techniques for Networked and Distributed Systems & FMOODS: Formal Methods for Open Object-Based Distributed Systems ","location":"Stockholm, Sweden","start_date":"2012-06-13","end_date":"2012-06-16"},"quality_controlled":"1","oa":1,"month":"06","volume":7273,"date_created":"2018-12-11T12:01:43Z","date_updated":"2021-01-12T07:41:26Z","author":[{"first_name":"Benoît","last_name":"Delahaye","full_name":"Delahaye, Benoît"},{"first_name":"Uli","last_name":"Fahrenberg","full_name":"Fahrenberg, Uli"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Legay, Axel","last_name":"Legay","first_name":"Axel"},{"last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","acknowledgement":"Research partially supported by the Danish-Chinese Center for Cyber Physical Systems (Grant No.61061130541) and VKR Center of Excellence MT-LAB.","year":"2012","publist_id":"3539","file_date_updated":"2020-07-14T12:46:01Z"},{"status":"public","ddc":["510"],"title":"Hierarchical ordering of reticular networks","intvolume":" 7","_id":"3159","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"5922","relation":"main_file","checksum":"515a98ad72e470752f03f13663dcaff8","date_created":"2019-02-05T12:38:43Z","date_updated":"2020-07-14T12:46:01Z","access_level":"open_access","file_name":"2012_PLoS_Mileyko.PDF","creator":"kschuh","content_type":"application/pdf","file_size":541583}],"oa_version":"Published Version","pubrep_id":"385","type":"journal_article","abstract":[{"lang":"eng","text":"The structure of hierarchical networks in biological and physical systems has long been characterized using the Horton-Strahler ordering scheme. The scheme assigns an integer order to each edge in the network based on the topology of branching such that the order increases from distal parts of the network (e.g., mountain streams or capillaries) to the "root" of the network (e.g., the river outlet or the aorta). However, Horton-Strahler ordering cannot be applied to networks with loops because they they create a contradiction in the edge ordering in terms of which edge precedes another in the hierarchy. Here, we present a generalization of the Horton-Strahler order to weighted planar reticular networks, where weights are assumed to correlate with the importance of network edges, e.g., weights estimated from edge widths may correlate to flow capacity. Our method assigns hierarchical levels not only to edges of the network, but also to its loops, and classifies the edges into reticular edges, which are responsible for loop formation, and tree edges. In addition, we perform a detailed and rigorous theoretical analysis of the sensitivity of the hierarchical levels to weight perturbations. In doing so, we show that the ordering of the reticular edges is more robust to noise in weight estimation than is the ordering of the tree edges. We discuss applications of this generalized Horton-Strahler ordering to the study of leaf venation and other biological networks."}],"issue":"6","publication":"PLoS One","citation":{"chicago":"Mileyko, Yuriy, Herbert Edelsbrunner, Charles Price, and Joshua Weitz. “Hierarchical Ordering of Reticular Networks.” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036715.","mla":"Mileyko, Yuriy, et al. “Hierarchical Ordering of Reticular Networks.” PLoS One, vol. 7, no. 6, e36715, Public Library of Science, 2012, doi:10.1371/journal.pone.0036715.","short":"Y. Mileyko, H. Edelsbrunner, C. Price, J. Weitz, PLoS One 7 (2012).","ista":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. 2012. Hierarchical ordering of reticular networks. PLoS One. 7(6), e36715.","ieee":"Y. Mileyko, H. Edelsbrunner, C. Price, and J. Weitz, “Hierarchical ordering of reticular networks,” PLoS One, vol. 7, no. 6. Public Library of Science, 2012.","apa":"Mileyko, Y., Edelsbrunner, H., Price, C., & Weitz, J. (2012). Hierarchical ordering of reticular networks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036715","ama":"Mileyko Y, Edelsbrunner H, Price C, Weitz J. Hierarchical ordering of reticular networks. PLoS One. 2012;7(6). doi:10.1371/journal.pone.0036715"},"date_published":"2012-06-06T00:00:00Z","scopus_import":1,"day":"06","has_accepted_license":"1","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"HeEd"}],"acknowledgement":"his work was supported by the National Science Foundation Plant Genome Research Program (grant 0820624 to H.E. and J.S.W.), the Defense Advanced Projects Research Agency (grant HR0011-09-1-0055 to H.E. and J.S.W.), and the European Science Foundation (under the Research Networking Programme on “Applied and Computational Algebraic Topology” run by H.E.). Joshua S. Weitz, Ph.D., holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.\r\n\r\n\r\n\r\nDuring preparation of this manuscript the authors became aware of a related work by Katifori and Magnasco (arXiv:1110.1412v1), concurrently submitted and accepted for publication in PLoS ONE.","year":"2012","date_updated":"2021-01-12T07:41:28Z","date_created":"2018-12-11T12:01:44Z","volume":7,"author":[{"full_name":"Mileyko, Yuriy","last_name":"Mileyko","first_name":"Yuriy"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Price, Charles","first_name":"Charles","last_name":"Price"},{"last_name":"Weitz","first_name":"Joshua","full_name":"Weitz, Joshua"}],"article_number":"e36715","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"3530","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0036715","month":"06"},{"publication":"Molecular Ecology","citation":{"short":"L.V. Ugelvig, A. Andersen, J. Boomsma, D. Nash, Molecular Ecology 21 (2012) 3224–3236.","mla":"Ugelvig, Line V., et al. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology, vol. 21, no. 13, Wiley-Blackwell, 2012, pp. 3224–36, doi:10.1111/j.1365-294X.2012.05592.x.","chicago":"Ugelvig, Line V, Anne Andersen, Jacobus Boomsma, and David Nash. “Dispersal and Gene Flow in the Rare Parasitic Large Blue Butterfly Maculinea Arion.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05592.x.","ama":"Ugelvig LV, Andersen A, Boomsma J, Nash D. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 2012;21(13):3224-3236. doi:10.1111/j.1365-294X.2012.05592.x","ieee":"L. V. Ugelvig, A. Andersen, J. Boomsma, and D. Nash, “Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion,” Molecular Ecology, vol. 21, no. 13. Wiley-Blackwell, pp. 3224–3236, 2012.","apa":"Ugelvig, L. V., Andersen, A., Boomsma, J., & Nash, D. (2012). Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05592.x","ista":"Ugelvig LV, Andersen A, Boomsma J, Nash D. 2012. Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion. Molecular Ecology. 21(13), 3224–3236."},"quality_controlled":"1","page":"3224 - 3236","doi":"10.1111/j.1365-294X.2012.05592.x","date_published":"2012-07-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"month":"07","day":"01","year":"2012","_id":"3156","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The work was financed by the Danish National Science Research Foundation via a grant to the Centre for Social Evolution.\r\nWe thank four anonymous reviewers for useful comments on the manuscript, J. Bergsten, P. Bina, B. Carlsson, M. Johannesson and A.E. Lomborg for providing additional wingtip samples, A. Illum for assistance in the field, and in particular P.S. Nielsen for mediating the contact to the collectors and the Swedish authorities. Collection was made possible through a permit by the Åtgärdsprogrammet, supported by the Swedish Environmental Protection Agency.","status":"public","publication_status":"published","title":"Dispersal and gene flow in the rare parasitic Large Blue butterfly Maculinea arion","intvolume":" 21","department":[{"_id":"SyCr"}],"publisher":"Wiley-Blackwell","author":[{"first_name":"Line V","last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V"},{"first_name":"Anne","last_name":"Andersen","full_name":"Andersen, Anne"},{"last_name":"Boomsma","first_name":"Jacobus","full_name":"Boomsma, Jacobus"},{"last_name":"Nash","first_name":"David","full_name":"Nash, David"}],"date_updated":"2021-01-12T07:41:27Z","date_created":"2018-12-11T12:01:43Z","oa_version":"None","volume":21,"type":"journal_article","abstract":[{"text":"Dispersal is crucial for gene flow and often determines the long-term stability of meta-populations, particularly in rare species with specialized life cycles. Such species are often foci of conservation efforts because they suffer disproportionally from degradation and fragmentation of their habitat. However, detailed knowledge of effective gene flow through dispersal is often missing, so that conservation strategies have to be based on mark-recapture observations that are suspected to be poor predictors of long-distance dispersal. These constraints have been especially severe in the study of butterfly populations, where microsatellite markers have been difficult to develop. We used eight microsatellite markers to analyse genetic population structure of the Large Blue butterfly Maculinea arion in Sweden. During recent decades, this species has become an icon of insect conservation after massive decline throughout Europe and extinction in Britain followed by reintroduction of a seed population from the Swedish island of Öland. We find that populations are highly structured genetically, but that gene flow occurs over distances 15 times longer than the maximum distance recorded from mark-recapture studies, which can only be explained by maximum dispersal distances at least twice as large as previously accepted. However, we also find evidence that gaps between sites with suitable habitat exceeding ∼ 20 km induce genetic erosion that can be detected from bottleneck analyses. Although further work is needed, our results suggest that M. arion can maintain fully functional metapopulations when they consist of optimal habitat patches that are no further apart than ∼10 km.","lang":"eng"}],"issue":"13","publist_id":"3538"},{"day":"01","scopus_import":1,"date_published":"2012-11-01T00:00:00Z","publication":"European Journal of Cell Biology","citation":{"ieee":"H. Schachtner et al., “Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo,” European Journal of Cell Biology, vol. 91, no. 11–12. Elsevier, pp. 923–929, 2012.","apa":"Schachtner, H., Li, A., Stevenson, D., Calaminus, S., Thomas, S., Watson, S., … Machesky, L. (2012). Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2012.04.002","ista":"Schachtner H, Li A, Stevenson D, Calaminus S, Thomas S, Watson S, Sixt MK, Wedlich Söldner R, Strathdee D, Machesky L. 2012. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 91(11–12), 923–929.","ama":"Schachtner H, Li A, Stevenson D, et al. Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo. European Journal of Cell Biology. 2012;91(11-12):923-929. doi:10.1016/j.ejcb.2012.04.002","chicago":"Schachtner, Hannah, Ang Li, David Stevenson, Simon Calaminus, Steven Thomas, Steve Watson, Michael K Sixt, Roland Wedlich Söldner, Douglas Strathdee, and Laura Machesky. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ejcb.2012.04.002.","short":"H. Schachtner, A. Li, D. Stevenson, S. Calaminus, S. Thomas, S. Watson, M.K. Sixt, R. Wedlich Söldner, D. Strathdee, L. Machesky, European Journal of Cell Biology 91 (2012) 923–929.","mla":"Schachtner, Hannah, et al. “Tissue Inducible Lifeact Expression Allows Visualization of Actin Dynamics in Vivo and Ex Vivo.” European Journal of Cell Biology, vol. 91, no. 11–12, Elsevier, 2012, pp. 923–29, doi:10.1016/j.ejcb.2012.04.002."},"page":"923 - 929","abstract":[{"lang":"eng","text":"We describe here the development and characterization of a conditionally inducible mouse model expressing Lifeact-GFP, a peptide that reports the dynamics of filamentous actin. We have used this model to study platelets, megakaryocytes and melanoblasts and we provide evidence that Lifeact-GFP is a useful reporter in these cell types ex vivo. In the case of platelets and megakaryocytes, these cells are not transfectable by traditional methods, so conditional activation of Lifeact allows the study of actin dynamics in these cells live. We studied melanoblasts in native skin explants from embryos, allowing the visualization of live actin dynamics during cytokinesis and migration. Our study revealed that melanoblasts lacking the small GTPase Rac1 show a delay in the formation of new pseudopodia following cytokinesis that accounts for the previously reported cytokinesis delay in these cells. Thus, through use of this mouse model, we were able to gain insights into the actin dynamics of cells that could only previously be studied using fixed specimens or following isolation from their native tissue environment."}],"issue":"11-12","type":"journal_article","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3158","title":"Tissue inducible Lifeact expression allows visualization of actin dynamics in vivo and ex vivo","status":"public","intvolume":" 91","month":"11","doi":"10.1016/j.ejcb.2012.04.002","language":[{"iso":"eng"}],"external_id":{"pmid":["22658956"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930012/","open_access":"1"}],"oa":1,"quality_controlled":"1","publist_id":"3534","author":[{"full_name":"Schachtner, Hannah","last_name":"Schachtner","first_name":"Hannah"},{"first_name":"Ang","last_name":"Li","full_name":"Li, Ang"},{"first_name":"David","last_name":"Stevenson","full_name":"Stevenson, David"},{"first_name":"Simon","last_name":"Calaminus","full_name":"Calaminus, Simon"},{"full_name":"Thomas, Steven","last_name":"Thomas","first_name":"Steven"},{"full_name":"Watson, Steve","last_name":"Watson","first_name":"Steve"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Wedlich Söldner, Roland","first_name":"Roland","last_name":"Wedlich Söldner"},{"full_name":"Strathdee, Douglas","last_name":"Strathdee","first_name":"Douglas"},{"full_name":"Machesky, Laura","last_name":"Machesky","first_name":"Laura"}],"date_created":"2018-12-11T12:01:44Z","date_updated":"2021-01-12T07:41:27Z","volume":91,"year":"2012","pmid":1,"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Elsevier"},{"publication_identifier":{"issn":["1861-8200"],"eissn":["1861-8219"]},"month":"03","doi":"10.1007/s11554-010-0168-3","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publist_id":"3417","file_date_updated":"2020-07-14T12:46:04Z","author":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"},{"full_name":"Peters, Jan","first_name":"Jan","last_name":"Peters"}],"volume":7,"date_updated":"2022-05-24T08:05:40Z","date_created":"2018-12-11T12:02:15Z","year":"2012","department":[{"_id":"ChLa"}],"publisher":"Springer","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2012-03-01T00:00:00Z","citation":{"ama":"Lampert C, Peters J. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 2012;7(1):31-41. doi:10.1007/s11554-010-0168-3","ieee":"C. Lampert and J. Peters, “Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components,” Journal of Real-Time Image Processing, vol. 7, no. 1. Springer, pp. 31–41, 2012.","apa":"Lampert, C., & Peters, J. (2012). Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. Springer. https://doi.org/10.1007/s11554-010-0168-3","ista":"Lampert C, Peters J. 2012. Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components. Journal of Real-Time Image Processing. 7(1), 31–41.","short":"C. Lampert, J. Peters, Journal of Real-Time Image Processing 7 (2012) 31–41.","mla":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal of Real-Time Image Processing, vol. 7, no. 1, Springer, 2012, pp. 31–41, doi:10.1007/s11554-010-0168-3.","chicago":"Lampert, Christoph, and Jan Peters. “Real-Time Detection of Colored Objects in Multiple Camera Streams with off-the-Shelf Hardware Components.” Journal of Real-Time Image Processing. Springer, 2012. https://doi.org/10.1007/s11554-010-0168-3."},"publication":"Journal of Real-Time Image Processing","page":"31 - 41","article_type":"original","issue":"1","abstract":[{"lang":"eng","text":"We describe RTblob, a high speed vision system that detects objects in cluttered scenes based on their color and shape at a speed of over 800 frames/s. Because the system is available as open-source software and relies only on off-the-shelf PC hardware components, it can provide the basis for multiple application scenarios. As an illustrative example, we show how RTblob can be used in a robotic table tennis scenario to estimate ball trajectories through 3D space simultaneously from four cameras images at a speed of 200 Hz."}],"type":"journal_article","file":[{"date_updated":"2020-07-14T12:46:04Z","date_created":"2019-02-12T10:52:25Z","checksum":"241be47ea50e81a283bcf4c45b07e8cc","relation":"main_file","file_id":"5958","file_size":2933187,"content_type":"application/pdf","creator":"kschuh","file_name":"2012_Springer_Lampert.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","_id":"3248","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","title":"Real-time detection of colored objects in multiple camera streams with off-the-shelf hardware components","ddc":["000"],"status":"public"},{"publication":"Conservation Genetics","citation":{"ama":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 2012;13(1):293-298. doi:10.1007/s10592-011-0262-5","ista":"Vilaça S, Fernandes Redondo RA, Lins L, Santos F. 2012. Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. 13(1), 293–298.","ieee":"S. Vilaça, R. A. Fernandes Redondo, L. Lins, and F. Santos, “Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus),” Conservation Genetics, vol. 13, no. 1. Springer, pp. 293–298, 2012.","apa":"Vilaça, S., Fernandes Redondo, R. A., Lins, L., & Santos, F. (2012). Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus). Conservation Genetics. Springer. https://doi.org/10.1007/s10592-011-0262-5","mla":"Vilaça, Sibelle, et al. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics, vol. 13, no. 1, Springer, 2012, pp. 293–98, doi:10.1007/s10592-011-0262-5.","short":"S. Vilaça, R.A. Fernandes Redondo, L. Lins, F. Santos, Conservation Genetics 13 (2012) 293–298.","chicago":"Vilaça, Sibelle, Rodrigo A Fernandes Redondo, Lívia Lins, and Fabrício Santos. “Remaining Genetic Diversity in Brazilian Merganser (Mergus Octosetaceus).” Conservation Genetics. Springer, 2012. https://doi.org/10.1007/s10592-011-0262-5."},"quality_controlled":"1","page":"293 - 298","date_published":"2012-02-01T00:00:00Z","doi":"10.1007/s10592-011-0262-5","language":[{"iso":"eng"}],"scopus_import":1,"month":"02","day":"01","_id":"3247","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The present study received grants from FAPEMIG, CNPq, Petrobras Ambiental and Fundação O Boticário de Conservação da Natureza, and followed all ethical guidelines and legal requirements of Brazil for sampling and studying an endangered species.\r\nWe thank the Specialist Work Group for the Conservation of Brazilian Merganser for valuable discussions and opinions on this manuscript. We also thank all the staff from Instituto Terra Brasilis and Funatura (Vivian S. Braz and Gislaine Disconzi) for collecting the samples at Serra da Canastra and Chapada dos Veadeiros, respectively; Dario A. Lijtmaerand and Pablo Tubaro for providing the samples from Argentina, Bradley C. Livezey for sending copies of his papers, and Geoff M. Hilton and Paulo de Tarso Z. Antas for useful suggestions that greatly improved this manuscript.","year":"2012","status":"public","publication_status":"published","title":"Remaining genetic diversity in Brazilian Merganser (Mergus octosetaceus)","intvolume":" 13","department":[{"_id":"JoBo"}],"publisher":"Springer","author":[{"first_name":"Sibelle","last_name":"Vilaça","full_name":"Vilaça, Sibelle"},{"full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","first_name":"Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lívia","last_name":"Lins","full_name":"Lins, Lívia"},{"last_name":"Santos","first_name":"Fabrício","full_name":"Santos, Fabrício"}],"date_created":"2018-12-11T12:02:15Z","date_updated":"2021-01-12T07:42:05Z","oa_version":"None","volume":13,"type":"journal_article","abstract":[{"text":"The Brazilian Merganser is a very rare and threatened species that nowadays inhabits only a few protected areas and their surroundings in the Brazilian territory. In order to estimate the remaining genetic diversity and population structure in this species, two mitochondrial genes were sequenced in 39 individuals belonging to two populations and in one individual collected in Argentina in 1950. We found a highly significant divergence between two major remaining populations of Mergus octosetaceus, which suggests a historical population structure in this species. Furthermore, two deeply divergent lineages were found in a single location, which could due to current or historical secondary contact. Based on the available genetic data, we point out future directions which would contribute to design strategies for conservation and management of this threatened species.","lang":"eng"}],"publist_id":"3420","issue":"1"},{"page":"3 - 4","quality_controlled":"1","citation":{"ista":"Behrndt M, Heisenberg C-PJ. 2012. Spurred by resistance mechanosensation in collective migration. Developmental Cell. 22(1), 3–4.","ieee":"M. Behrndt and C.-P. J. Heisenberg, “Spurred by resistance mechanosensation in collective migration,” Developmental Cell, vol. 22, no. 1. Cell Press, pp. 3–4, 2012.","apa":"Behrndt, M., & Heisenberg, C.-P. J. (2012). Spurred by resistance mechanosensation in collective migration. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.12.018","ama":"Behrndt M, Heisenberg C-PJ. Spurred by resistance mechanosensation in collective migration. Developmental Cell. 2012;22(1):3-4. doi:10.1016/j.devcel.2011.12.018","chicago":"Behrndt, Martin, and Carl-Philipp J Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” Developmental Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2011.12.018.","mla":"Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Spurred by Resistance Mechanosensation in Collective Migration.” Developmental Cell, vol. 22, no. 1, Cell Press, 2012, pp. 3–4, doi:10.1016/j.devcel.2011.12.018.","short":"M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 22 (2012) 3–4."},"publication":"Developmental Cell","language":[{"iso":"eng"}],"date_published":"2012-01-17T00:00:00Z","doi":"10.1016/j.devcel.2011.12.018","scopus_import":1,"day":"17","month":"01","intvolume":" 22","department":[{"_id":"CaHe"}],"publisher":"Cell Press","status":"public","publication_status":"published","title":"Spurred by resistance mechanosensation in collective migration","_id":"3245","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","volume":22,"oa_version":"None","date_updated":"2021-01-12T07:42:05Z","date_created":"2018-12-11T12:02:14Z","author":[{"full_name":"Behrndt, Martin","last_name":"Behrndt","first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"type":"journal_article","publist_id":"3426","issue":"1","abstract":[{"lang":"eng","text":"How cells orchestrate their behavior during collective migration is a long-standing question. Using magnetic tweezers to apply mechanical stimuli to Xenopus mesendoderm cells, Weber etal. (2012) now reveal, in this issue of Developmental Cell, a cadherin-mediated mechanosensitive response that promotes cell polarization and movement persistence during the collective mesendoderm migration in gastrulation."}]},{"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"American Institute of Physics","year":"2012","acknowledgement":"We thank T. Gregor, E. F. Wieschaus, and, especially, C. G. Callan for helpful discussions.\r\nWork at Princeton was supported in part by NSF Grants No. PHY–0957573 and No. CCF–0939370, by NIH Grant No. R01 GM077599, and by the W. M. Keck Foundation. For part of this work, G.T. was supported in part by NSF Grant No. EF–0928048 and by the Vice Provost for Research at the University of Pennsylvania.","date_created":"2018-12-11T12:02:20Z","date_updated":"2021-01-12T07:42:14Z","volume":85,"author":[{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"},{"full_name":"Walczak, Aleksandra","first_name":"Aleksandra","last_name":"Walczak"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"}],"article_number":"041903","publist_id":"3386","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1112.5026"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.85.041903","month":"04","title":"Optimizing information flow in small genetic networks. III. A self-interacting gene","status":"public","intvolume":" 85","_id":"3262","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point."}],"issue":"4","publication":" Physical Review E statistical nonlinear and soft matter physics ","citation":{"ista":"Tkačik G, Walczak A, Bialek W. 2012. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 85(4), 041903.","apa":"Tkačik, G., Walczak, A., & Bialek, W. (2012). Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.85.041903","ieee":"G. Tkačik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks. III. A self-interacting gene,” Physical Review E statistical nonlinear and soft matter physics , vol. 85, no. 4. American Institute of Physics, 2012.","ama":"Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. III. A self-interacting gene. Physical Review E statistical nonlinear and soft matter physics . 2012;85(4). doi:10.1103/PhysRevE.85.041903","chicago":"Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2012. https://doi.org/10.1103/PhysRevE.85.041903.","mla":"Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 85, no. 4, 041903, American Institute of Physics, 2012, doi:10.1103/PhysRevE.85.041903.","short":"G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 85 (2012)."},"date_published":"2012-04-01T00:00:00Z","scopus_import":1,"day":"01"},{"issue":"4-5","abstract":[{"text":"Consider a convex relaxation f̂ of a pseudo-Boolean function f. We say that the relaxation is totally half-integral if f̂(x) is a polyhedral function with half-integral extreme points x, and this property is preserved after adding an arbitrary combination of constraints of the form x i=x j, x i=1-x j, and x i=γ where γ∈{0,1,1/2} is a constant. A well-known example is the roof duality relaxation for quadratic pseudo-Boolean functions f. We argue that total half-integrality is a natural requirement for generalizations of roof duality to arbitrary pseudo-Boolean functions. Our contributions are as follows. First, we provide a complete characterization of totally half-integral relaxations f̂ by establishing a one-to-one correspondence with bisubmodular functions. Second, we give a new characterization of bisubmodular functions. Finally, we show some relationships between general totally half-integral relaxations and relaxations based on the roof duality. On the conceptual level, our results show that bisubmodular functions provide a natural generalization of the roof duality approach to higher-order terms. This can be viewed as a non-submodular analogue of the fact that submodular functions generalize the s-t minimum cut problem with non-negative weights to higher-order terms.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3257","intvolume":" 160","status":"public","title":"Generalized roof duality and bisubmodular functions","day":"01","scopus_import":1,"date_published":"2012-03-01T00:00:00Z","citation":{"ista":"Kolmogorov V. 2012. Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. 160(4–5), 416–426.","ieee":"V. Kolmogorov, “Generalized roof duality and bisubmodular functions,” Discrete Applied Mathematics, vol. 160, no. 4–5. Elsevier, pp. 416–426, 2012.","apa":"Kolmogorov, V. (2012). Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2011.10.026","ama":"Kolmogorov V. Generalized roof duality and bisubmodular functions. Discrete Applied Mathematics. 2012;160(4-5):416-426. doi:10.1016/j.dam.2011.10.026","chicago":"Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2011.10.026.","mla":"Kolmogorov, Vladimir. “Generalized Roof Duality and Bisubmodular Functions.” Discrete Applied Mathematics, vol. 160, no. 4–5, Elsevier, 2012, pp. 416–26, doi:10.1016/j.dam.2011.10.026.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 416–426."},"publication":"Discrete Applied Mathematics","page":"416 - 426","publist_id":"3397","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2934"}]},"author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"volume":160,"date_updated":"2023-02-23T11:04:49Z","date_created":"2018-12-11T12:02:18Z","year":"2012","publisher":"Elsevier","department":[{"_id":"VlKo"}],"publication_status":"published","month":"03","doi":"10.1016/j.dam.2011.10.026","language":[{"iso":"eng"}],"external_id":{"arxiv":["1005.2305"]},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1005.2305","open_access":"1"}],"quality_controlled":"1"},{"_id":"3277","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","publisher":"Springer","department":[{"_id":"NiBa"}],"title":"Can the evolution of multicellularity be anticipated in the exploration of the solar system?","publication_status":"published","status":"public","author":[{"full_name":"de Vladar, Harold","last_name":"de Vladar","first_name":"Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chela Flores, Julian","last_name":"Chela Flores","first_name":"Julian"}],"volume":24,"oa_version":"None","date_created":"2018-12-11T12:02:25Z","date_updated":"2021-01-12T07:42:20Z","type":"book_chapter","alternative_title":["Cellular Origin, Life in Extreme Habitats and Astrobiology"],"publist_id":"3369","abstract":[{"text":"The problem of the origin of metazoa is becoming more urgent in the context of astrobiology. By now it is clear that clues to the understanding of this crucial transition in the evolution of life can arise in a fourth pathway besides the three possibilities in the quest for simplicity outlined by Bonner in his classical book. In other words, solar system exploration seems to be one way in the long-term to elucidate the simplicity of evolutionary development. We place these ideas in the context of different inheritance systems, namely the genotypic and phenotypic replicators with limited or unlimited heredity, and ask which of these can support multicellular development, and to which degree of complexity. However, the quest for evidence on the evolution of biotas from planets around other stars does not seem to be feasible with present technology with direct visualization of living organisms on exoplanets. But this may be attempted on the Galilean moons of Jupiter where there is a possibility of detecting reliable biomarkers in the next decade with the Europa Jupiter System Mission, in view of recent progress by landing micropenetrators on planetary, or satellite surfaces. Mars is a second possibility in the inner Solar System, in spite of the multiple difficulties faced by the fleet of past, present and future missions. We discuss a series of preliminary ideas for elucidating the origin of metazoan analogues with available instrumentation in potential payloads of feasible space missions to the Galilean moons.","lang":"eng"}],"citation":{"ama":"de Vladar H, Chela Flores J. Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and Other Planetary Bodies. Vol 24. Springer; 2012:387-405. doi:10.1007/978-94-007-4966-5_22","ista":"de Vladar H, Chela Flores J. 2012.Can the evolution of multicellularity be anticipated in the exploration of the solar system? In: Life on Earth and other planetary bodies. Cellular Origin, Life in Extreme Habitats and Astrobiology, vol. 24, 387–405.","apa":"de Vladar, H., & Chela Flores, J. (2012). Can the evolution of multicellularity be anticipated in the exploration of the solar system? In Life on Earth and other planetary bodies (Vol. 24, pp. 387–405). Springer. https://doi.org/10.1007/978-94-007-4966-5_22","ieee":"H. de Vladar and J. Chela Flores, “Can the evolution of multicellularity be anticipated in the exploration of the solar system?,” in Life on Earth and other planetary bodies, vol. 24, Springer, 2012, pp. 387–405.","mla":"de Vladar, Harold, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” Life on Earth and Other Planetary Bodies, vol. 24, Springer, 2012, pp. 387–405, doi:10.1007/978-94-007-4966-5_22.","short":"H. de Vladar, J. Chela Flores, in:, Life on Earth and Other Planetary Bodies, Springer, 2012, pp. 387–405.","chicago":"Vladar, Harold de, and Julian Chela Flores. “Can the Evolution of Multicellularity Be Anticipated in the Exploration of the Solar System?” In Life on Earth and Other Planetary Bodies, 24:387–405. Springer, 2012. https://doi.org/10.1007/978-94-007-4966-5_22."},"publication":"Life on Earth and other planetary bodies","page":"387 - 405","quality_controlled":"1","date_published":"2012-01-01T00:00:00Z","doi":"10.1007/978-94-007-4966-5_22","language":[{"iso":"eng"}],"month":"01","day":"01"},{"_id":"3279","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 7194","status":"public","title":"Hardness preserving constructions of pseudorandom functions","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We show a hardness-preserving construction of a PRF from any length doubling PRG which improves upon known constructions whenever we can put a non-trivial upper bound q on the number of queries to the PRF. Our construction requires only O(logq) invocations to the underlying PRG with each query. In comparison, the number of invocations by the best previous hardness-preserving construction (GGM using Levin's trick) is logarithmic in the hardness of the PRG. For example, starting from an exponentially secure PRG {0,1} n → {0,1} 2n, we get a PRF which is exponentially secure if queried at most q = exp(√n)times and where each invocation of the PRF requires Θ(√n) queries to the underlying PRG. This is much less than the Θ(n) required by known constructions. \r\n"}],"citation":{"chicago":"Jain, Abhishek, Krzysztof Z Pietrzak, and Aris Tentes. “Hardness Preserving Constructions of Pseudorandom Functions,” 7194:369–82. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_21.","short":"A. Jain, K.Z. Pietrzak, A. Tentes, in:, Springer, 2012, pp. 369–382.","mla":"Jain, Abhishek, et al. Hardness Preserving Constructions of Pseudorandom Functions. Vol. 7194, Springer, 2012, pp. 369–82, doi:10.1007/978-3-642-28914-9_21.","ieee":"A. Jain, K. Z. Pietrzak, and A. Tentes, “Hardness preserving constructions of pseudorandom functions,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 369–382.","apa":"Jain, A., Pietrzak, K. Z., & Tentes, A. (2012). Hardness preserving constructions of pseudorandom functions (Vol. 7194, pp. 369–382). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_21","ista":"Jain A, Pietrzak KZ, Tentes A. 2012. Hardness preserving constructions of pseudorandom functions. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 369–382.","ama":"Jain A, Pietrzak KZ, Tentes A. Hardness preserving constructions of pseudorandom functions. In: Vol 7194. Springer; 2012:369-382. doi:10.1007/978-3-642-28914-9_21"},"page":"369 - 382","date_published":"2012-05-04T00:00:00Z","scopus_import":1,"day":"04","year":"2012","acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC)","publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","author":[{"last_name":"Jain","first_name":"Abhishek","full_name":"Jain, Abhishek"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Aris","last_name":"Tentes","full_name":"Tentes, Aris"}],"volume":7194,"date_updated":"2021-01-12T07:42:21Z","date_created":"2018-12-11T12:02:25Z","ec_funded":1,"publist_id":"3367","main_file_link":[{"url":"http://www.iacr.org/archive/tcc2012/tcc2012-index.html"}],"project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"quality_controlled":"1","doi":"10.1007/978-3-642-28914-9_21","conference":{"name":"TCC: Theory of Cryptography Conference","end_date":"2012-03-21","start_date":"2012-03-19","location":"Taormina, Sicily, Italy"},"language":[{"iso":"eng"}],"month":"05"},{"scopus_import":1,"month":"06","day":"01","quality_controlled":"1","page":"960 - 967","publication":" Engineering Analysis with Boundary Elements","citation":{"ama":"Rieckh G, Kreuzer W, Waubke H, Balazs P. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 2012;36(6):960-967. doi:10.1016/j.enganabound.2011.12.014","apa":"Rieckh, G., Kreuzer, W., Waubke, H., & Balazs, P. (2012). A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. Elsevier. https://doi.org/10.1016/j.enganabound.2011.12.014","ieee":"G. Rieckh, W. Kreuzer, H. Waubke, and P. Balazs, “A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil,” Engineering Analysis with Boundary Elements, vol. 36, no. 6. Elsevier, pp. 960–967, 2012.","ista":"Rieckh G, Kreuzer W, Waubke H, Balazs P. 2012. A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil. Engineering Analysis with Boundary Elements. 36(6), 960–967.","short":"G. Rieckh, W. Kreuzer, H. Waubke, P. Balazs, Engineering Analysis with Boundary Elements 36 (2012) 960–967.","mla":"Rieckh, Georg, et al. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.” Engineering Analysis with Boundary Elements, vol. 36, no. 6, Elsevier, 2012, pp. 960–67, doi:10.1016/j.enganabound.2011.12.014.","chicago":"Rieckh, Georg, Wolfgang Kreuzer, Holger Waubke, and Peter Balazs. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.” Engineering Analysis with Boundary Elements. Elsevier, 2012. https://doi.org/10.1016/j.enganabound.2011.12.014."},"language":[{"iso":"eng"}],"doi":"10.1016/j.enganabound.2011.12.014","date_published":"2012-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"A boundary element model of a tunnel running through horizontally layered soil with anisotropic material properties is presented. Since there is no analytical fundamental solution for wave propagation inside a layered orthotropic medium in 3D, the fundamental displacements and stresses have to be calculated numerically. In our model this is done in the Fourier domain with respect to space and time. The assumption of a straight tunnel with infinite extension in the x direction makes it possible to decouple the system for every wave number kx, leading to a 2.5D-problem, which is suited for parallel computation. The special form of the fundamental solution, resulting from our Fourier ansatz, and the fact, that the calculation of the boundary integral equation is performed in the Fourier domain, enhances the stability and efficiency of the numerical calculations."}],"issue":"6","publist_id":"3372","status":"public","title":"A 2.5D-Fourier-BEM model for vibrations in a tunnel running through layered anisotropic soil","publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaTk"}],"intvolume":" 36","_id":"3274","acknowledgement":"This work was supported by the Austrian Federal Ministry of Transport, Innovation and Technology under the Grant Bmvit-isb2 and the FFG under the project Pr. Nr. 809089.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","date_updated":"2021-01-12T07:42:19Z","date_created":"2018-12-11T12:02:24Z","volume":36,"oa_version":"None","author":[{"full_name":"Rieckh, Georg","last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kreuzer, Wolfgang","last_name":"Kreuzer","first_name":"Wolfgang"},{"last_name":"Waubke","first_name":"Holger","full_name":"Waubke, Holger"},{"full_name":"Balazs, Peter","first_name":"Peter","last_name":"Balazs"}]},{"month":"01","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255887/","open_access":"1"}],"external_id":{"pmid":["22031940"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1128/JVI.05638-11","publist_id":"3356","department":[{"_id":"JoBo"}],"publisher":"ASM","publication_status":"published","pmid":1,"year":"2012","acknowledgement":"This work was supported by grants from Fundação de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG), the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES), and the National Council for Scientific and Technological Development (CNPq). A.C.T.C.P., B.S.A.F.B., F.G.G.L., and J.A.P.S.-M. were recipients of predoctoral fellowships from CNPq. C.A.B., E.G.K., T.S.-P., P.F.P.P., and P.C.P.F. are recipients of research fellowships from CNPq. \r\n\r\n\r\nWe are grateful to Angela S. Lopes, Ilda M. V. Gama, João R. dos Santos, and Andreza A. Carvalho for their secretarial/technical assistance and to Fernanda Gambogi for help with immunofluorescence microscopy. We also thank M. C. Sogayar (Department of Biochemistry, University of São Paulo, São Paulo, Brazil), who kindly provided us with the A31 cell line, and R. Davis (Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA) for the WT and JNK1/2-, MKK4-, MKK7-, and MKK4/7-KO cells. VACV WR was from C. Jungwirth (Universität Würzburg, Würzburg, Germany). The recombinant VACV vF13L-GFP and the rabbit polyclonal antibodies against viral proteins, B5R, D8L, L1R, and A36R, were from B. Moss (NIAID, Bethesda, MD). The pcDNA3-Myc-JNK2-MKK7 WT plasmid was from Eugen Kerkhoff (Universität Würzburg, Würzburg, Germany). We also thank Flávio G. da Fonseca (UFMG, Belo Horizonte, MG, Brazil) and Kathleen A. Boyle (Medical College of Wisconsin, Milwaukee, WI) for critically reading the manuscript.","volume":86,"date_created":"2018-12-11T12:02:29Z","date_updated":"2021-01-12T07:42:25Z","author":[{"full_name":"Pereira, Anna","last_name":"Pereira","first_name":"Anna"},{"id":"36705F98-F248-11E8-B48F-1D18A9856A87","last_name":"Leite","first_name":"Flávia","full_name":"Leite, Flávia"},{"full_name":"Brasil, Bruno","first_name":"Bruno","last_name":"Brasil"},{"full_name":"Soares Martins, Jamaria","last_name":"Soares Martins","first_name":"Jamaria"},{"full_name":"Torres, Alice","last_name":"Torres","first_name":"Alice"},{"first_name":"Paulo","last_name":"Pimenta","full_name":"Pimenta, Paulo"},{"full_name":"Souto Padrón, Thais","first_name":"Thais","last_name":"Souto Padrón"},{"last_name":"Tranktman","first_name":"Paula","full_name":"Tranktman, Paula"},{"first_name":"Paulo","last_name":"Ferreira","full_name":"Ferreira, Paulo"},{"first_name":"Erna","last_name":"Kroon","full_name":"Kroon, Erna"},{"full_name":"Bonjardim, Cláudio","first_name":"Cláudio","last_name":"Bonjardim"}],"scopus_import":1,"day":"01","page":"172 - 184","citation":{"ama":"Pereira A, Leite F, Brasil B, et al. A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology. 2012;86(1):172-184. doi:10.1128/JVI.05638-11","ista":"Pereira A, Leite F, Brasil B, Soares Martins J, Torres A, Pimenta P, Souto Padrón T, Tranktman P, Ferreira P, Kroon E, Bonjardim C. 2012. A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology. 86(1), 172–184.","apa":"Pereira, A., Leite, F., Brasil, B., Soares Martins, J., Torres, A., Pimenta, P., … Bonjardim, C. (2012). A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization. Journal of Virology. ASM. https://doi.org/10.1128/JVI.05638-11","ieee":"A. Pereira et al., “A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization,” Journal of Virology, vol. 86, no. 1. ASM, pp. 172–184, 2012.","mla":"Pereira, Anna, et al. “A Vaccinia Virus-Driven Interplay between the MKK4/7-JNK1/2 Pathway and Cytoskeleton Reorganization.” Journal of Virology, vol. 86, no. 1, ASM, 2012, pp. 172–84, doi:10.1128/JVI.05638-11.","short":"A. Pereira, F. Leite, B. Brasil, J. Soares Martins, A. Torres, P. Pimenta, T. Souto Padrón, P. Tranktman, P. Ferreira, E. Kroon, C. Bonjardim, Journal of Virology 86 (2012) 172–184.","chicago":"Pereira, Anna, Flávia Leite, Bruno Brasil, Jamaria Soares Martins, Alice Torres, Paulo Pimenta, Thais Souto Padrón, et al. “A Vaccinia Virus-Driven Interplay between the MKK4/7-JNK1/2 Pathway and Cytoskeleton Reorganization.” Journal of Virology. ASM, 2012. https://doi.org/10.1128/JVI.05638-11."},"publication":"Journal of Virology","date_published":"2012-01-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Viral manipulation of transduction pathways associated with key cellular functions such as survival, response to microbial infection, and cytoskeleton reorganization can provide the supportive milieu for a productive infection. Here, we demonstrate that vaccinia virus (VACV) infection leads to activation of the stress-activated protein kinase (SAPK)/extracellular signal-regulated kinase (ERK) 4/7 (MKK4/7)-c-Jun N-terminal protein kinase 1/2 (JNK1/2) pathway; further, the stimulation of this pathway requires postpenetration, prereplicative events in the viral replication cycle. Although the formation of intracellular mature virus (IMV) was not affected in MKK4/7- or JNK1/2-knockout (KO) cells, we did note an accentuated deregulation of microtubule and actin network organization in infected JNK1/2-KO cells. This was followed by deregulated viral trafficking to the periphery and enhanced enveloped particle release. Furthermore, VACV infection induced alterations in the cell contractility and morphology, and cell migration was reduced in the JNK-KO cells. In addition, phosphorylation of proteins implicated with early cell contractility and cell migration, such as microtubule-associated protein 1B and paxillin, respectively, was not detected in the VACV-infected KO cells. In sum, our findings uncover a regulatory role played by the MKK4/7-JNK1/2 pathway in cytoskeleton reorganization during VACV infection.\r\n"}],"intvolume":" 86","title":"A vaccinia virus-driven interplay between the MKK4/7-JNK1/2 pathway and cytoskeleton reorganization","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3289","oa_version":"Submitted Version"},{"publisher":"Elsevier","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"Research by the third author is partially supported by the National Science Foundation (NSF) under grant DBI-0820624.","year":"2012","volume":33,"date_created":"2018-12-11T12:02:36Z","date_updated":"2021-01-12T07:42:34Z","author":[{"id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","last_name":"Bendich","first_name":"Paul","full_name":"Bendich, Paul"},{"last_name":"Cabello","first_name":"Sergio","full_name":"Cabello, Sergio"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"publist_id":"3330","file_date_updated":"2020-07-14T12:46:06Z","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.patrec.2011.10.007","month":"08","intvolume":" 33","status":"public","title":"A point calculus for interlevel set homology","ddc":["000"],"_id":"3310","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":280280,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-542-v1+1_2012-J-01-Poinculus.pdf","access_level":"open_access","date_created":"2018-12-12T10:15:00Z","date_updated":"2020-07-14T12:46:06Z","checksum":"d65f79775b51258a604ca5ec741297cc","relation":"main_file","file_id":"5116"}],"oa_version":"Submitted Version","pubrep_id":"542","type":"journal_article","issue":"11","abstract":[{"text":"The theory of persistent homology opens up the possibility to reason about topological features of a space or a function quantitatively and in combinatorial terms. We refer to this new angle at a classical subject within algebraic topology as a point calculus, which we present for the family of interlevel sets of a real-valued function. Our account of the subject is expository, devoid of proofs, and written for non-experts in algebraic topology.","lang":"eng"}],"page":"1436 - 1444","citation":{"mla":"Bendich, Paul, et al. “A Point Calculus for Interlevel Set Homology.” Pattern Recognition Letters, vol. 33, no. 11, Elsevier, 2012, pp. 1436–44, doi:10.1016/j.patrec.2011.10.007.","short":"P. Bendich, S. Cabello, H. Edelsbrunner, Pattern Recognition Letters 33 (2012) 1436–1444.","chicago":"Bendich, Paul, Sergio Cabello, and Herbert Edelsbrunner. “A Point Calculus for Interlevel Set Homology.” Pattern Recognition Letters. Elsevier, 2012. https://doi.org/10.1016/j.patrec.2011.10.007.","ama":"Bendich P, Cabello S, Edelsbrunner H. A point calculus for interlevel set homology. Pattern Recognition Letters. 2012;33(11):1436-1444. doi:10.1016/j.patrec.2011.10.007","ista":"Bendich P, Cabello S, Edelsbrunner H. 2012. A point calculus for interlevel set homology. Pattern Recognition Letters. 33(11), 1436–1444.","ieee":"P. Bendich, S. Cabello, and H. Edelsbrunner, “A point calculus for interlevel set homology,” Pattern Recognition Letters, vol. 33, no. 11. Elsevier, pp. 1436–1444, 2012.","apa":"Bendich, P., Cabello, S., & Edelsbrunner, H. (2012). A point calculus for interlevel set homology. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2011.10.007"},"publication":"Pattern Recognition Letters","date_published":"2012-08-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"acknowledgement":"This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, MAT2010-15138, ENE2008-03277-E/CON, CSD2009-00050, and CSD2009-00013. M.I. thanks the Spanish MICINN for her Ph.D. grant. J.A. and R.Z. also acknowledge Generalitat de Catalunya 2009-SGR-770 and XaRMAE. A.C. is grateful for financial support through the Ramon y Cajal program of the Spanish MICINN.\r\n\r\n","_id":"338","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","publication_status":"published","status":"public","title":"Extending the nanocrystal synthesis control to quaternary compositions","publisher":"American Chemical Society (ACS)","intvolume":" 12","author":[{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"full_name":"Zamani, Reza","first_name":"Reza","last_name":"Zamani"},{"full_name":"Li, Wenhua","last_name":"Li","first_name":"Wenhua"},{"first_name":"Alexey","last_name":"Shavel","full_name":"Shavel, Alexey"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"full_name":"Morante, Joan","first_name":"Joan","last_name":"Morante"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"date_updated":"2021-01-12T07:43:05Z","date_created":"2018-12-11T11:45:54Z","volume":12,"oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"The ample chemical and structural freedom of quaternary compounds permits engineering materials that fulfill the requirements of a wide variety of applications. In this work, the mechanisms to achieve unprecedented size, shape, and composition control in quaternary nanocrystals are detailed. The described procedure allows obtaining tetrahedral and penta-tetrahedral quaternary nanocrystals with tuned size distributions and controlled compositions from a plethora of I 2-II-IV-VI 4 semiconductors."}],"issue":"3","publist_id":"7488","extern":"1","publication":"Crystal Growth and Design ","citation":{"ama":"Ibáñez M, Zamani R, Li W, et al. Extending the nanocrystal synthesis control to quaternary compositions. Crystal Growth and Design . 2012;12(3):1085-1090. doi:10.1021/cg201709c","ista":"Ibáñez M, Zamani R, Li W, Shavel A, Arbiol J, Morante J, Cabot A. 2012. Extending the nanocrystal synthesis control to quaternary compositions. Crystal Growth and Design . 12(3), 1085–1090.","apa":"Ibáñez, M., Zamani, R., Li, W., Shavel, A., Arbiol, J., Morante, J., & Cabot, A. (2012). Extending the nanocrystal synthesis control to quaternary compositions. Crystal Growth and Design . American Chemical Society (ACS). https://doi.org/10.1021/cg201709c","ieee":"M. Ibáñez et al., “Extending the nanocrystal synthesis control to quaternary compositions,” Crystal Growth and Design , vol. 12, no. 3. American Chemical Society (ACS), pp. 1085–1090, 2012.","mla":"Ibáñez, Maria, et al. “Extending the Nanocrystal Synthesis Control to Quaternary Compositions.” Crystal Growth and Design , vol. 12, no. 3, American Chemical Society (ACS), 2012, pp. 1085–90, doi:10.1021/cg201709c.","short":"M. Ibáñez, R. Zamani, W. Li, A. Shavel, J. Arbiol, J. Morante, A. Cabot, Crystal Growth and Design 12 (2012) 1085–1090.","chicago":"Ibáñez, Maria, Reza Zamani, Wenhua Li, Alexey Shavel, Jordi Arbiol, Joan Morante, and Andreu Cabot. “Extending the Nanocrystal Synthesis Control to Quaternary Compositions.” Crystal Growth and Design . American Chemical Society (ACS), 2012. https://doi.org/10.1021/cg201709c."},"quality_controlled":"1","article_type":"original","page":"1085 - 1090","date_published":"2012-01-01T00:00:00Z","doi":"10.1021/cg201709c","language":[{"iso":"eng"}],"month":"01","day":"01","article_processing_charge":"No"},{"_id":"339","acknowledgement":"This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, MAT2010-15138, ENE2008-03277-E/CON, CSD2009-00050. and CSD2009-00013. M.I. and N.G.-C. thank the Spanish MICINN for the PhD grant. J.A. and R.Z. also acknowledge Generalitat de Catalunya 2009-SGR-770 and XaRMAE. A.C. is thankful for financial support through the Ramon y Cajal program of the Spanish MICINN. N.G.-C. and J.D.P. are thankful for the computer resources, technical expertise and assistance provided by the Barcelona Supercomputing Center - Centro Nacional de Supercomputación.","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4","publication_status":"published","intvolume":" 24","publisher":"American Chemical Society","author":[{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"first_name":"Doris","last_name":"Cadavid","full_name":"Cadavid, Doris"},{"full_name":"Zamani, Reza","first_name":"Reza","last_name":"Zamani"},{"full_name":"García Castelló, Nuria","last_name":"García Castelló","first_name":"Nuria"},{"full_name":"Izquierdo Roca, Victora","last_name":"Izquierdo Roca","first_name":"Victora"},{"first_name":"Wenhua","last_name":"Li","full_name":"Li, Wenhua"},{"full_name":"Fairbrother, Andrew","first_name":"Andrew","last_name":"Fairbrother"},{"first_name":"Joan","last_name":"Prades","full_name":"Prades, Joan"},{"last_name":"Shavel","first_name":"Alexey","full_name":"Shavel, Alexey"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"first_name":"Alejandro","last_name":"Pérez Rodríguez","full_name":"Pérez Rodríguez, Alejandro"},{"last_name":"Morante","first_name":"Joan","full_name":"Morante, Joan"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"date_created":"2018-12-11T11:45:54Z","date_updated":"2021-01-12T07:43:09Z","oa_version":"None","volume":24,"type":"journal_article","abstract":[{"lang":"eng","text":"A high-yield and upscalable colloidal synthesis route for the production of quaternary I 2-II-IV-VI 4 nanocrystals, particularly stannite Cu 2+xCd 1-xSnSe 4, with narrow size distribution and precisely controlled composition is presented. It is also shown here how the diversity of valences in the constituent elements allows an effective control of their electrical conductivity through the adjustment of the cation ratios. At the same time, while the crystallographic complexity of quaternary chalcogenides is associated with intrinsically low thermal conductivities, the reduction of the lattice dimensions to the nanoscale further reduces the materials thermal conductivity. In the specific case of the stannite crystal structure, a convenient slab distribution of the valence band maximum states permits a partial decoupling of the p-type electrical conductivity from both the Seebeck coefficient and the thermal conductivity. Combining these features, we demonstrate how an initial optimization of the nanocrystals Cd/Cu ratio allowed us to obtain low-temperature solution-processed materials with ZT values up to 0.71 at 685 K."}],"publist_id":"7489","issue":"3","extern":"1","publication":"Chemistry of Materials","citation":{"ama":"Ibáñez M, Cadavid D, Zamani R, et al. Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4. Chemistry of Materials. 2012;24(3):562-570. doi:10.1021/cm2031812","apa":"Ibáñez, M., Cadavid, D., Zamani, R., García Castelló, N., Izquierdo Roca, V., Li, W., … Cabot, A. (2012). Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/cm2031812","ieee":"M. Ibáñez et al., “Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4,” Chemistry of Materials, vol. 24, no. 3. American Chemical Society, pp. 562–570, 2012.","ista":"Ibáñez M, Cadavid D, Zamani R, García Castelló N, Izquierdo Roca V, Li W, Fairbrother A, Prades J, Shavel A, Arbiol J, Pérez Rodríguez A, Morante J, Cabot A. 2012. Composition control and thermoelectric properties of quaternary chalcogenide nanocrystals: The case of stannite Cu2CdSnSe4. Chemistry of Materials. 24(3), 562–570.","short":"M. Ibáñez, D. Cadavid, R. Zamani, N. García Castelló, V. Izquierdo Roca, W. Li, A. Fairbrother, J. Prades, A. Shavel, J. Arbiol, A. Pérez Rodríguez, J. Morante, A. Cabot, Chemistry of Materials 24 (2012) 562–570.","mla":"Ibáñez, Maria, et al. “Composition Control and Thermoelectric Properties of Quaternary Chalcogenide Nanocrystals: The Case of Stannite Cu2CdSnSe4.” Chemistry of Materials, vol. 24, no. 3, American Chemical Society, 2012, pp. 562–70, doi:10.1021/cm2031812.","chicago":"Ibáñez, Maria, Doris Cadavid, Reza Zamani, Nuria García Castelló, Victora Izquierdo Roca, Wenhua Li, Andrew Fairbrother, et al. “Composition Control and Thermoelectric Properties of Quaternary Chalcogenide Nanocrystals: The Case of Stannite Cu2CdSnSe4.” Chemistry of Materials. American Chemical Society, 2012. https://doi.org/10.1021/cm2031812."},"quality_controlled":"1","article_type":"original","page":"562 - 570","date_published":"2012-01-31T00:00:00Z","doi":"10.1021/cm2031812","language":[{"iso":"eng"}],"month":"01","day":"31","article_processing_charge":"No"},{"extern":"1","issue":"3","publist_id":"7490","abstract":[{"lang":"eng","text":"A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles with controlled composition is presented. CZTS nanoparticles were prepared through the reaction of the metals' amino complexes with elemental sulfur in a continuous-flow reactor at moderate temperatures (300-330 °C). High-resolution transmission electron microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic structure compatible with that of the kesterite. Chemical characterization of the materials showed the presence of the four elements in each individual nanocrystal. Composition control was achieved by adjusting the solution flow rate through the reactor and the proper choice of the nominal precursor concentration within the flowing solution. Single-particle analysis revealed a composition distribution within each sample, which was optimized at the highest synthesis temperatures used. "}],"type":"journal_article","oa_version":"None","volume":134,"date_updated":"2021-01-12T07:43:13Z","date_created":"2018-12-11T11:45:54Z","author":[{"first_name":"Alexey","last_name":"Shavel","full_name":"Shavel, Alexey"},{"full_name":"Cadavid, Doris","last_name":"Cadavid","first_name":"Doris"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Carrete, Alex","last_name":"Carrete","first_name":"Alex"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"intvolume":" 134","publisher":"ACS","publication_status":"published","status":"public","title":"Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor","_id":"340","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, CDS2009-00050, CSD2009-00013, and ENE2008-03277-E/CON. M.I. thanks the Spanish MICINN for her Ph.D. grant. A.C. is thankful for financial support through the Ramón y Cajal Program.","year":"2012","article_processing_charge":"No","day":"02","month":"01","language":[{"iso":"eng"}],"doi":"10.1021/ja209688a","date_published":"2012-01-02T00:00:00Z","page":"1438 - 1441","article_type":"original","quality_controlled":"1","citation":{"short":"A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, A. Cabot, Journal of the American Chemical Society 134 (2012) 1438–1441.","mla":"Shavel, Alexey, et al. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society, vol. 134, no. 3, ACS, 2012, pp. 1438–41, doi:10.1021/ja209688a.","chicago":"Shavel, Alexey, Doris Cadavid, Maria Ibáñez, Alex Carrete, and Andreu Cabot. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja209688a.","ama":"Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 2012;134(3):1438-1441. doi:10.1021/ja209688a","ieee":"A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, and A. Cabot, “Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor,” Journal of the American Chemical Society, vol. 134, no. 3. ACS, pp. 1438–1441, 2012.","apa":"Shavel, A., Cadavid, D., Ibáñez, M., Carrete, A., & Cabot, A. (2012). Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja209688a","ista":"Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. 2012. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 134(3), 1438–1441."},"publication":"Journal of the American Chemical Society"}]