[{"publist_id":"4639","author":[{"first_name":"Yohann","last_name":"Boutté","full_name":"Boutté, Yohann"},{"full_name":"Jonsson, Kristoffer","first_name":"Kristoffer","last_name":"Jonsson"},{"last_name":"Mcfarlane","first_name":"Heather","full_name":"Mcfarlane, Heather"},{"last_name":"Johnson","first_name":"Errin","full_name":"Johnson, Errin"},{"first_name":"Delphine","last_name":"Gendre","full_name":"Gendre, Delphine"},{"full_name":"Swarup, Ranjan","first_name":"Ranjan","last_name":"Swarup"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lacey","last_name":"Samuels","full_name":"Samuels, Lacey"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"first_name":"Rishikesh","last_name":"Bhalerao","full_name":"Bhalerao, Rishikesh"}],"date_updated":"2021-01-12T06:56:33Z","date_created":"2018-12-11T11:56:48Z","volume":110,"year":"2013","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"month":"10","doi":"10.1073/pnas.1309057110","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791722/","open_access":"1"}],"external_id":{"pmid":["24043780"]},"quality_controlled":"1","abstract":[{"lang":"eng","text":"The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development."}],"issue":"40","type":"journal_article","oa_version":"Submitted Version","_id":"2290","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation","status":"public","intvolume":" 110","day":"01","scopus_import":1,"date_published":"2013-10-01T00:00:00Z","publication":"PNAS","citation":{"chicago":"Boutté, Yohann, Kristoffer Jonsson, Heather Mcfarlane, Errin Johnson, Delphine Gendre, Ranjan Swarup, Jiří Friml, Lacey Samuels, Stéphanie Robert, and Rishikesh Bhalerao. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1309057110.","mla":"Boutté, Yohann, et al. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS, vol. 110, no. 40, National Academy of Sciences, 2013, pp. 16259–64, doi:10.1073/pnas.1309057110.","short":"Y. Boutté, K. Jonsson, H. Mcfarlane, E. Johnson, D. Gendre, R. Swarup, J. Friml, L. Samuels, S. Robert, R. Bhalerao, PNAS 110 (2013) 16259–16264.","ista":"Boutté Y, Jonsson K, Mcfarlane H, Johnson E, Gendre D, Swarup R, Friml J, Samuels L, Robert S, Bhalerao R. 2013. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 110(40), 16259–16264.","ieee":"Y. Boutté et al., “ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation,” PNAS, vol. 110, no. 40. National Academy of Sciences, pp. 16259–16264, 2013.","apa":"Boutté, Y., Jonsson, K., Mcfarlane, H., Johnson, E., Gendre, D., Swarup, R., … Bhalerao, R. (2013). ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1309057110","ama":"Boutté Y, Jonsson K, Mcfarlane H, et al. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 2013;110(40):16259-16264. doi:10.1073/pnas.1309057110"},"page":"16259 - 16264"},{"type":"conference","ec_funded":1,"publist_id":"4634","abstract":[{"lang":"eng","text":"In this work we propose a system for automatic classification of Drosophila embryos into developmental stages.\r\nWhile the system is designed to solve an actual problem in biological research, we believe that the principle underly-\r\ning it is interesting not only for biologists, but also for researchers in computer vision. The main idea is to combine two orthogonal sources of information: one is a classifier trained on strongly invariant features, which makes it applicable to images of very different conditions, but also leads to rather noisy predictions. The other is a label propagation step based on a more powerful similarity measure that however is only consistent within specific subsets of the data at a time.\r\nIn our biological setup, the information sources are the shape and the staining patterns of embryo images. We show\r\nexperimentally that while neither of the methods can be used by itself to achieve satisfactory results, their combina-\r\ntion achieves prediction quality comparable to human performance."}],"publisher":"IEEE","department":[{"_id":"ChLa"}],"publication_status":"published","status":"public","title":"Drosophila Embryo Stage Annotation using Label Propagation","_id":"2294","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","date_created":"2018-12-11T11:56:49Z","date_updated":"2021-01-12T06:56:35Z","author":[{"full_name":"Kazmar, Tomas","first_name":"Tomas","last_name":"Kazmar"},{"first_name":"Evgeny","last_name":"Kvon","full_name":"Kvon, Evgeny"},{"full_name":"Stark, Alexander","first_name":"Alexander","last_name":"Stark"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"scopus_import":1,"day":"01","month":"12","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"http://www.cv-foundation.org/openaccess/ICCV2013.py","open_access":"1"}],"oa":1,"citation":{"short":"T. Kazmar, E. Kvon, A. Stark, C. Lampert, in:, IEEE, 2013.","mla":"Kazmar, Tomas, et al. Drosophila Embryo Stage Annotation Using Label Propagation. IEEE, 2013, doi:10.1109/ICCV.2013.139.","chicago":"Kazmar, Tomas, Evgeny Kvon, Alexander Stark, and Christoph Lampert. “Drosophila Embryo Stage Annotation Using Label Propagation.” IEEE, 2013. https://doi.org/10.1109/ICCV.2013.139.","ama":"Kazmar T, Kvon E, Stark A, Lampert C. Drosophila Embryo Stage Annotation using Label Propagation. In: IEEE; 2013. doi:10.1109/ICCV.2013.139","apa":"Kazmar, T., Kvon, E., Stark, A., & Lampert, C. (2013). Drosophila Embryo Stage Annotation using Label Propagation. Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.139","ieee":"T. Kazmar, E. Kvon, A. Stark, and C. Lampert, “Drosophila Embryo Stage Annotation using Label Propagation,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013.","ista":"Kazmar T, Kvon E, Stark A, Lampert C. 2013. Drosophila Embryo Stage Annotation using Label Propagation. ICCV: International Conference on Computer Vision."},"language":[{"iso":"eng"}],"doi":"10.1109/ICCV.2013.139","date_published":"2013-12-01T00:00:00Z","conference":{"end_date":"2013-12-08","start_date":"2013-12-01","location":"Sydney, Australia","name":"ICCV: International Conference on Computer Vision"}},{"alternative_title":["LNCS"],"type":"conference_editor","abstract":[{"text":"This book constitutes the thoroughly refereed conference proceedings of the 38th International Symposium on Mathematical Foundations of Computer Science, MFCS 2013, held in Klosterneuburg, Austria, in August 2013. The 67 revised full papers presented together with six invited talks were carefully selected from 191 submissions. Topics covered include algorithmic game theory, algorithmic learning theory, algorithms and data structures, automata, formal languages, bioinformatics, complexity, computational geometry, computer-assisted reasoning, concurrency theory, databases and knowledge-based systems, foundations of computing, logic in computer science, models of computation, semantics and verification of programs, and theoretical issues in artificial intelligence.","lang":"eng"}],"publist_id":"4636","status":"public","title":"Mathematical Foundations of Computer Science 2013","publication_status":"published","editor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Sgall, Jiri","first_name":"Jiri","last_name":"Sgall"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","intvolume":" 8087","year":"2013","_id":"2292","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2020-08-11T10:09:45Z","date_created":"2018-12-11T11:56:48Z","oa_version":"None","volume":8087,"series_title":"Lecture Notes in Computer Science","scopus_import":1,"day":"08","month":"08","publication_identifier":{"isbn":["978-3-642-40312-5"]},"quality_controlled":"1","page":"VI - 854","citation":{"ama":"Chatterjee K, Sgall J, eds. Mathematical Foundations of Computer Science 2013. Vol 8087. Springer; 2013:VI-854. doi:10.1007/978-3-642-40313-2","apa":"Chatterjee, K., & Sgall, J. (Eds.). (2013). Mathematical Foundations of Computer Science 2013 (Vol. 8087, p. VI-854). Presented at the MFCS: Mathematical Foundations of Computer Science, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40313-2","ieee":"K. Chatterjee and J. Sgall, Eds., Mathematical Foundations of Computer Science 2013, vol. 8087. Springer, 2013, p. VI-854.","ista":"Chatterjee K, Sgall J eds. 2013. Mathematical Foundations of Computer Science 2013, Springer,p.","short":"K. Chatterjee, J. Sgall, eds., Mathematical Foundations of Computer Science 2013, Springer, 2013.","mla":"Chatterjee, Krishnendu, and Jiri Sgall, editors. Mathematical Foundations of Computer Science 2013. Vol. 8087, Springer, 2013, p. VI-854, doi:10.1007/978-3-642-40313-2.","chicago":"Chatterjee, Krishnendu, and Jiri Sgall, eds. Mathematical Foundations of Computer Science 2013. Vol. 8087. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40313-2."},"language":[{"iso":"eng"}],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2013-08-30","location":"Klosterneuburg, Austria","start_date":"2013-08-26"},"date_published":"2013-08-08T00:00:00Z","doi":"10.1007/978-3-642-40313-2"},{"scopus_import":1,"month":"12","day":"01","main_file_link":[{"open_access":"1","url":"www.cv-foundation.org/openaccess/content_iccv_2013/papers/Sharmanska_Learning_to_Rank_2013_ICCV_paper.pdf"}],"citation":{"short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, IEEE, 2013, pp. 825–832.","mla":"Sharmanska, Viktoriia, et al. Learning to Rank Using Privileged Information. IEEE, 2013, pp. 825–32, doi:10.1109/ICCV.2013.107.","chicago":"Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Learning to Rank Using Privileged Information,” 825–32. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.107.","ama":"Sharmanska V, Quadrianto N, Lampert C. Learning to rank using privileged information. In: IEEE; 2013:825-832. doi:10.1109/ICCV.2013.107","ieee":"V. Sharmanska, N. Quadrianto, and C. Lampert, “Learning to rank using privileged information,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013, pp. 825–832.","apa":"Sharmanska, V., Quadrianto, N., & Lampert, C. (2013). Learning to rank using privileged information (pp. 825–832). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.107","ista":"Sharmanska V, Quadrianto N, Lampert C. 2013. Learning to rank using privileged information. ICCV: International Conference on Computer Vision, 825–832."},"oa":1,"quality_controlled":"1","page":"825 - 832","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"conference":{"end_date":"2013-12-08","start_date":"2013-12-01","location":"Sydney, Australia","name":"ICCV: International Conference on Computer Vision"},"doi":"10.1109/ICCV.2013.107","date_published":"2013-12-01T00:00:00Z","language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"Many computer vision problems have an asymmetric distribution of information between training and test time. In this work, we study the case where we are given additional information about the training data, which however will not be available at test time. This situation is called learning using privileged information (LUPI). We introduce two maximum-margin techniques that are able to make use of this additional source of information, and we show that the framework is applicable to several scenarios that have been studied in computer vision before. Experiments with attributes, bounding boxes, image tags and rationales as additional information in object classification show promising results.","lang":"eng"}],"ec_funded":1,"publist_id":"4635","_id":"2293","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Learning to rank using privileged information","publication_status":"published","status":"public","publisher":"IEEE","department":[{"_id":"ChLa"}],"author":[{"first_name":"Viktoriia","last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia"},{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"date_created":"2018-12-11T11:56:49Z","date_updated":"2023-02-23T10:36:41Z","oa_version":"Submitted Version"},{"quality_controlled":"1","page":"115 - 129","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2013/492"}],"citation":{"chicago":"Ferrara, Anna, Georg Fuchsbauer, and Bogdan Warinschi. “Cryptographically Enforced RBAC,” 115–29. IEEE, 2013. https://doi.org/10.1109/CSF.2013.15.","short":"A. Ferrara, G. Fuchsbauer, B. Warinschi, in:, IEEE, 2013, pp. 115–129.","mla":"Ferrara, Anna, et al. Cryptographically Enforced RBAC. IEEE, 2013, pp. 115–29, doi:10.1109/CSF.2013.15.","ieee":"A. Ferrara, G. Fuchsbauer, and B. Warinschi, “Cryptographically enforced RBAC,” presented at the CSF: Computer Security Foundations, New Orleans, LA, United States, 2013, pp. 115–129.","apa":"Ferrara, A., Fuchsbauer, G., & Warinschi, B. (2013). Cryptographically enforced RBAC (pp. 115–129). Presented at the CSF: Computer Security Foundations, New Orleans, LA, United States: IEEE. https://doi.org/10.1109/CSF.2013.15","ista":"Ferrara A, Fuchsbauer G, Warinschi B. 2013. Cryptographically enforced RBAC. CSF: Computer Security Foundations, 115–129.","ama":"Ferrara A, Fuchsbauer G, Warinschi B. Cryptographically enforced RBAC. In: IEEE; 2013:115-129. doi:10.1109/CSF.2013.15"},"oa":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2013-09-26","location":"New Orleans, LA, United States","end_date":"2013-09-28","name":"CSF: Computer Security Foundations"},"date_published":"2013-09-01T00:00:00Z","doi":"10.1109/CSF.2013.15","scopus_import":1,"month":"09","day":"01","title":"Cryptographically enforced RBAC","publication_status":"published","status":"public","department":[{"_id":"KrPi"}],"publisher":"IEEE","_id":"2291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","date_created":"2018-12-11T11:56:48Z","date_updated":"2021-01-12T06:56:34Z","oa_version":"Submitted Version","author":[{"full_name":"Ferrara, Anna","last_name":"Ferrara","first_name":"Anna"},{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg"},{"first_name":"Bogdan","last_name":"Warinschi","full_name":"Warinschi, Bogdan"}],"type":"conference","abstract":[{"lang":"eng","text":"Cryptographic access control promises to offer easily distributed trust and broader applicability, while reducing reliance on low-level online monitors. Traditional implementations of cryptographic access control rely on simple cryptographic primitives whereas recent endeavors employ primitives with richer functionality and security guarantees. Worryingly, few of the existing cryptographic access-control schemes come with precise guarantees, the gap between the policy specification and the implementation being analyzed only informally, if at all. In this paper we begin addressing this shortcoming. Unlike prior work that targeted ad-hoc policy specification, we look at the well-established Role-Based Access Control (RBAC) model, as used in a typical file system. In short, we provide a precise syntax for a computational version of RBAC, offer rigorous definitions for cryptographic policy enforcement of a large class of RBAC security policies, and demonstrate that an implementation based on attribute-based encryption meets our security notions. We view our main contribution as being at the conceptual level. Although we work with RBAC for concreteness, our general methodology could guide future research for uses of cryptography in other access-control models. \r\n"}],"publist_id":"4637"},{"alternative_title":["LNCS"],"type":"conference_editor","abstract":[{"lang":"eng","text":"This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms."}],"publist_id":"4643","publication_status":"published","title":"Computational Methods in Systems Biology","status":"public","intvolume":" 8130","publisher":"Springer","department":[{"_id":"ToHe"}],"editor":[{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-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"}],"_id":"2288","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","date_updated":"2019-08-02T12:37:44Z","date_created":"2018-12-11T11:56:47Z","volume":8130,"oa_version":"None","day":"01","month":"07","publication_identifier":{"isbn":["978-3-642-40707-9"]},"quality_controlled":"1","citation":{"ista":"Gupta A, Henzinger TA eds. 2013. Computational Methods in Systems Biology, Springer,p.","ieee":"A. Gupta and T. A. Henzinger, Eds., Computational Methods in Systems Biology, vol. 8130. Springer, 2013.","apa":"Gupta, A., & Henzinger, T. A. (Eds.). (2013). Computational Methods in Systems Biology (Vol. 8130). Presented at the CMSB: Computational Methods in Systems Biology, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40708-6","ama":"Gupta A, Henzinger TA, eds. Computational Methods in Systems Biology. Vol 8130. Springer; 2013. doi:10.1007/978-3-642-40708-6","chicago":"Gupta, Ashutosh, and Thomas A Henzinger, eds. Computational Methods in Systems Biology. Vol. 8130. Springer, 2013. https://doi.org/10.1007/978-3-642-40708-6.","mla":"Gupta, Ashutosh, and Thomas A. Henzinger, editors. Computational Methods in Systems Biology. Vol. 8130, Springer, 2013, doi:10.1007/978-3-642-40708-6.","short":"A. Gupta, T.A. Henzinger, eds., Computational Methods in Systems Biology, Springer, 2013."},"language":[{"iso":"eng"}],"conference":{"name":"CMSB: Computational Methods in Systems Biology","end_date":"2013-09-24","start_date":"2013-09-22","location":"Klosterneuburg, Austria"},"date_published":"2013-07-01T00:00:00Z","doi":"10.1007/978-3-642-40708-6"},{"month":"01","oa":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"quality_controlled":"1","doi":"10.1007/978-3-642-38856-9_10","conference":{"location":"Seattle, WA, United States","start_date":"2013-06-20","end_date":"2013-06-22","name":"SAS: Static Analysis Symposium"},"language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"4630","file_date_updated":"2020-07-14T12:45:37Z","year":"2013","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","author":[{"full_name":"Dragoi, Cezara","last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Enea","first_name":"Constantin","full_name":"Enea, Constantin"},{"full_name":"Sighireanu, Mihaela","last_name":"Sighireanu","first_name":"Mihaela"}],"volume":7935,"date_created":"2018-12-11T11:56:50Z","date_updated":"2021-01-12T06:56:36Z","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"short":"C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2013, pp. 150–171.","mla":"Dragoi, Cezara, et al. Local Shape Analysis for Overlaid Data Structures. Vol. 7935, Springer, 2013, pp. 150–71, doi:10.1007/978-3-642-38856-9_10.","chicago":"Dragoi, Cezara, Constantin Enea, and Mihaela Sighireanu. “Local Shape Analysis for Overlaid Data Structures,” 7935:150–71. Springer, 2013. https://doi.org/10.1007/978-3-642-38856-9_10.","ama":"Dragoi C, Enea C, Sighireanu M. Local shape analysis for overlaid data structures. In: Vol 7935. Springer; 2013:150-171. doi:10.1007/978-3-642-38856-9_10","ieee":"C. Dragoi, C. Enea, and M. Sighireanu, “Local shape analysis for overlaid data structures,” presented at the SAS: Static Analysis Symposium, Seattle, WA, United States, 2013, vol. 7935, pp. 150–171.","apa":"Dragoi, C., Enea, C., & Sighireanu, M. (2013). Local shape analysis for overlaid data structures (Vol. 7935, pp. 150–171). Presented at the SAS: Static Analysis Symposium, Seattle, WA, United States: Springer. https://doi.org/10.1007/978-3-642-38856-9_10","ista":"Dragoi C, Enea C, Sighireanu M. 2013. Local shape analysis for overlaid data structures. SAS: Static Analysis Symposium, LNCS, vol. 7935, 150–171."},"page":"150 - 171","date_published":"2013-01-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We present a shape analysis for programs that manipulate overlaid data structures which share sets of objects. The abstract domain contains Separation Logic formulas that (1) combine a per-object separating conjunction with a per-field separating conjunction and (2) constrain a set of variables interpreted as sets of objects. The definition of the abstract domain operators is based on a notion of homomorphism between formulas, viewed as graphs, used recently to define optimal decision procedures for fragments of the Separation Logic. Based on a Frame Rule that supports the two versions of the separating conjunction, the analysis is able to reason in a modular manner about non-overlaid data structures and then, compose information only at a few program points, e.g., procedure returns. We have implemented this analysis in a prototype tool and applied it on several interesting case studies that manipulate overlaid and nested linked lists.\r\n","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2298","intvolume":" 7935","status":"public","ddc":["000","004"],"title":"Local shape analysis for overlaid data structures","pubrep_id":"196","file":[{"file_name":"IST-2014-196-v1+1_sas13.pdf","access_level":"open_access","content_type":"application/pdf","file_size":299004,"creator":"system","relation":"main_file","file_id":"4824","date_updated":"2020-07-14T12:45:37Z","date_created":"2018-12-12T10:10:36Z","checksum":"907edd33a5892e3af093365f1fd57ed7"}],"oa_version":"Submitted Version"},{"abstract":[{"text":"The standard hardware design flow involves: (a) design of an integrated circuit using a hardware description language, (b) extensive functional and formal verification, and (c) logical synthesis. However, the above-mentioned processes consume significant effort and time. An alternative approach is to use a formal specification language as a high-level hardware description language and synthesize hardware from formal specifications. Our work is a case study of the synthesis of the widely and industrially used AMBA AHB protocol from formal specifications. Bloem et al. presented the first formal specifications for the AMBA AHB Arbiter and synthesized the AHB Arbiter circuit. However, in the first formal specification some important assumptions were missing. Our contributions are as follows: (a) We present detailed formal specifications for the AHB Arbiter incorporating the missing details, and obtain significant improvements in the synthesis results (both with respect to the number of gates in the synthesized circuit and with respect to the time taken to synthesize the circuit), and (b) we present formal specifications to generate compact circuits for the remaining two main components of AMBA AHB, namely, AHB Master and AHB Slave. Thus with systematic description we are able to automatically and completely synthesize an important and widely used industrial protocol.","lang":"eng"}],"issue":"5-6","type":"journal_article","pubrep_id":"87","oa_version":"Submitted Version","file":[{"date_created":"2018-12-12T10:11:53Z","date_updated":"2020-07-14T12:45:37Z","checksum":"57b06a732dd8d6349190dba6b5b0d33b","relation":"main_file","file_id":"4910","file_size":277372,"content_type":"application/pdf","creator":"system","file_name":"IST-2012-87-v1+1_Synthesis_of_AMBA_AHB_from_formal_specifications-_A_case_study.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2299","ddc":["000"],"title":"Synthesis of AMBA AHB from formal specification: A case study","status":"public","intvolume":" 15","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2013-10-01T00:00:00Z","publication":"International Journal on Software Tools for Technology Transfer","citation":{"short":"Y. Godhal, K. Chatterjee, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 15 (2013) 585–601.","mla":"Godhal, Yashdeep, et al. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” International Journal on Software Tools for Technology Transfer, vol. 15, no. 5–6, Springer, 2013, pp. 585–601, doi:10.1007/s10009-011-0207-9.","chicago":"Godhal, Yashdeep, Krishnendu Chatterjee, and Thomas A Henzinger. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” International Journal on Software Tools for Technology Transfer. Springer, 2013. https://doi.org/10.1007/s10009-011-0207-9.","ama":"Godhal Y, Chatterjee K, Henzinger TA. Synthesis of AMBA AHB from formal specification: A case study. International Journal on Software Tools for Technology Transfer. 2013;15(5-6):585-601. doi:10.1007/s10009-011-0207-9","apa":"Godhal, Y., Chatterjee, K., & Henzinger, T. A. (2013). Synthesis of AMBA AHB from formal specification: A case study. 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Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. 2013;8(2):185-232. doi:10.1007/s11537-013-1264-5","ista":"Seiringer R. 2013. Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. 8(2), 185–232.","ieee":"R. Seiringer, “Hot topics in cold gases: A mathematical physics perspective,” Japanese Journal of Mathematics, vol. 8, no. 2. Springer, pp. 185–232, 2013.","apa":"Seiringer, R. (2013). Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. Springer. https://doi.org/10.1007/s11537-013-1264-5","mla":"Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” Japanese Journal of Mathematics, vol. 8, no. 2, Springer, 2013, pp. 185–232, doi:10.1007/s11537-013-1264-5.","short":"R. Seiringer, Japanese Journal of Mathematics 8 (2013) 185–232.","chicago":"Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” Japanese Journal of Mathematics. Springer, 2013. https://doi.org/10.1007/s11537-013-1264-5."},"publication":"Japanese Journal of Mathematics","page":"185 - 232","date_published":"2013-09-24T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We present an overview of mathematical results on the low temperature properties of dilute quantum gases, which have been obtained in the past few years. The presentation includes a discussion of Bose-Einstein condensation, the excitation spectrum for trapped gases and its relation to superfluidity, as well as the appearance of quantized vortices in rotating systems. All these properties are intensely being studied in current experiments on cold atomic gases. 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Hierzu werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement, die noch nicht mit dem Thema vertraut sind.","lang":"ger"}],"citation":{"mla":"Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken. Vol. 50, De Gruyter, 2013, doi:10.1515/9783110278736.","short":"P. Danowski, A. Pohl, (Open) Linked Data in Bibliotheken, De Gruyter, 2013.","chicago":"Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken. Vol. 50. De Gruyter, 2013. https://doi.org/10.1515/9783110278736.","ama":"Danowski P, Pohl A. (Open) Linked Data in Bibliotheken. Vol 50. De Gruyter; 2013. doi:10.1515/9783110278736","ista":"Danowski P, Pohl A. 2013. (Open) Linked Data in Bibliotheken, De Gruyter,p.","apa":"Danowski, P., & Pohl, A. (2013). (Open) Linked Data in Bibliotheken (Vol. 50). De Gruyter. https://doi.org/10.1515/9783110278736","ieee":"P. Danowski and A. 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Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, D. Zufferey, in:, Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–331.","mla":"Desai, Ankush, et al. “P: Safe Asynchronous Event-Driven Programming.” Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–31, doi:10.1145/2491956.2462184.","chicago":"Desai, Ankush, Vivek Gupta, Ethan Jackson, Shaz Qadeer, Sriram Rajamani, and Damien Zufferey. “P: Safe Asynchronous Event-Driven Programming.” In Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, 321–31. ACM, 2013. https://doi.org/10.1145/2491956.2462184.","ama":"Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. P: Safe asynchronous event-driven programming. In: Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. ACM; 2013:321-331. doi:10.1145/2491956.2462184","ieee":"A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, and D. Zufferey, “P: Safe asynchronous event-driven programming,” in Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, Seattle, WA, United States, 2013, pp. 321–331.","apa":"Desai, A., Gupta, V., Jackson, E., Qadeer, S., Rajamani, S., & Zufferey, D. (2013). P: Safe asynchronous event-driven programming. In Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 321–331). Seattle, WA, United States: ACM. https://doi.org/10.1145/2491956.2462184","ista":"Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. 2013. P: Safe asynchronous event-driven programming. Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. 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P allows the programmer to specify the system as a collection of interacting state machines, which communicate with each other using events. P unifies modeling and programming into one activity for the programmer. Not only can a P program be compiled into executable code, but it can also be tested using model checking techniques. P allows the programmer to specify the environment, used to "close" the system during testing, as nondeterministic ghost machines. Ghost machines are erased during compilation to executable code; a type system ensures that the erasure is semantics preserving. The P language is designed so that a P program can be checked for responsiveness-the ability to handle every event in a timely manner. By default, a machine needs to handle every event that arrives in every state. But handling every event in every state is impractical. The language provides a notion of deferred events where the programmer can annotate when she wants to delay processing an event. The default safety checker looks for presence of unhan-dled events. The language also provides default liveness checks that an event cannot be potentially deferred forever. P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P."}],"ec_funded":1,"publist_id":"4626","type":"conference"},{"publist_id":"4627","article_number":"064401","author":[{"full_name":"Giuliani, Alessandro","last_name":"Giuliani","first_name":"Alessandro"},{"last_name":"Lieb","first_name":"Élliott","full_name":"Lieb, Élliott"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"date_created":"2018-12-11T11:56:51Z","date_updated":"2021-01-12T06:56:38Z","volume":88,"year":"2013","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"American Physical Society","month":"08","doi":"10.1103/PhysRevB.88.064401","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1305.5323"]},"main_file_link":[{"url":"http://arxiv.org/abs/1305.5323","open_access":"1"}],"quality_controlled":"1","abstract":[{"text":"We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Preprint","_id":"2300","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Realization of stripes and slabs in two and three dimensions","status":"public","intvolume":" 88","day":"01","scopus_import":1,"date_published":"2013-08-01T00:00:00Z","publication":"Physical Review B","citation":{"apa":"Giuliani, A., Lieb, É., & Seiringer, R. (2013). Realization of stripes and slabs in two and three dimensions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.88.064401","ieee":"A. Giuliani, É. Lieb, and R. Seiringer, “Realization of stripes and slabs in two and three dimensions,” Physical Review B, vol. 88, no. 6. American Physical Society, 2013.","ista":"Giuliani A, Lieb É, Seiringer R. 2013. Realization of stripes and slabs in two and three dimensions. Physical Review B. 88(6), 064401.","ama":"Giuliani A, Lieb É, Seiringer R. Realization of stripes and slabs in two and three dimensions. Physical Review B. 2013;88(6). doi:10.1103/PhysRevB.88.064401","chicago":"Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.064401.","short":"A. Giuliani, É. Lieb, R. Seiringer, Physical Review B 88 (2013).","mla":"Giuliani, Alessandro, et al. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B, vol. 88, no. 6, 064401, American Physical Society, 2013, doi:10.1103/PhysRevB.88.064401."}},{"type":"journal_article","issue":"6","publist_id":"4624","abstract":[{"text":"MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools.","lang":"eng"}],"intvolume":" 8","publisher":"Springer","department":[{"_id":"SiHi"}],"status":"public","title":"Dissection of gene function at clonal level using mosaic analysis with double markers","publication_status":"published","year":"2013","_id":"2303","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by IST Austria institutional funds.","oa_version":"None","volume":8,"date_created":"2018-12-11T11:56:52Z","date_updated":"2021-01-12T06:56:39Z","author":[{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon"}],"scopus_import":1,"day":"03","month":"09","page":"557 - 568","quality_controlled":"1","article_type":"review","citation":{"chicago":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology. Springer, 2013. https://doi.org/10.1007/s11515-013-1279-6.","mla":"Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology, vol. 8, no. 6, Springer, 2013, pp. 557–68, doi:10.1007/s11515-013-1279-6.","short":"S. Hippenmeyer, Frontiers in Biology 8 (2013) 557–568.","ista":"Hippenmeyer S. 2013. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 8(6), 557–568.","apa":"Hippenmeyer, S. (2013). Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. Springer. https://doi.org/10.1007/s11515-013-1279-6","ieee":"S. Hippenmeyer, “Dissection of gene function at clonal level using mosaic analysis with double markers,” Frontiers in Biology, vol. 8, no. 6. Springer, pp. 557–568, 2013.","ama":"Hippenmeyer S. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 2013;8(6):557-568. doi:10.1007/s11515-013-1279-6"},"publication":"Frontiers in Biology","language":[{"iso":"eng"}],"date_published":"2013-09-03T00:00:00Z","doi":"10.1007/s11515-013-1279-6"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2304","acknowledgement":"This research is supported by the Graduate school of IST Austria (Institute of Science and Technology Austria).","year":"2013","publication_status":"published","status":"public","title":"Van der Corput sequences and linear permutations","intvolume":" 43","department":[{"_id":"HeEd"}],"publisher":"Elsevier","author":[{"first_name":"Florian","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian"}],"date_updated":"2021-01-12T06:56:39Z","date_created":"2018-12-11T11:56:53Z","oa_version":"None","volume":43,"type":"journal_article","abstract":[{"lang":"eng","text":"This extended abstract is concerned with the irregularities of distribution of one-dimensional permuted van der Corput sequences that are generated from linear permutations. We show how to obtain upper bounds for the discrepancy and diaphony of these sequences, by relating them to Kronecker sequences and applying earlier results of Faure and Niederreiter."}],"publist_id":"4623","publication":"Electronic Notes in Discrete Mathematics","citation":{"chicago":"Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” Electronic Notes in Discrete Mathematics. Elsevier, 2013. https://doi.org/10.1016/j.endm.2013.07.008.","mla":"Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” Electronic Notes in Discrete Mathematics, vol. 43, Elsevier, 2013, pp. 43–50, doi:10.1016/j.endm.2013.07.008.","short":"F. Pausinger, Electronic Notes in Discrete Mathematics 43 (2013) 43–50.","ista":"Pausinger F. 2013. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 43, 43–50.","apa":"Pausinger, F. (2013). Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2013.07.008","ieee":"F. Pausinger, “Van der Corput sequences and linear permutations,” Electronic Notes in Discrete Mathematics, vol. 43. Elsevier, pp. 43–50, 2013.","ama":"Pausinger F. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 2013;43:43-50. doi:10.1016/j.endm.2013.07.008"},"quality_controlled":"1","page":"43 - 50","doi":"10.1016/j.endm.2013.07.008","date_published":"2013-09-05T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"month":"09","day":"05"},{"status":"public","title":"Disordered Bose-Einstein condensates with interaction","publication_status":"published","publisher":"World Scientific Publishing","year":"2013","_id":"2315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:56:57Z","date_updated":"2021-01-12T06:56:43Z","oa_version":"None","author":[{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"},{"last_name":"Zagrebnov","first_name":"Valentin","full_name":"Zagrebnov, Valentin"}],"type":"conference","extern":"1","abstract":[{"text":" We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the interval. ","lang":"eng"}],"publist_id":"4612","page":"610-619","citation":{"short":"R. Seiringer, J. Yngvason, V. Zagrebnov, in:, World Scientific Publishing, 2013, pp. 610–619.","mla":"Seiringer, Robert, et al. Disordered Bose-Einstein Condensates with Interaction. World Scientific Publishing, 2013, pp. 610–19, doi:10.1142/9789814449243_0063.","chicago":"Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Disordered Bose-Einstein Condensates with Interaction,” 610–19. World Scientific Publishing, 2013. https://doi.org/10.1142/9789814449243_0063.","ama":"Seiringer R, Yngvason J, Zagrebnov V. Disordered Bose-Einstein condensates with interaction. In: World Scientific Publishing; 2013:610-619. doi:10.1142/9789814449243_0063","ieee":"R. Seiringer, J. Yngvason, and V. Zagrebnov, “Disordered Bose-Einstein condensates with interaction,” presented at the ICMP: International Congress on Mathematical Physics, 2013, pp. 610–619.","apa":"Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Disordered Bose-Einstein condensates with interaction (pp. 610–619). Presented at the ICMP: International Congress on Mathematical Physics, World Scientific Publishing. https://doi.org/10.1142/9789814449243_0063","ista":"Seiringer R, Yngvason J, Zagrebnov V. 2013. Disordered Bose-Einstein condensates with interaction. ICMP: International Congress on Mathematical Physics, 610–619."},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1209.4046","open_access":"1"}],"external_id":{"arxiv":["1209.4046"]},"language":[{"iso":"eng"}],"conference":{"name":"ICMP: International Congress on Mathematical Physics"},"date_published":"2013-01-01T00:00:00Z","doi":"10.1142/9789814449243_0063","article_processing_charge":"No"},{"conference":{"name":"OTAMP: Operator Theory, Analysis and Mathematical Physics"},"date_published":"2013-01-01T00:00:00Z","doi":"10.1007/978-3-0348-0531-5_3","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1103.1866"}],"oa":1,"citation":{"ista":"Frank R, Hainzl C, Seiringer R, Solovej J. 2013. Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction. OTAMP: Operator Theory, Analysis and Mathematical Physics, 57–88.","apa":"Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2013). Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction (pp. 57–88). Presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, Springer. https://doi.org/10.1007/978-3-0348-0531-5_3","ieee":"R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “ Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction,” presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, 2013, pp. 57–88.","ama":"Frank R, Hainzl C, Seiringer R, Solovej J. Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction. In: Springer; 2013:57-88. doi:10.1007/978-3-0348-0531-5_3","chicago":"Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “ Derivation of Ginzburg-Landau Theory for a One-Dimensional System with Contact Interaction,” 57–88. Springer, 2013. https://doi.org/10.1007/978-3-0348-0531-5_3.","mla":"Frank, Rupert, et al. Derivation of Ginzburg-Landau Theory for a One-Dimensional System with Contact Interaction. Springer, 2013, pp. 57–88, doi:10.1007/978-3-0348-0531-5_3.","short":"R. Frank, C. Hainzl, R. Seiringer, J. Solovej, in:, Springer, 2013, pp. 57–88."},"quality_controlled":0,"page":"57 - 88","month":"01","day":"01","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert L"},{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Robert Seiringer"},{"last_name":"Solovej","first_name":"Jan","full_name":"Solovej, Jan P"}],"date_updated":"2021-01-12T06:56:45Z","date_created":"2018-12-11T11:56:58Z","_id":"2319","year":"2013","publication_status":"published","status":"public","title":" Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction","publisher":"Springer","abstract":[{"lang":"eng","text":"In a recent paper [7] we give the first rigorous derivation of the celebrated Ginzburg-Landau (GL)theory, starting from the microscopic Bardeen- Cooper-Schrieffer (BCS)model. Here we present our results in the simplified case of a one-dimensional system of particles interacting via a δ-potential."}],"publist_id":"4608","extern":1,"type":"conference"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2328","ddc":["000","004"],"status":"public","title":"Aspect-oriented linearizability proofs","intvolume":" 8052","pubrep_id":"197","oa_version":"Submitted Version","file":[{"file_id":"4721","relation":"main_file","checksum":"bdbb520de91751fe0136309ad4ef67e4","date_created":"2018-12-12T10:08:58Z","date_updated":"2020-07-14T12:45:39Z","access_level":"open_access","file_name":"IST-2014-197-v1+1_main-queue-verification.pdf","creator":"system","content_type":"application/pdf","file_size":337059}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates.\r\nIn response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof.","lang":"eng"}],"citation":{"short":"T.A. Henzinger, A. Sezgin, V. Vafeiadis, 8052 (2013) 242–256.","mla":"Henzinger, Thomas A., et al. Aspect-Oriented Linearizability Proofs. Vol. 8052, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 242–56, doi:10.1007/978-3-642-40184-8_18.","chicago":"Henzinger, Thomas A, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Lecture Notes in Computer Science. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.1007/978-3-642-40184-8_18.","ama":"Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. 2013;8052:242-256. doi:10.1007/978-3-642-40184-8_18","ieee":"T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” vol. 8052. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 242–256, 2013.","apa":"Henzinger, T. A., Sezgin, A., & Vafeiadis, V. (2013). Aspect-oriented linearizability proofs. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-40184-8_18","ista":"Henzinger TA, Sezgin A, Vafeiadis V. 2013. Aspect-oriented linearizability proofs. 8052, 242–256."},"page":"242 - 256","date_published":"2013-08-01T00:00:00Z","scopus_import":1,"series_title":"Lecture Notes in Computer Science","day":"01","has_accepted_license":"1","year":"2013","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali"},{"last_name":"Vafeiadis","first_name":"Viktor","full_name":"Vafeiadis, Viktor"}],"related_material":{"record":[{"id":"1832","relation":"later_version","status":"public"}]},"date_updated":"2023-02-23T10:16:27Z","date_created":"2018-12-11T11:57:01Z","volume":8052,"file_date_updated":"2020-07-14T12:45:39Z","ec_funded":1,"publist_id":"4598","oa":1,"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"conference":{"name":"CONCUR: Concurrency Theory","end_date":"2013-08-30","location":"Buenos Aires, Argentina","start_date":"2013-08-27"},"doi":"10.1007/978-3-642-40184-8_18","language":[{"iso":"eng"}],"month":"08"},{"type":"journal_article","publist_id":"4521","issue":"3","abstract":[{"text":"The Lieb-Thirring inequalities give a bound on the negative eigenvalues of a Schrödinger operator in terms of an Lp-norm of the potential. These are dual to bounds on the H1-norms of a system of orthonormal functions. Here we extend these bounds to analogous inequalities for perturbations of the Fermi sea of noninteracting particles (i.e., for perturbations of the continuous spectrum of the Laplacian by local potentials).","lang":"eng"}],"extern":1,"_id":"2404","year":"2013","publisher":"Duke University Press","intvolume":" 162","publication_status":"published","status":"public","title":"A positive density analogue of the Lieb-Thirring inequality","author":[{"full_name":"Frank, Rupert L","last_name":"Frank","first_name":"Rupert"},{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"last_name":"Lieb","first_name":"Élliott","full_name":"Lieb, Élliott H"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Robert Seiringer"}],"volume":162,"date_created":"2018-12-11T11:57:28Z","date_updated":"2021-01-12T06:57:17Z","month":"02","day":"01","oa":1,"citation":{"ista":"Frank R, Lewin M, Lieb É, Seiringer R. 2013. A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. 162(3), 435–495.","ieee":"R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “A positive density analogue of the Lieb-Thirring inequality,” Duke Mathematical Journal, vol. 162, no. 3. Duke University Press, pp. 435–495, 2013.","apa":"Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2013). A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2019477","ama":"Frank R, Lewin M, Lieb É, Seiringer R. A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. 2013;162(3):435-495. doi:10.1215/00127094-2019477","chicago":"Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “A Positive Density Analogue of the Lieb-Thirring Inequality.” Duke Mathematical Journal. Duke University Press, 2013. https://doi.org/10.1215/00127094-2019477.","mla":"Frank, Rupert, et al. “A Positive Density Analogue of the Lieb-Thirring Inequality.” Duke Mathematical Journal, vol. 162, no. 3, Duke University Press, 2013, pp. 435–95, doi:10.1215/00127094-2019477.","short":"R. Frank, M. Lewin, É. Lieb, R. Seiringer, Duke Mathematical Journal 162 (2013) 435–495."},"main_file_link":[{"url":"http://arxiv.org/abs/1108.4246","open_access":"1"}],"publication":"Duke Mathematical Journal","page":"435 - 495","quality_controlled":0,"date_published":"2013-02-01T00:00:00Z","doi":"10.1215/00127094-2019477"},{"volume":217,"date_created":"2018-12-11T11:57:29Z","date_updated":"2021-01-12T06:57:17Z","author":[{"full_name":"Robert Seiringer","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"},{"full_name":"Zagrebnov, Valentin A","last_name":"Zagrebnov","first_name":"Valentin"}],"intvolume":" 217","publisher":"Springer","publication_status":"published","status":"public","title":"Condensation of interacting bosons in a random potential","year":"2013","_id":"2406","extern":1,"issue":"1","publist_id":"4520","abstract":[{"lang":"eng","text":"We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval. We prove that, in the Gross-Pitaevskii limit, Bose Einstein condensation takes place in the whole parameter range considered. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the unit interval."}],"type":"journal_article","doi":"10.1140/epjst/e2013-01759-5","date_published":"2013-02-01T00:00:00Z","page":"103 - 107","quality_controlled":0,"citation":{"short":"R. Seiringer, J. Yngvason, V. Zagrebnov, European Physical Journal: Special Topics 217 (2013) 103–107.","mla":"Seiringer, Robert, et al. “Condensation of Interacting Bosons in a Random Potential.” European Physical Journal: Special Topics, vol. 217, no. 1, Springer, 2013, pp. 103–07, doi:10.1140/epjst/e2013-01759-5.","chicago":"Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Condensation of Interacting Bosons in a Random Potential.” European Physical Journal: Special Topics. Springer, 2013. https://doi.org/10.1140/epjst/e2013-01759-5.","ama":"Seiringer R, Yngvason J, Zagrebnov V. Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. 2013;217(1):103-107. doi:10.1140/epjst/e2013-01759-5","ieee":"R. Seiringer, J. Yngvason, and V. Zagrebnov, “Condensation of interacting bosons in a random potential,” European Physical Journal: Special Topics, vol. 217, no. 1. Springer, pp. 103–107, 2013.","apa":"Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. Springer. https://doi.org/10.1140/epjst/e2013-01759-5","ista":"Seiringer R, Yngvason J, Zagrebnov V. 2013. Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. 217(1), 103–107."},"publication":"European Physical Journal: Special Topics","month":"02","day":"01"},{"month":"04","day":"01","doi":"10.1007/s00220-012-1604-y","date_published":"2013-04-01T00:00:00Z","quality_controlled":0,"page":"557 - 573","publication":"Communications in Mathematical Physics","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1201.3954","open_access":"1"}],"citation":{"ieee":"R. Frank, É. Lieb, and R. Seiringer, “Symmetry of bipolaron bound states for small Coulomb repulsion,” Communications in Mathematical Physics, vol. 319, no. 2. Springer, pp. 557–573, 2013.","apa":"Frank, R., Lieb, É., & Seiringer, R. (2013). Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-012-1604-y","ista":"Frank R, Lieb É, Seiringer R. 2013. Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. 319(2), 557–573.","ama":"Frank R, Lieb É, Seiringer R. Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. 2013;319(2):557-573. doi:10.1007/s00220-012-1604-y","chicago":"Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-012-1604-y.","short":"R. Frank, É. Lieb, R. Seiringer, Communications in Mathematical Physics 319 (2013) 557–573.","mla":"Frank, Rupert, et al. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” Communications in Mathematical Physics, vol. 319, no. 2, Springer, 2013, pp. 557–73, doi:10.1007/s00220-012-1604-y."},"extern":1,"abstract":[{"lang":"eng","text":"We consider the bipolaron in the Pekar-Tomasevich approximation and address the question whether the ground state is spherically symmetric or not. Numerical analysis has, so far, not completely settled the question. Our contribution is to prove rigorously that the ground state remains spherical for small values of the electron-electron Coulomb repulsion."}],"publist_id":"4522","issue":"2","type":"journal_article","date_created":"2018-12-11T11:57:28Z","date_updated":"2021-01-12T06:57:17Z","volume":319,"author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert L"},{"full_name":"Lieb, Élliott H","last_name":"Lieb","first_name":"Élliott"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Robert Seiringer"}],"publication_status":"published","title":"Symmetry of bipolaron bound states for small Coulomb repulsion","status":"public","intvolume":" 319","publisher":"Springer","_id":"2405","year":"2013"},{"doi":"10.1007/s00220-013-1736-8","date_published":"2013-09-01T00:00:00Z","page":"559 - 591","quality_controlled":0,"oa":1,"citation":{"short":"P. Grech, R. Seiringer, Communications in Mathematical Physics 322 (2013) 559–591.","mla":"Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” Communications in Mathematical Physics, vol. 322, no. 2, Springer, 2013, pp. 559–91, doi:10.1007/s00220-013-1736-8.","chicago":"Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-013-1736-8.","ama":"Grech P, Seiringer R. The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. 2013;322(2):559-591. doi:10.1007/s00220-013-1736-8","apa":"Grech, P., & Seiringer, R. (2013). The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-013-1736-8","ieee":"P. Grech and R. Seiringer, “The excitation spectrum for weakly interacting Bosons in a trap,” Communications in Mathematical Physics, vol. 322, no. 2. Springer, pp. 559–591, 2013.","ista":"Grech P, Seiringer R. 2013. The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. 322(2), 559–591."},"main_file_link":[{"url":"http://arxiv.org/abs/1205.5259","open_access":"1"}],"publication":"Communications in Mathematical Physics","day":"01","month":"09","volume":322,"date_created":"2018-12-11T11:57:29Z","date_updated":"2021-01-12T06:57:18Z","author":[{"last_name":"Grech","first_name":"Philip","full_name":"Grech, Philip"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Robert Seiringer"}],"intvolume":" 322","publisher":"Springer","title":"The excitation spectrum for weakly interacting Bosons in a trap","status":"public","publication_status":"published","_id":"2408","year":"2013","extern":1,"issue":"2","publist_id":"4518","abstract":[{"text":"We investigate the low-energy excitation spectrum of a Bose gas confined in a trap, with weak long-range repulsive interactions. In particular, we prove that the spectrum can be described in terms of the eigenvalues of an effective one-particle operator, as predicted by the Bogoliubov approximation.","lang":"eng"}],"type":"journal_article"},{"publist_id":"4514","file_date_updated":"2020-07-14T12:45:40Z","year":"2013","department":[{"_id":"JoBo"}],"publisher":"BioMed Central","publication_status":"published","author":[{"full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","last_name":"Kupczok"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"volume":13,"date_updated":"2021-01-12T06:57:20Z","date_created":"2018-12-11T11:57:31Z","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"},"quality_controlled":"1","doi":"10.1186/1471-2148-13-54","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates."}],"_id":"2412","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","title":"Probabilistic models for CRISPR spacer content evolution ","ddc":["576"],"status":"public","pubrep_id":"397","file":[{"file_id":"5268","relation":"main_file","date_created":"2018-12-12T10:17:15Z","date_updated":"2020-07-14T12:45:40Z","checksum":"029c7e0b198c19312b66ecce3cabb22f","file_name":"IST-2015-397-v1+1_1471-2148-13-54.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":518729}],"oa_version":"Published Version","scopus_import":1,"has_accepted_license":"1","day":"26","citation":{"chicago":"Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-54.","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:10.1186/1471-2148-13-54.","short":"A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.","ista":"Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54.","apa":"Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54","ieee":"A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013.","ama":"Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54"},"publication":"BMC Evolutionary Biology","page":"54 - 54","date_published":"2013-02-26T00:00:00Z"},{"language":[{"iso":"eng"}],"date_published":"2013-08-01T00:00:00Z","doi":"10.1002/9783527671632.ch08","quality_controlled":"1","citation":{"mla":"Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson, Wiley-VCH, 2013, doi:10.1002/9783527671632.ch08.","short":"M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH, 2013.","chicago":"Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” In Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson. Wiley-VCH, 2013. https://doi.org/10.1002/9783527671632.ch08.","ama":"Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH; 2013. doi:10.1002/9783527671632.ch08","ista":"Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity, .","apa":"Valderrama, M., Botella Soler, V., & Le Van Quyen, M. (2013). Neuronal oscillations scale up and scale down the brain dynamics . In M. Meyer & Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH. https://doi.org/10.1002/9783527671632.ch08","ieee":"M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations scale up and scale down the brain dynamics ,” in Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, M. Meyer and Z. Pesenson, Eds. Wiley-VCH, 2013."},"publication":"Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain","publication_identifier":{"eisbn":["9783527671632"],"isbn":["9783527411986 "]},"month":"08","day":"01","scopus_import":1,"oa_version":"None","date_updated":"2021-01-12T06:57:20Z","date_created":"2018-12-11T11:57:31Z","author":[{"last_name":"Valderrama","first_name":"Mario","full_name":"Valderrama, Mario"},{"full_name":"Botella Soler, Vicente","first_name":"Vicente","last_name":"Botella Soler","id":"421234E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8790-1914"},{"last_name":"Le Van Quyen","first_name":"Michel","full_name":"Le Van Quyen, Michel"}],"editor":[{"full_name":"Meyer, Misha","last_name":"Meyer","first_name":"Misha"},{"full_name":"Pesenson, Z.","last_name":"Pesenson","first_name":"Z."}],"publisher":"Wiley-VCH","department":[{"_id":"GaTk"}],"title":"Neuronal oscillations scale up and scale down the brain dynamics ","status":"public","publication_status":"published","_id":"2413","year":"2013","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"4513","abstract":[{"lang":"eng","text":"Progress in understanding the global brain dynamics has remained slow to date in large part because of the highly multiscale nature of brain activity. Indeed, normal brain dynamics is characterized by complex interactions between multiple levels: from the microscopic scale of single neurons to the mesoscopic level of local groups of neurons, and finally to the macroscopic level of the whole brain. Among the most difficult tasks are those of identifying which scales are significant for a given particular function and describing how the scales affect each other. It is important to realize that the scales of time and space are linked together, or even intertwined, and that causal inference is far more ambiguous between than within levels. We approach this problem from the perspective of our recent work on simultaneous recording from micro- and macroelectrodes in the human brain. We propose a physiological description of these multilevel interactions, based on phase–amplitude coupling of neuronal oscillations that operate at multiple frequencies and on different spatial scales. Specifically, the amplitude of the oscillations on a particular spatial scale is modulated by phasic variations in neuronal excitability induced by lower frequency oscillations that emerge on a larger spatial scale. Following this general principle, it is possible to scale up or scale down the multiscale brain dynamics. It is expected that large-scale network oscillations in the low-frequency range, mediating downward effects, may play an important role in attention and consciousness."}],"alternative_title":["Reviews of Nonlinear Dynamics and Complexity"],"type":"book_chapter"},{"doi":"10.1128/genomeA.00216-13","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"06","author":[{"full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A"},{"last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne"},{"last_name":"Stift","first_name":"Gertraud","id":"2DB195CA-F248-11E8-B48F-1D18A9856A87","full_name":"Stift, Gertraud"},{"full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:57:30Z","date_updated":"2021-01-12T06:57:19Z","volume":1,"year":"2013","publication_status":"published","department":[{"_id":"JoBo"},{"_id":"LifeSc"}],"publisher":"American Society for Microbiology","file_date_updated":"2020-07-14T12:45:40Z","publist_id":"4516","date_published":"2013-06-13T00:00:00Z","publication":"Genome Announcements","citation":{"short":"R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).","mla":"Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements, vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13.","chicago":"Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements. American Society for Microbiology, 2013. https://doi.org/10.1128/genomeA.00216-13.","ama":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 2013;1(3). doi:10.1128/genomeA.00216-13","apa":"Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13","ieee":"R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” Genome Announcements, vol. 1, no. 3. American Society for Microbiology, 2013.","ista":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3)."},"day":"13","has_accepted_license":"1","scopus_import":1,"pubrep_id":"398","oa_version":"Published Version","file":[{"checksum":"0751ec74b695567e0cdf02aaf9c26829","date_updated":"2020-07-14T12:45:40Z","date_created":"2018-12-12T10:17:36Z","file_id":"5291","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":130026,"access_level":"open_access","file_name":"IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf"}],"_id":"2410","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"status":"public","title":"Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis","intvolume":" 1","abstract":[{"text":"Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. ","lang":"eng"}],"issue":"3","type":"journal_article"},{"abstract":[{"lang":"eng","text":"Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.\r\n"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","file":[{"checksum":"2e866932ab688f47ecd504acb4d5c7d4","date_created":"2020-05-15T11:13:01Z","date_updated":"2020-07-14T12:45:41Z","file_id":"7859","relation":"main_file","creator":"dernst","file_size":309182,"content_type":"application/pdf","access_level":"open_access","file_name":"2013_CAV_Piskac.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2447","ddc":["000"],"status":"public","title":"Automating separation logic using SMT","intvolume":" 8044","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"series_title":"Lecture Notes in Computer Science","date_published":"2013-07-01T00:00:00Z","citation":{"short":"R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.","mla":"Piskac, Ruzica, et al. Automating Separation Logic Using SMT. Vol. 8044, Springer, 2013, pp. 773–89, doi:10.1007/978-3-642-39799-8_54.","chicago":"Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_54.","ama":"Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789. doi:10.1007/978-3-642-39799-8_54","apa":"Piskac, R., Wies, T., & Zufferey, D. (2013). Automating separation logic using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_54","ieee":"R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013.","ista":"Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT. 8044, 773–789."},"page":"773 - 789","file_date_updated":"2020-07-14T12:45:41Z","publist_id":"4456","author":[{"full_name":"Piskac, Ruzica","last_name":"Piskac","first_name":"Ruzica"},{"full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies","first_name":"Thomas"},{"full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","first_name":"Damien"}],"date_updated":"2020-08-11T10:09:47Z","date_created":"2018-12-11T11:57:43Z","volume":8044,"year":"2013","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"month":"07","conference":{"name":"CAV: Computer Aided Verification","end_date":"2013-07-19","location":"St. Petersburg, Russia","start_date":"2013-07-13"},"doi":"10.1007/978-3-642-39799-8_54","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1"},{"_id":"2443","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","status":"public","intvolume":" 200","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery."}],"issue":"4","publication":"New Phytologist","citation":{"ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 2013;200(4):1034-1048. doi:10.1111/nph.12437","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","ieee":"S. Simon et al., “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” New Phytologist, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. Wiley. https://doi.org/10.1111/nph.12437","mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:10.1111/nph.12437.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist. Wiley, 2013. https://doi.org/10.1111/nph.12437."},"article_type":"original","page":"1034 - 1048","date_published":"2013-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","year":"2013","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Wiley","author":[{"last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu"},{"full_name":"Kubeš, Martin","first_name":"Martin","last_name":"Kubeš"},{"full_name":"Baster, Pawel","last_name":"Baster","first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"full_name":"Dobrev, Petre","last_name":"Dobrev","first_name":"Petre"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"}],"date_updated":"2022-06-07T08:57:52Z","date_created":"2018-12-11T11:57:41Z","volume":200,"ec_funded":1,"publist_id":"4460","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.12437"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"doi":"10.1111/nph.12437","language":[{"iso":"eng"}],"month":"12"},{"day":"01","series_title":"Lecture Notes in Computer Science","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","page":"559 - 575","citation":{"ama":"Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:10.1007/978-3-642-39799-8_37","ista":"Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575.","apa":"Chatterjee, K., Gaiser, A., & Kretinsky, J. (2013). Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_37","ieee":"K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer, pp. 559–575, 2013.","mla":"Chatterjee, Krishnendu, et al. Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis. Vol. 8044, Springer, 2013, pp. 559–75, doi:10.1007/978-3-642-39799-8_37.","short":"K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.","chicago":"Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_37."},"abstract":[{"text":"The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 8044","status":"public","title":"Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis","_id":"2446","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-39799-8_37","conference":{"name":"CAV: Computer Aided Verification","start_date":"2013-07-13","location":"St. Petersburg, Russia","end_date":"2013-07-19"},"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1304.5281","open_access":"1"}],"external_id":{"arxiv":["1304.5281"]},"ec_funded":1,"publist_id":"4457","volume":8044,"date_updated":"2020-08-11T10:09:47Z","date_created":"2018-12-11T11:57:42Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Gaiser, Andreas","first_name":"Andreas","last_name":"Gaiser"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2013"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-39799-8_36","conference":{"name":"CAV: Computer Aided Verification","end_date":"2013-07-19","start_date":"2013-07-13","location":"St. Petersburg, Russia"},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1304.0084","open_access":"1"}],"external_id":{"arxiv":["1304.0084"]},"month":"07","volume":8044,"date_created":"2018-12-11T11:57:42Z","date_updated":"2020-08-11T10:09:47Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Jakub","last_name":"Ła̧Cki","full_name":"Ła̧Cki, Jakub"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","year":"2013","publist_id":"4459","ec_funded":1,"date_published":"2013-07-01T00:00:00Z","page":"543 - 558","citation":{"ama":"Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:10.1007/978-3-642-39799-8_36","ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558.","apa":"Chatterjee, K., & Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_36","ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.","mla":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. Faster Algorithms for Markov Decision Processes with Low Treewidth. Vol. 8044, Springer, 2013, pp. 543–58, doi:10.1007/978-3-642-39799-8_36.","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.","chicago":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_36."},"day":"01","series_title":"Lecture Notes in Computer Science","scopus_import":1,"oa_version":"Preprint","intvolume":" 8044","status":"public","title":"Faster algorithms for Markov decision processes with low treewidth","_id":"2444","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time."}],"alternative_title":["LNCS"],"type":"conference"},{"day":"01","month":"11","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2013-11-01T00:00:00Z","doi":"10.1093/mp/sst044","page":"1849 - 1862","quality_controlled":"1","citation":{"apa":"Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene, J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. Cell Press. https://doi.org/10.1093/mp/sst044","ieee":"T. Nodzyński et al., “Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis,” Molecular Plant, vol. 6, no. 6. Cell Press, pp. 1849–1862, 2013.","ista":"Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862.","ama":"Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 2013;6(6):1849-1862. doi:10.1093/mp/sst044","chicago":"Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” Molecular Plant. Cell Press, 2013. https://doi.org/10.1093/mp/sst044.","short":"T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene, G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862.","mla":"Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” Molecular Plant, vol. 6, no. 6, Cell Press, 2013, pp. 1849–62, doi:10.1093/mp/sst044."},"publication":"Molecular Plant","issue":"6","publist_id":"4454","abstract":[{"text":"Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. ","lang":"eng"}],"type":"journal_article","volume":6,"oa_version":"None","date_created":"2018-12-11T11:57:44Z","date_updated":"2021-01-12T06:57:33Z","author":[{"last_name":"Nodzyński","first_name":"Tomasz","full_name":"Nodzyński, Tomasz"},{"first_name":"Murguel","last_name":"Feraru","full_name":"Feraru, Murguel"},{"last_name":"Hirsch","first_name":"Sibylle","full_name":"Hirsch, Sibylle"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"full_name":"Nicuales, Claudiu","first_name":"Claudiu","last_name":"Nicuales"},{"full_name":"Van Leene, Jelle","last_name":"Van Leene","first_name":"Jelle"},{"full_name":"De Jaeger, Geert","last_name":"De Jaeger","first_name":"Geert"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"department":[{"_id":"JiFr"}],"intvolume":" 6","publisher":"Cell Press","title":"Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2449","year":"2013"},{"doi":"10.1186/1471-2229-13-20","date_published":"2013-02-01T00:00:00Z","citation":{"short":"E. Barbez, M. Laňková, M. Pařezová, A. Maizel, E. Zažímalová, J. Petrášek, J. Friml, J. Kleine Vehn, BMC Plant Biology 13 (2013).","mla":"Barbez, Elke, et al. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology, vol. 13, no. 1, BioMed Central, 2013, doi:10.1186/1471-2229-13-20.","chicago":"Barbez, Elke, Martina Laňková, Markéta Pařezová, Alexis Maizel, Eva Zažímalová, Jan Petrášek, Jiří Friml, and Jürgen Kleine Vehn. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2229-13-20.","ama":"Barbez E, Laňková M, Pařezová M, et al. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 2013;13(1). doi:10.1186/1471-2229-13-20","ieee":"E. Barbez et al., “Single-cell-based system to monitor carrier driven cellular auxin homeostasis,” BMC Plant Biology, vol. 13, no. 1. BioMed Central, 2013.","apa":"Barbez, E., Laňková, M., Pařezová, M., Maizel, A., Zažímalová, E., Petrášek, J., … Kleine Vehn, J. (2013). Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-13-20","ista":"Barbez E, Laňková M, Pařezová M, Maizel A, Zažímalová E, Petrášek J, Friml J, Kleine Vehn J. 2013. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 13(1)."},"publication":"BMC Plant Biology","quality_controlled":0,"month":"02","day":"01","author":[{"first_name":"Elke","last_name":"Barbez","full_name":"Barbez, Elke"},{"full_name":"Laňková, Martina","first_name":"Martina","last_name":"Laňková"},{"first_name":"Markéta","last_name":"Pařezová","full_name":"Pařezová, Markéta"},{"full_name":"Maizel, Alexis","last_name":"Maizel","first_name":"Alexis"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"}],"volume":13,"date_created":"2018-12-11T11:57:45Z","date_updated":"2021-01-12T06:57:34Z","year":"2013","_id":"2452","publisher":"BioMed Central","intvolume":" 13","title":"Single-cell-based system to monitor carrier driven cellular auxin homeostasis","status":"public","publication_status":"published","issue":"1","publist_id":"4451","abstract":[{"text":"Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.","lang":"eng"}],"extern":1,"type":"journal_article"},{"author":[{"full_name":"Liu, Junli","last_name":"Liu","first_name":"Junli"},{"full_name":"Menhi, Saher","first_name":"Saher","last_name":"Menhi"},{"first_name":"Jennifer","last_name":"Topping","full_name":"Topping, Jennifer"},{"full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lindsey","first_name":"Keith","full_name":"Lindsey, Keith"}],"date_updated":"2021-01-12T06:57:34Z","date_created":"2018-12-11T11:57:44Z","volume":4,"_id":"2450","year":"2013","publication_status":"published","title":"Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development","status":"public","publisher":"Frontiers Research Foundation","intvolume":" 4","abstract":[{"lang":"eng","text":"Understanding how hormones and genes interact to coordinate plant growth is a major challenge in developmental biology. The activities of auxin, ethylene, and cytokinin depend on cellular context and exhibit either synergistic or antagonistic interactions. Here we use experimentation and network construction to elucidate the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants such as polaris (pls), we show experimentally that expression of both PIN1 and PIN2 significantly increases. This relationship is analyzed in the context of the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin, ethylene and cytokinin concentration decreases, approximately remains unchanged and increases, respectively. Experimental data are integrated into a hormonal crosstalk network through combination with information in literature. Network construction reveals that the regulation of both PIN1 and PIN2 is predominantly via ethylene signaling. In addition, it is deduced that the relationship between cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition to its regulation to auxin, ethylene, and PLS levels. We discuss how the network of hormones and genes coordinates plant growth by simultaneously regulating the activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk, root development, auxin flux, PIN proteins, PLS protein, signaling network"}],"publist_id":"4453","issue":"75","extern":1,"type":"journal_article","date_published":"2013-04-01T00:00:00Z","doi":"10.3389/fpls.2013.00075","publication":"Frontiers in Plant Science","citation":{"ista":"Liu J, Menhi S, Topping J, Friml J, Lindsey K. 2013. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 4(75).","apa":"Liu, J., Menhi, S., Topping, J., Friml, J., & Lindsey, K. (2013). Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00075","ieee":"J. Liu, S. Menhi, J. Topping, J. Friml, and K. Lindsey, “Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development,” Frontiers in Plant Science, vol. 4, no. 75. Frontiers Research Foundation, 2013.","ama":"Liu J, Menhi S, Topping J, Friml J, Lindsey K. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 2013;4(75). doi:10.3389/fpls.2013.00075","chicago":"Liu, Junli, Saher Menhi, Jennifer Topping, Jiří Friml, and Keith Lindsey. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00075.","mla":"Liu, Junli, et al. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” Frontiers in Plant Science, vol. 4, no. 75, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00075.","short":"J. Liu, S. Menhi, J. Topping, J. Friml, K. Lindsey, Frontiers in Plant Science 4 (2013)."},"quality_controlled":0,"day":"01","month":"04"},{"doi":"10.1515/crelle.2012.039","date_published":"2013-07-01T00:00:00Z","publication":"Journal fur die Reine und Angewandte Mathematik","oa":1,"citation":{"chicago":"Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, 2013. https://doi.org/10.1515/crelle.2012.039.","short":"S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik (2013) 69–151.","mla":"Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:10.1515/crelle.2012.039.","apa":"Baier, S., & Browning, T. D. (2013). Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle.2012.039","ieee":"S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational points on del Pezzo surfaces,” Journal fur die Reine und Angewandte Mathematik, no. 680. Walter de Gruyter, pp. 69–151, 2013.","ista":"Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680), 69–151.","ama":"Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2013;(680):69-151. doi:10.1515/crelle.2012.039"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1011.3434"}],"quality_controlled":0,"page":"69 - 151","day":"01","month":"07","author":[{"full_name":"Baier, Stephan","first_name":"Stephan","last_name":"Baier"},{"full_name":"Timothy Browning","first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177"}],"date_updated":"2021-01-12T06:57:33Z","date_created":"2018-12-11T11:45:24Z","_id":"245","year":"2013","status":"public","publication_status":"published","title":"Inhomogeneous cubic congruences and rational points on del Pezzo surfaces","publisher":"Walter de Gruyter","abstract":[{"lang":"eng","text":"For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ."}],"publist_id":"7659","issue":"680","extern":1,"type":"journal_article"},{"issue":"1","publist_id":"4446","extern":"1","type":"journal_article","author":[{"last_name":"Viaene","first_name":"Tom","full_name":"Viaene, Tom"},{"full_name":"Delwiche, Charles","first_name":"Charles","last_name":"Delwiche"},{"last_name":"Rensing","first_name":"Stefan","full_name":"Rensing, Stefan"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"date_created":"2018-12-11T11:57:46Z","date_updated":"2021-01-12T06:57:36Z","volume":18,"oa_version":"None","_id":"2457","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2013","title":"Origin and evolution of PIN auxin transporters in the green lineage","status":"public","publication_status":"published","intvolume":" 18","publisher":"Cell Press","month":"01","day":"01","date_published":"2013-01-01T00:00:00Z","doi":"10.1016/j.tplants.2012.08.009","language":[{"iso":"eng"}],"publication":"Trends in Plant Science","citation":{"short":"T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18 (2013) 5–10.","mla":"Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science, vol. 18, no. 1, Cell Press, 2013, pp. 5–10, doi:10.1016/j.tplants.2012.08.009.","chicago":"Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science. Cell Press, 2013. https://doi.org/10.1016/j.tplants.2012.08.009.","ama":"Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 2013;18(1):5-10. doi:10.1016/j.tplants.2012.08.009","ieee":"T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of PIN auxin transporters in the green lineage,” Trends in Plant Science, vol. 18, no. 1. Cell Press, pp. 5–10, 2013.","apa":"Viaene, T., Delwiche, C., Rensing, S., & Friml, J. (2013). Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2012.08.009","ista":"Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10."},"quality_controlled":"1","page":"5 - 10"},{"day":"01","month":"09","date_published":"2013-09-01T00:00:00Z","doi":"10.1112/S0010437X13007185","publication":"Compositio Mathematica","citation":{"short":"T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494.","mla":"Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica, vol. 149, no. 9, Cambridge University Press, 2013, pp. 1457–94, doi:10.1112/S0010437X13007185.","chicago":"Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica. Cambridge University Press, 2013. https://doi.org/10.1112/S0010437X13007185.","ama":"Browning TD, Munshi R. Rational points on singular intersections of quadrics. Compositio Mathematica. 2013;149(9):1457-1494. doi:10.1112/S0010437X13007185","apa":"Browning, T. D., & Munshi, R. (2013). Rational points on singular intersections of quadrics. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X13007185","ieee":"T. D. Browning and R. Munshi, “Rational points on singular intersections of quadrics,” Compositio Mathematica, vol. 149, no. 9. Cambridge University Press, pp. 1457–1494, 2013.","ista":"Browning TD, Munshi R. 2013. Rational points on singular intersections of quadrics. Compositio Mathematica. 149(9), 1457–1494."},"quality_controlled":0,"page":"1457 - 1494","abstract":[{"lang":"eng","text":"Given an intersection of two quadrics X Pm1, with m > 9, the quantitative arithmetic of the set X(Q) is investigated under the assumption that the singular locus of X consists of a pair of conjugate singular points defined over Q(i)."}],"issue":"9","publist_id":"7658","extern":1,"type":"journal_article","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Timothy Browning"},{"full_name":"Munshi, Ritabrata","last_name":"Munshi","first_name":"Ritabrata"}],"date_updated":"2021-01-12T06:57:37Z","date_created":"2018-12-11T11:45:25Z","volume":149,"_id":"246","acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","year":"2013","publication_status":"published","title":"Rational points on singular intersections of quadrics","status":"public","publisher":"Cambridge University Press","intvolume":" 149"},{"month":"07","doi":"10.1371/journal.pone.0070013","language":[{"iso":"eng"}],"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,"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:41Z","publist_id":"4430","article_number":"e70013","author":[{"last_name":"Sanchez Romero","first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada"},{"full_name":"Ariza, Antonio","first_name":"Antonio","last_name":"Ariza"},{"full_name":"Wilson, Keith","last_name":"Wilson","first_name":"Keith"},{"last_name":"Skjøt","first_name":"Michael","full_name":"Skjøt, Michael"},{"first_name":"Jesper","last_name":"Vind","full_name":"Vind, Jesper"},{"full_name":"De Maria, Leonardo","last_name":"De Maria","first_name":"Leonardo"},{"last_name":"Skov","first_name":"Lars","full_name":"Skov, Lars"},{"full_name":"Sánchez Ruiz, Jose","first_name":"Jose","last_name":"Sánchez Ruiz"}],"date_created":"2018-12-11T11:57:51Z","date_updated":"2021-01-12T06:57:41Z","volume":8,"year":"2013","publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Public Library of Science","day":"30","has_accepted_license":"1","scopus_import":1,"date_published":"2013-07-30T00:00:00Z","publication":"PLoS One","citation":{"ieee":"I. Sanchez-Romero et al., “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013.","apa":"Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070013","ista":"Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013.","ama":"Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070013","chicago":"Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070013.","short":"I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013).","mla":"Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:10.1371/journal.pone.0070013."},"abstract":[{"text":"The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation.","lang":"eng"}],"issue":"7","type":"journal_article","pubrep_id":"414","oa_version":"Published Version","file":[{"file_id":"5124","relation":"main_file","checksum":"c0c96cc76ed7ef0d036a31a7e33c9a37","date_updated":"2020-07-14T12:45:41Z","date_created":"2018-12-12T10:15:07Z","access_level":"open_access","file_name":"IST-2016-414-v1+1_journal.pone.0070013.pdf","creator":"system","content_type":"application/pdf","file_size":1323666}],"_id":"2471","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mechanism of protein kinetic stabilization by engineered disulfide crosslinks","status":"public","ddc":["570"],"intvolume":" 8"},{"intvolume":" 8","ddc":["580","570"],"status":"public","title":"Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development","_id":"2472","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":9003465,"creator":"system","file_name":"IST-2015-393-v1+1_journal.pone.0070069.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:34Z","date_updated":"2020-07-14T12:45:41Z","checksum":"3be71828b6c2ba9c90eb7056e3f7f57a","relation":"main_file","file_id":"5222"}],"oa_version":"Published Version","pubrep_id":"393","type":"journal_article","issue":"7","abstract":[{"text":"Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development.","lang":"eng"}],"citation":{"short":"C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar, G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml, B. Pogson, PLoS One 8 (2013).","mla":"Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One, vol. 8, no. 7, e70069, Public Library of Science, 2013, doi:10.1371/journal.pone.0070069.","chicago":"Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070069.","ama":"Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070069","ieee":"C. Cazzonelli et al., “Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013.","apa":"Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar, N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070069","ista":"Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 8(7), e70069."},"publication":"PLoS One","date_published":"2013-07-29T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"29","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"Public Library of Science","publication_status":"published","year":"2013","volume":8,"date_created":"2018-12-11T11:57:52Z","date_updated":"2021-01-12T06:57:41Z","author":[{"full_name":"Cazzonelli, Christopher","last_name":"Cazzonelli","first_name":"Christopher"},{"full_name":"Vanstraelen, Marleen","first_name":"Marleen","last_name":"Vanstraelen"},{"full_name":"Simon, Sibu","first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741"},{"full_name":"Yin, Kuide","first_name":"Kuide","last_name":"Yin"},{"last_name":"Carron Arthur","first_name":"Ashley","full_name":"Carron Arthur, Ashley"},{"full_name":"Nisar, Nazia","first_name":"Nazia","last_name":"Nisar"},{"full_name":"Tarle, Gauri","last_name":"Tarle","first_name":"Gauri"},{"full_name":"Cuttriss, Abby","last_name":"Cuttriss","first_name":"Abby"},{"full_name":"Searle, Iain","first_name":"Iain","last_name":"Searle"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"first_name":"Ulrike","last_name":"Mathesius","full_name":"Mathesius, Ulrike"},{"last_name":"Masle","first_name":"Josette","full_name":"Masle, Josette"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"},{"full_name":"Pogson, Barry","last_name":"Pogson","first_name":"Barry"}],"article_number":"e70069","publist_id":"4431","ec_funded":1,"file_date_updated":"2020-07-14T12:45:41Z","project":[{"grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"},{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"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.0070069","month":"07"},{"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.0070050","month":"07","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Public Library of Science","year":"2013","date_updated":"2021-01-12T06:57:40Z","date_created":"2018-12-11T11:57:51Z","volume":8,"author":[{"full_name":"Čovanová, Milada","last_name":"Čovanová","first_name":"Milada"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"full_name":"Rychtář, Jan","first_name":"Jan","last_name":"Rychtář"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"}],"article_number":"e70050","file_date_updated":"2020-07-14T12:45:41Z","publist_id":"4432","publication":"PLoS One","citation":{"chicago":"Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070050.","mla":"Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One, vol. 8, no. 7, e70050, Public Library of Science, 2013, doi:10.1371/journal.pone.0070050.","short":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013).","ista":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 8(7), e70050.","ieee":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová, “Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013.","apa":"Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., & Zažímalová, E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070050","ama":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070050"},"date_published":"2013-07-23T00:00:00Z","scopus_import":1,"day":"23","has_accepted_license":"1","ddc":["570"],"title":"Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells","status":"public","intvolume":" 8","_id":"2470","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":2294955,"access_level":"open_access","file_name":"IST-2016-413-v1+1_journal.pone.0070050.pdf","checksum":"2d47ef47616ef4de1d517d146548184e","date_updated":"2020-07-14T12:45:41Z","date_created":"2018-12-12T10:08:21Z","file_id":"4681","relation":"main_file"}],"pubrep_id":"413","type":"journal_article","abstract":[{"lang":"eng","text":"Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients."}],"issue":"7"},{"publist_id":"4436","file_date_updated":"2020-07-14T12:45:41Z","article_number":"103","author":[{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"volume":32,"date_created":"2018-12-11T11:57:50Z","date_updated":"2023-02-23T10:44:14Z","year":"2013","department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","month":"07","doi":"10.1145/2461912.2461982","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","issue":"4","abstract":[{"lang":"eng","text":"We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation."}],"type":"journal_article","pubrep_id":"605","file":[{"file_id":"5279","relation":"main_file","date_updated":"2020-07-14T12:45:41Z","date_created":"2018-12-12T10:17:25Z","checksum":"aeea6b0ff2b27c695aeb8408c7d2fc50","file_name":"IST-2016-605-v1+1_tetflip_fixed.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":8601561}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2466","intvolume":" 32","ddc":["000"],"title":"Highly adaptive liquid simulations on tetrahedral meshes","status":"public","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","citation":{"chicago":"Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461982.","short":"R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics, vol. 32, no. 4, 103, ACM, 2013, doi:10.1145/2461912.2461982.","ieee":"R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on tetrahedral meshes,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.","apa":"Ando, R., Thuerey, N., & Wojtan, C. (2013). Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461982","ista":"Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 32(4), 103.","ama":"Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461982"},"publication":"ACM Transactions on Graphics"},{"publist_id":"4435","file_date_updated":"2020-07-14T12:45:41Z","article_number":"34","author":[{"full_name":"Bernstein, Gilbert","last_name":"Bernstein","first_name":"Gilbert"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"volume":32,"date_updated":"2023-02-23T10:44:16Z","date_created":"2018-12-11T11:57:50Z","year":"2013","department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","month":"07","doi":"10.1145/2461912.2462027","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","issue":"4","abstract":[{"text":"This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors.","lang":"eng"}],"type":"journal_article","pubrep_id":"604","file":[{"relation":"main_file","file_id":"4768","checksum":"9c8425d62246996ca632c5a01870515b","date_created":"2018-12-12T10:09:43Z","date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","file_name":"IST-2016-604-v1+1_toptop2013.pdf","content_type":"application/pdf","file_size":3514674,"creator":"system"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2467","intvolume":" 32","title":"Putting holes in holey geometry: Topology change for arbitrary surfaces","status":"public","ddc":["000"],"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","citation":{"short":"G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics, vol. 32, no. 4, 34, ACM, 2013, doi:10.1145/2461912.2462027.","chicago":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2462027.","ama":"Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2462027","ieee":"G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change for arbitrary surfaces,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.","apa":"Bernstein, G., & Wojtan, C. (2013). Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2462027","ista":"Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34."},"publication":"ACM Transactions on Graphics"},{"article_number":"68","file_date_updated":"2020-07-14T12:45:41Z","publist_id":"4434","year":"2013","publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"author":[{"full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","last_name":"Bojsen-Hansen","first_name":"Morten"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"date_updated":"2023-02-23T10:44:18Z","date_created":"2018-12-11T11:57:50Z","volume":32,"month":"07","oa":1,"quality_controlled":"1","doi":"10.1145/2461912.2461991","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers.","lang":"eng"}],"issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2468","status":"public","title":"Liquid surface tracking with error compensation","ddc":["000"],"intvolume":" 32","pubrep_id":"603","file":[{"checksum":"53d905e0180e23ef3e813b969ffed4e1","date_created":"2018-12-12T10:09:37Z","date_updated":"2020-07-14T12:45:41Z","file_id":"4761","relation":"main_file","creator":"system","file_size":5813685,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-603-v1+1_liquidError_web.pdf"}],"oa_version":"Submitted Version","scopus_import":1,"day":"01","has_accepted_license":"1","publication":"ACM Transactions on Graphics","citation":{"chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461991.","short":"M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” ACM Transactions on Graphics, vol. 32, no. 4, 68, ACM, 2013, doi:10.1145/2461912.2461991.","apa":"Bojsen-Hansen, M., & Wojtan, C. (2013). Liquid surface tracking with error compensation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461991","ieee":"M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.","ista":"Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68.","ama":"Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461991"},"date_published":"2013-07-01T00:00:00Z"},{"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":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"volume":23,"date_updated":"2021-01-12T06:57:40Z","date_created":"2018-12-11T11:57:51Z","pmid":1,"year":"2013","department":[{"_id":"CaHe"}],"publisher":"Cell Press","publication_status":"published","publist_id":"4433","file_date_updated":"2020-07-14T12:45:41Z","doi":"10.1016/j.cub.2013.06.019","language":[{"iso":"eng"}],"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"},"external_id":{"pmid":["23885883"]},"quality_controlled":"1","month":"07","oa_version":"Published Version","file":[{"creator":"dernst","file_size":247320,"content_type":"application/pdf","access_level":"open_access","file_name":"2013_CurrentBiology_Maitre.pdf","checksum":"6a424b2f007b41d4955a9135793b2162","date_created":"2019-01-24T15:40:22Z","date_updated":"2020-07-14T12:45:41Z","file_id":"5881","relation":"main_file"}],"_id":"2469","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 23","ddc":["570"],"status":"public","title":"Three functions of cadherins in cell adhesion","issue":"14","abstract":[{"text":"Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals. By regulating contact formation and stability, cadherins play a crucial role in tissue morphogenesis and homeostasis. Here, we review the three major unctions of cadherins in cell–cell contact formation and stability. Two of those functions lead to a decrease in interfacial ension at the forming cell–cell contact, thereby promoting contact expansion — first, by providing adhesion tension that lowers interfacial tension at the cell–cell contact, and second, by signaling to the actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial tension at the contact. The third function of cadherins in cell–cell contact formation is to stabilize the contact by resisting mechanical forces that pull on the contact.","lang":"eng"}],"type":"journal_article","date_published":"2013-07-22T00:00:00Z","citation":{"ama":"Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion. Current Biology. 2013;23(14):R626-R633. doi:10.1016/j.cub.2013.06.019","apa":"Maître, J.-L., & Heisenberg, C.-P. J. (2013). Three functions of cadherins in cell adhesion. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.06.019","ieee":"J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell adhesion,” Current Biology, vol. 23, no. 14. Cell Press, pp. R626–R633, 2013.","ista":"Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion. Current Biology. 23(14), R626–R633.","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.","mla":"Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” Current Biology, vol. 23, no. 14, Cell Press, 2013, pp. R626–33, doi:10.1016/j.cub.2013.06.019.","chicago":"Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.06.019."},"publication":"Current Biology","page":"R626 - R633","has_accepted_license":"1","day":"22","scopus_import":1},{"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Timothy Browning"}],"volume":56,"date_created":"2018-12-11T11:45:25Z","date_updated":"2021-01-12T06:57:40Z","year":"2013","_id":"247","acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","intvolume":" 56","publisher":"Unknown","publication_status":"published","title":"The Lang-Weil estimate for cubic hypersurfaces","status":"public","issue":"3","publist_id":"7657","abstract":[{"text":"An improved estimate is provided for the number of Fq-rational points on a geometrically irreducible, projective, cubic hypersurface that is not equal to a cone.","lang":"eng"}],"extern":1,"type":"journal_article","doi":"10.4153/CMB-2011-177-4","date_published":"2013-08-31T00:00:00Z","citation":{"ieee":"T. D. Browning, “The Lang-Weil estimate for cubic hypersurfaces,” Canadian Mathematical Bulletin, vol. 56, no. 3. Unknown, pp. 500–502, 2013.","apa":"Browning, T. D. (2013). The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. Unknown. https://doi.org/10.4153/CMB-2011-177-4","ista":"Browning TD. 2013. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. 56(3), 500–502.","ama":"Browning TD. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. 2013;56(3):500-502. doi:10.4153/CMB-2011-177-4","chicago":"Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” Canadian Mathematical Bulletin. Unknown, 2013. https://doi.org/10.4153/CMB-2011-177-4.","short":"T.D. Browning, Canadian Mathematical Bulletin 56 (2013) 500–502.","mla":"Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” Canadian Mathematical Bulletin, vol. 56, no. 3, Unknown, 2013, pp. 500–02, doi:10.4153/CMB-2011-177-4."},"publication":"Canadian Mathematical Bulletin","page":"500 - 502","quality_controlled":0,"day":"31","month":"08"},{"oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5376","checksum":"4274ec1f433b838a7d5b941cc9684ca7","date_created":"2018-12-12T10:18:54Z","date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","file_size":1706282,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"118","intvolume":" 87","title":"Genetic hitch-hiking in spatially extended populations","ddc":["570"],"status":"public","_id":"2473","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"8","abstract":[{"lang":"eng","text":"When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift, . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis."}],"type":"journal_article","date_published":"2013-01-03T00:00:00Z","page":"75 - 89","citation":{"short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","mla":"Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population Biology, vol. 87, no. 8, Elsevier, 2013, pp. 75–89, doi:10.1016/j.tpb.2012.12.001.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Genetic Hitch-Hiking in Spatially Extended Populations.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2012.12.001.","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 2013;87(8):75-89. doi:10.1016/j.tpb.2012.12.001","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking in spatially extended populations,” Theoretical Population Biology, vol. 87, no. 8. Elsevier, pp. 75–89, 2013.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2012.12.001","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89."},"publication":"Theoretical Population Biology","has_accepted_license":"1","day":"03","scopus_import":1,"volume":87,"date_updated":"2021-01-12T06:57:42Z","date_created":"2018-12-11T11:57:52Z","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"}],"publisher":"Elsevier","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2013","ec_funded":1,"publist_id":"4428","file_date_updated":"2020-07-14T12:45:41Z","language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2012.12.001","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"quality_controlled":"1","oa":1,"month":"01"},{"type":"journal_article","abstract":[{"text":"Despite the pivotal functions of the NMDA receptor (NMDAR) for neural circuit development and synaptic plasticity, the molecular mechanisms underlying the dynamics of NMDAR trafficking are poorly understood. The cell adhesion molecule neuroligin-1 (NL1) modifies NMDAR-dependent synaptic transmission and synaptic plasticity, but it is unclear whether NL1 controls synaptic accumulation or function of the receptors. Here, we provide evidence that NL1 regulates the abundance of NMDARs at postsynaptic sites. This function relies on extracellular, NL1 isoform-specific sequences that facilitate biochemical interactions between NL1 and the NMDAR GluN1 subunit. Our work uncovers NL1 isoform-specific cisinteractions with ionotropic glutamate receptors as a key mechanism for controlling synaptic properties.","lang":"eng"}],"issue":"2","publist_id":"4423","extern":1,"_id":"2478","year":"2013","title":"Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling","status":"public","publication_status":"published","publisher":"National Academy of Sciences","intvolume":" 110","author":[{"last_name":"Budreck","first_name":"Elaine","full_name":"Budreck, Elaine C"},{"full_name":"Kwon, Oh-Bin","first_name":"Oh","last_name":"Kwon"},{"first_name":"Jung","last_name":"Jung","full_name":"Jung, Jung-Hoon"},{"full_name":"Baudouin, Stéphane J","last_name":"Baudouin","first_name":"Stéphane"},{"first_name":"Albert","last_name":"Thommen","full_name":"Thommen, Albert"},{"last_name":"Kim","first_name":"Hye","full_name":"Kim, Hye-Sun"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","first_name":"Harumi","full_name":"Harumi Harada"},{"first_name":"Katsuhiko","last_name":"Tabuchi","full_name":"Tabuchi, Katsuhiko"},{"full_name":"Ryuichi Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"full_name":"Scheiffele, Peter","last_name":"Scheiffele","first_name":"Peter"},{"last_name":"Kim","first_name":"Joung","full_name":"Kim, Joung-Hun"}],"date_created":"2018-12-11T11:57:54Z","date_updated":"2021-01-12T06:57:43Z","volume":110,"day":"08","month":"01","publication":"PNAS","citation":{"chicago":"Budreck, Elaine, Oh Kwon, Jung Jung, Stéphane Baudouin, Albert Thommen, Hye Kim, Yugo Fukazawa, et al. “Neuroligin-1 Controls Synaptic Abundance of NMDA-Type Glutamate Receptors through Extracellular Coupling.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1214718110.","short":"E. Budreck, O. Kwon, J. Jung, S. Baudouin, A. Thommen, H. Kim, Y. Fukazawa, H. Harada, K. Tabuchi, R. Shigemoto, P. Scheiffele, J. Kim, PNAS 110 (2013) 725–730.","mla":"Budreck, Elaine, et al. “Neuroligin-1 Controls Synaptic Abundance of NMDA-Type Glutamate Receptors through Extracellular Coupling.” PNAS, vol. 110, no. 2, National Academy of Sciences, 2013, pp. 725–30, doi:10.1073/pnas.1214718110.","ieee":"E. Budreck et al., “Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling,” PNAS, vol. 110, no. 2. National Academy of Sciences, pp. 725–730, 2013.","apa":"Budreck, E., Kwon, O., Jung, J., Baudouin, S., Thommen, A., Kim, H., … Kim, J. (2013). Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1214718110","ista":"Budreck E, Kwon O, Jung J, Baudouin S, Thommen A, Kim H, Fukazawa Y, Harada H, Tabuchi K, Shigemoto R, Scheiffele P, Kim J. 2013. Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling. PNAS. 110(2), 725–730.","ama":"Budreck E, Kwon O, Jung J, et al. Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling. PNAS. 2013;110(2):725-730. doi:10.1073/pnas.1214718110"},"quality_controlled":0,"page":"725 - 730","doi":"10.1073/pnas.1214718110","date_published":"2013-01-08T00:00:00Z"},{"doi":"10.1112/plms/pdt060","date_published":"2013-11-29T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1210.4010"}],"oa":1,"citation":{"ista":"De La Bretèche R, Browning TD. 2013. Density of Châtelet surfaces failing the Hasse principle. Proceedings of the London Mathematical Society. 108(4), 1030–1078.","ieee":"R. De La Bretèche and T. D. Browning, “Density of Châtelet surfaces failing the Hasse principle,” Proceedings of the London Mathematical Society, vol. 108, no. 4. Oxford University Press, pp. 1030–1078, 2013.","apa":"De La Bretèche, R., & Browning, T. D. (2013). Density of Châtelet surfaces failing the Hasse principle. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms/pdt060","ama":"De La Bretèche R, Browning TD. Density of Châtelet surfaces failing the Hasse principle. Proceedings of the London Mathematical Society. 2013;108(4):1030-1078. doi:10.1112/plms/pdt060","chicago":"De La Bretèche, Régis, and Timothy D Browning. “Density of Châtelet Surfaces Failing the Hasse Principle.” Proceedings of the London Mathematical Society. Oxford University Press, 2013. https://doi.org/10.1112/plms/pdt060.","mla":"De La Bretèche, Régis, and Timothy D. Browning. “Density of Châtelet Surfaces Failing the Hasse Principle.” Proceedings of the London Mathematical Society, vol. 108, no. 4, Oxford University Press, 2013, pp. 1030–78, doi:10.1112/plms/pdt060.","short":"R. De La Bretèche, T.D. Browning, Proceedings of the London Mathematical Society 108 (2013) 1030–1078."},"publication":"Proceedings of the London Mathematical Society","page":"1030 - 1078","quality_controlled":0,"day":"29","month":"11","author":[{"last_name":"De La Bretèche","first_name":"Régis","full_name":"de la Bretèche, Régis"},{"first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Timothy Browning"}],"volume":108,"date_updated":"2021-01-12T06:57:51Z","date_created":"2018-12-11T11:45:26Z","_id":"250","year":"2013","acknowledgement":"While working on this paper, the first author was supported by an IUF Junior and ANR while the second author was supported by ERC grant 306457.","publisher":"Oxford University Press","intvolume":" 108","status":"public","title":"Density of Châtelet surfaces failing the Hasse principle","publication_status":"published","issue":"4","publist_id":"7652","abstract":[{"text":"Châtelet surfaces provide a rich source of geometrically rational surfaces that do not always satisfy the Hasse principle. Restricting attention to a special class of Châtelet surfaces, we investigate the frequency that such counter-examples arise over the rational numbers.","lang":"eng"}],"extern":1,"type":"journal_article"},{"citation":{"ieee":"R. De La Bretèche and T. D. Browning, “Counter examples to the Hasse principle among certain coflasque tori,” Journal de Theorie des Nombres de Bordeaux, vol. 26, no. 1. Universite de Bordeaux I, pp. 25–44, 2013.","apa":"De La Bretèche, R., & Browning, T. D. (2013). Counter examples to the Hasse principle among certain coflasque tori. Journal de Theorie Des Nombres de Bordeaux. Universite de Bordeaux I. https://doi.org/10.5802/jtnb.857","ista":"De La Bretèche R, Browning TD. 2013. Counter examples to the Hasse principle among certain coflasque tori. Journal de Theorie des Nombres de Bordeaux. 26(1), 25–44.","ama":"De La Bretèche R, Browning TD. Counter examples to the Hasse principle among certain coflasque tori. Journal de Theorie des Nombres de Bordeaux. 2013;26(1):25-44. doi:10.5802/jtnb.857","chicago":"De La Bretèche, Régis, and Timothy D Browning. “Counter Examples to the Hasse Principle among Certain Coflasque Tori.” Journal de Theorie Des Nombres de Bordeaux. Universite de Bordeaux I, 2013. https://doi.org/10.5802/jtnb.857.","short":"R. De La Bretèche, T.D. Browning, Journal de Theorie Des Nombres de Bordeaux 26 (2013) 25–44.","mla":"De La Bretèche, Régis, and Timothy D. Browning. “Counter Examples to the Hasse Principle among Certain Coflasque Tori.” Journal de Theorie Des Nombres de Bordeaux, vol. 26, no. 1, Universite de Bordeaux I, 2013, pp. 25–44, doi:10.5802/jtnb.857."},"publication":"Journal de Theorie des Nombres de Bordeaux","page":"25 - 44","quality_controlled":0,"doi":"10.5802/jtnb.857","date_published":"2013-05-14T00:00:00Z","day":"14","month":"05","year":"2013","_id":"251","publisher":"Universite de Bordeaux I","intvolume":" 26","publication_status":"published","status":"public","title":"Counter examples to the Hasse principle among certain coflasque tori","author":[{"first_name":"Régis","last_name":"De La Bretèche","full_name":"de la Bretèche, Régis"},{"orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D","full_name":"Timothy Browning"}],"volume":26,"date_updated":"2021-01-12T06:57:55Z","date_created":"2018-12-11T11:45:26Z","type":"journal_article","publist_id":"7651","issue":"1","abstract":[{"lang":"eng","text":"We study the density of varieties in a certain family which do not satisfy the Hasse principle. This work relies on results recently obtained by Colliot-Thélène [3]."}],"extern":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2517","intvolume":" 7966","title":"Formalizing and reasoning about quality","ddc":["000"],"status":"public","file":[{"file_id":"7860","relation":"main_file","checksum":"85afbf6c18a2c7e377c52c9410e2d824","date_updated":"2020-07-14T12:45:42Z","date_created":"2020-05-15T11:16:12Z","access_level":"open_access","file_name":"2013_ICALP_Almagor.pdf","creator":"dernst","content_type":"application/pdf","file_size":363031}],"oa_version":"Submitted Version","type":"conference","alternative_title":["LNCS"],"issue":"Part 2","abstract":[{"text":"Traditional formal methods are based on a Boolean satisfaction notion: a reactive system satisfies, or not, a given specification. We generalize formal methods to also address the quality of systems. As an adequate specification formalism we introduce the linear temporal logic LTL[F]. The satisfaction value of an LTL[F] formula is a number between 0 and 1, describing the quality of the satisfaction. The logic generalizes traditional LTL by augmenting it with a (parameterized) set F of arbitrary functions over the interval [0,1]. For example, F may contain the maximum or minimum between the satisfaction values of subformulas, their product, and their average. The classical decision problems in formal methods, such as satisfiability, model checking, and synthesis, are generalized to search and optimization problems in the quantitative setting. For example, model checking asks for the quality in which a specification is satisfied, and synthesis returns a system satisfying the specification with the highest quality. Reasoning about quality gives rise to other natural questions, like the distance between specifications. We formalize these basic questions and study them for LTL[F]. By extending the automata-theoretic approach for LTL to a setting that takes quality into an account, we are able to solve the above problems and show that reasoning about LTL[F] has roughly the same complexity as reasoning about traditional LTL.","lang":"eng"}],"citation":{"ista":"Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality. 7966(Part 2), 15–27.","apa":"Almagor, S., Boker, U., & Kupferman, O. (2013). Formalizing and reasoning about quality. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. https://doi.org/10.1007/978-3-642-39212-2_3","ieee":"S. Almagor, U. Boker, and O. Kupferman, “Formalizing and reasoning about quality,” vol. 7966, no. Part 2. Springer, pp. 15–27, 2013.","ama":"Almagor S, Boker U, Kupferman O. Formalizing and reasoning about quality. 2013;7966(Part 2):15-27. doi:10.1007/978-3-642-39212-2_3","chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “Formalizing and Reasoning about Quality.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39212-2_3.","mla":"Almagor, Shaull, et al. Formalizing and Reasoning about Quality. Vol. 7966, no. Part 2, Springer, 2013, pp. 15–27, doi:10.1007/978-3-642-39212-2_3.","short":"S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27."},"page":"15 - 27","date_published":"2013-07-01T00:00:00Z","scopus_import":1,"series_title":"Lecture Notes in Computer Science","article_processing_charge":"No","has_accepted_license":"1","day":"01","year":"2013","acknowledgement":"ERC Grant QUALITY. ","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","author":[{"first_name":"Shaull","last_name":"Almagor","full_name":"Almagor, Shaull"},{"full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","last_name":"Boker"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"volume":7966,"date_created":"2018-12-11T11:58:08Z","date_updated":"2020-08-11T10:09:47Z","ec_funded":1,"publist_id":"4384","file_date_updated":"2020-07-14T12:45:42Z","oa":1,"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"}],"quality_controlled":"1","doi":"10.1007/978-3-642-39212-2_3","conference":{"end_date":"2013-07-12","start_date":"2013-07-08","location":"Riga, Latvia","name":"ICALP: Automata, Languages and Programming"},"language":[{"iso":"eng"}],"month":"07"},{"external_id":{"arxiv":["1207.7213"]},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1207.7213","open_access":"1"}],"quality_controlled":"1","doi":"10.1007/978-3-642-39206-1_53","conference":{"end_date":"2013-07-12","location":"Riga, Latvia","start_date":"2013-07-08","name":"ICALP: Automata, Languages and Programming"},"language":[{"iso":"eng"}],"month":"07","year":"2013","department":[{"_id":"VlKo"}],"publisher":"Springer","publication_status":"published","related_material":{"record":[{"id":"2271","relation":"later_version","status":"public"}]},"author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"volume":7965,"date_created":"2018-12-11T11:58:08Z","date_updated":"2023-02-23T10:35:42Z","publist_id":"4383","citation":{"ieee":"V. Kolmogorov, “The power of linear programming for finite-valued CSPs: A constructive characterization,” presented at the ICALP: Automata, Languages and Programming, Riga, Latvia, 2013, vol. 7965, no. 1, pp. 625–636.","apa":"Kolmogorov, V. (2013). The power of linear programming for finite-valued CSPs: A constructive characterization (Vol. 7965, pp. 625–636). Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. https://doi.org/10.1007/978-3-642-39206-1_53","ista":"Kolmogorov V. 2013. The power of linear programming for finite-valued CSPs: A constructive characterization. ICALP: Automata, Languages and Programming, LNCS, vol. 7965, 625–636.","ama":"Kolmogorov V. The power of linear programming for finite-valued CSPs: A constructive characterization. In: Vol 7965. Springer; 2013:625-636. doi:10.1007/978-3-642-39206-1_53","chicago":"Kolmogorov, Vladimir. “The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization,” 7965:625–36. Springer, 2013. https://doi.org/10.1007/978-3-642-39206-1_53.","short":"V. Kolmogorov, in:, Springer, 2013, pp. 625–636.","mla":"Kolmogorov, Vladimir. The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization. Vol. 7965, no. 1, Springer, 2013, pp. 625–36, doi:10.1007/978-3-642-39206-1_53."},"page":"625 - 636","date_published":"2013-07-01T00:00:00Z","scopus_import":1,"day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2518","intvolume":" 7965","title":"The power of linear programming for finite-valued CSPs: A constructive characterization","status":"public","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"issue":"1","abstract":[{"lang":"eng","text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. An instance of the problem is specified by a sum of cost functions from the language with the goal to minimise the sum. We study which classes of finite-valued languages can be solved exactly by the basic linear programming relaxation (BLP). Thapper and Živný showed [20] that if BLP solves the language then the language admits a binary commutative fractional polymorphism. We prove that the converse is also true. This leads to a necessary and a sufficient condition which can be checked in polynomial time for a given language. In contrast, the previous necessary and sufficient condition due to [20] involved infinitely many inequalities. More recently, Thapper and Živný [21] showed (using, in particular, a technique introduced in this paper) that core languages that do not satisfy our condition are NP-hard. Taken together, these results imply that a finite-valued language can either be solved using Linear Programming or is NP-hard."}]},{"abstract":[{"text":"We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes.","lang":"eng"}],"issue":"3","publist_id":"4385","type":"journal_article","author":[{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"last_name":"Nickisch","first_name":"Hannes","full_name":"Nickisch, Hannes"},{"first_name":"Stefan","last_name":"Harmeling","full_name":"Harmeling, Stefan"}],"date_updated":"2021-01-12T06:57:58Z","date_created":"2018-12-11T11:58:08Z","oa_version":"None","volume":36,"_id":"2516","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","status":"public","title":"Attribute-based classification for zero-shot learning of object categories","publication_status":"published","intvolume":" 36","publisher":"IEEE","department":[{"_id":"ChLa"}],"month":"07","day":"30","scopus_import":1,"doi":"10.1109/TPAMI.2013.140","date_published":"2013-07-30T00:00:00Z","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","citation":{"ama":"Lampert C, Nickisch H, Harmeling S. Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2013;36(3):453-465. doi:10.1109/TPAMI.2013.140","apa":"Lampert, C., Nickisch, H., & Harmeling, S. (2013). Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2013.140","ieee":"C. Lampert, H. Nickisch, and S. Harmeling, “Attribute-based classification for zero-shot learning of object categories,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 36, no. 3. IEEE, pp. 453–465, 2013.","ista":"Lampert C, Nickisch H, Harmeling S. 2013. Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(3), 453–465.","short":"C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2013) 453–465.","mla":"Lampert, Christoph, et al. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 36, no. 3, IEEE, 2013, pp. 453–65, doi:10.1109/TPAMI.2013.140.","chicago":"Lampert, Christoph, Hannes Nickisch, and Stefan Harmeling. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2013. https://doi.org/10.1109/TPAMI.2013.140."},"quality_controlled":"1","page":"453 - 465"},{"publication_status":"published","publisher":"AUAI Press","department":[{"_id":"ChLa"}],"year":"2013","date_created":"2018-12-11T11:58:09Z","date_updated":"2023-02-23T10:46:36Z","author":[{"full_name":"Quadrianto, Novi","last_name":"Quadrianto","first_name":"Novi"},{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","first_name":"Viktoriia","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia"},{"last_name":"Knowles","first_name":"David","full_name":"Knowles, David"},{"full_name":"Ghahramani, Zoubin","first_name":"Zoubin","last_name":"Ghahramani"}],"file_date_updated":"2020-07-14T12:45:42Z","publist_id":"4381","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"conference":{"name":"UAI: Uncertainty in Artificial Intelligence","location":"Bellevue, WA, United States","start_date":"2013-07-11","end_date":"2013-07-15"},"month":"07","publication_identifier":{"isbn":["9780974903996"]},"ddc":["000"],"status":"public","title":"The supervised IBP: Neighbourhood preserving infinite latent feature models","_id":"2520","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"325f20c4b926bd74d39006b97df572bd","date_updated":"2020-07-14T12:45:42Z","date_created":"2018-12-12T10:15:16Z","file_id":"5134","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1117100,"access_level":"open_access","file_name":"IST-2013-137-v1+1_QuaShaKnoGha13.pdf"}],"oa_version":"Submitted Version","pubrep_id":"137","type":"conference","abstract":[{"lang":"eng","text":"We propose a probabilistic model to infer supervised latent variables in\r\nthe Hamming space from observed data. Our model allows simultaneous\r\ninference of the number of binary latent variables, and their values. The\r\nlatent variables preserve neighbourhood structure of the data in a sense\r\nthat objects in the same semantic concept have similar latent values, and\r\nobjects in different concepts have dissimilar latent values. We formulate\r\nthe supervised infinite latent variable problem based on an intuitive\r\nprinciple of pulling objects together if they are of the same type, and\r\npushing them apart if they are not. We then combine this principle with a\r\nflexible Indian Buffet Process prior on the latent variables. We show that\r\nthe inferred supervised latent variables can be directly used to perform a\r\nnearest neighbour search for the purpose of retrieval. We introduce a new\r\napplication of dynamically extending hash codes, and show how to\r\neffectively couple the structure of the hash codes with continuously\r\ngrowing structure of the neighbourhood preserving infinite latent feature\r\nspace."}],"page":"527 - 536","publication":"Proceedings of the 29th conference uncertainty in Artificial Intelligence","citation":{"mla":"Quadrianto, Novi, et al. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” Proceedings of the 29th Conference Uncertainty in Artificial Intelligence, AUAI Press, 2013, pp. 527–36.","short":"N. Quadrianto, V. Sharmanska, D. Knowles, Z. Ghahramani, in:, Proceedings of the 29th Conference Uncertainty in Artificial Intelligence, AUAI Press, 2013, pp. 527–536.","chicago":"Quadrianto, Novi, Viktoriia Sharmanska, David Knowles, and Zoubin Ghahramani. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” In Proceedings of the 29th Conference Uncertainty in Artificial Intelligence, 527–36. AUAI Press, 2013.","ama":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. The supervised IBP: Neighbourhood preserving infinite latent feature models. In: Proceedings of the 29th Conference Uncertainty in Artificial Intelligence. AUAI Press; 2013:527-536.","ista":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. 2013. The supervised IBP: Neighbourhood preserving infinite latent feature models. Proceedings of the 29th conference uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, 527–536.","ieee":"N. Quadrianto, V. Sharmanska, D. Knowles, and Z. Ghahramani, “The supervised IBP: Neighbourhood preserving infinite latent feature models,” in Proceedings of the 29th conference uncertainty in Artificial Intelligence, Bellevue, WA, United States, 2013, pp. 527–536.","apa":"Quadrianto, N., Sharmanska, V., Knowles, D., & Ghahramani, Z. (2013). The supervised IBP: Neighbourhood preserving infinite latent feature models. In Proceedings of the 29th conference uncertainty in Artificial Intelligence (pp. 527–536). Bellevue, WA, United States: AUAI Press."},"date_published":"2013-07-11T00:00:00Z","scopus_import":1,"day":"11","has_accepted_license":"1"},{"_id":"253","year":"2013","intvolume":" 60","publisher":"Unknown","title":"Counting rational points on cubic hypersurfaces: Corrigendum","publication_status":"published","status":"public","author":[{"first_name":"Timothy D","last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Timothy Browning"}],"volume":60,"date_created":"2018-12-11T11:45:27Z","date_updated":"2021-01-12T06:58:03Z","type":"journal_article","issue":"1","publist_id":"7649","extern":1,"citation":{"short":"T.D. Browning, Mathematika 60 (2013) 101–107.","mla":"Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” Mathematika, vol. 60, no. 1, Unknown, 2013, pp. 101–07, doi:10.1112/S0025579313000132.","chicago":"Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” Mathematika. Unknown, 2013. https://doi.org/10.1112/S0025579313000132.","ama":"Browning TD. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 2013;60(1):101-107. doi:10.1112/S0025579313000132","apa":"Browning, T. D. (2013). Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. Unknown. https://doi.org/10.1112/S0025579313000132","ieee":"T. D. Browning, “Counting rational points on cubic hypersurfaces: Corrigendum,” Mathematika, vol. 60, no. 1. Unknown, pp. 101–107, 2013.","ista":"Browning TD. 2013. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 60(1), 101–107."},"publication":"Mathematika","page":"101 - 107","quality_controlled":0,"date_published":"2013-09-06T00:00:00Z","doi":"10.1112/S0025579313000132","month":"09","day":"06"},{"intvolume":" 66","publisher":"Elsevier","publication_status":"published","title":"Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice","status":"public","_id":"2692","year":"2013","volume":66,"date_updated":"2021-01-12T06:59:05Z","date_created":"2018-12-11T11:59:06Z","author":[{"full_name":"Dobi, Alice","last_name":"Dobi","first_name":"Alice"},{"last_name":"Sartori","first_name":"Simone","full_name":"Sartori, Simone B"},{"last_name":"Busti","first_name":"Daniela","full_name":"Busti, Daniela"},{"last_name":"Van Der Putten","first_name":"Herman","full_name":"Van Der Putten, Herman V"},{"full_name":"Singewald, Nicolas","last_name":"Singewald","first_name":"Nicolas"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Ryuichi Shigemoto"},{"full_name":"Ferraguti, Francesco","first_name":"Francesco","last_name":"Ferraguti"}],"type":"journal_article","extern":1,"publist_id":"4205","abstract":[{"lang":"eng","text":"The group III metabotropic glutamate (mGlu) receptors mGlu7 and mGlu8 are receiving increased attention as potential novel therapeutic targets for anxiety disorders. The effects mediated by these receptors appear to result from a complex interplay of facilitatory and inhibitory actions at different brain sites in the anxiety/fear circuits. To better understand the effect of mGlu7 and mGlu8 receptors on extinction of contextual fear and their critical sites of action in the fear networks, we focused on the amygdala. Direct injection into the basolateral complex of the amygdala of the mGlu7 receptor agonist AMN082 facilitated extinction, whereas the mGlu8 receptor agonist (S)-3,4-DCPG sustained freezing during the extinction acquisition trial. We also determined at the ultrastructural level the synaptic distribution of these receptors in the basal nucleus (BA) and intercalated cell clusters (ITCs) of the amygdala. Both areas are thought to exert key roles in fear extinction. We demonstrate that mGlu7 and mGlu8 receptors are located in different presynaptic terminals forming both asymmetric and symmetric synapses, and that they preferentially target neurons expressing mGlu1α receptors mostly located around ITCs. In addition we show that mGlu7 and mGlu8 receptors were segregated to different inputs to a significant extent. In particular, mGlu7a receptors were primarily onto glutamatergic afferents arising from the BA or midline thalamic nuclei, but not the medial prefrontal cortex (mPFC), as revealed by combined anterograde tracing and pre-embedding electron microscopy. On the other hand, mGlu8a showed a more restricted distribution in the BA and appeared absent from thalamic, mPFC and intrinsic inputs. This segregation of mGlu7 and mGlu8 receptors in different neuronal pathways of the fear circuit might explain the distinct effects on fear extinction training observed with mGlu7 and mGlu8 receptor agonists."}],"page":"274 - 289","quality_controlled":0,"citation":{"chicago":"Dobi, Alice, Simone Sartori, Daniela Busti, Herman Van Der Putten, Nicolas Singewald, Ryuichi Shigemoto, and Francesco Ferraguti. “Neural Substrates for the Distinct Effects of Presynaptic Group III Metabotropic Glutamate Receptors on Extinction of Contextual Fear Conditioning in Mice.” Neuropharmacology. Elsevier, 2013. https://doi.org/10.1016/j.neuropharm.2012.05.025.","mla":"Dobi, Alice, et al. “Neural Substrates for the Distinct Effects of Presynaptic Group III Metabotropic Glutamate Receptors on Extinction of Contextual Fear Conditioning in Mice.” Neuropharmacology, vol. 66, Elsevier, 2013, pp. 274–89, doi:10.1016/j.neuropharm.2012.05.025.","short":"A. Dobi, S. Sartori, D. Busti, H. Van Der Putten, N. Singewald, R. Shigemoto, F. Ferraguti, Neuropharmacology 66 (2013) 274–289.","ista":"Dobi A, Sartori S, Busti D, Van Der Putten H, Singewald N, Shigemoto R, Ferraguti F. 2013. Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology. 66, 274–289.","ieee":"A. Dobi et al., “Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice,” Neuropharmacology, vol. 66. Elsevier, pp. 274–289, 2013.","apa":"Dobi, A., Sartori, S., Busti, D., Van Der Putten, H., Singewald, N., Shigemoto, R., & Ferraguti, F. (2013). Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology. Elsevier. https://doi.org/10.1016/j.neuropharm.2012.05.025","ama":"Dobi A, Sartori S, Busti D, et al. Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice. Neuropharmacology. 2013;66:274-289. doi:10.1016/j.neuropharm.2012.05.025"},"publication":"Neuropharmacology","date_published":"2013-03-01T00:00:00Z","doi":"10.1016/j.neuropharm.2012.05.025","month":"03","day":"01"},{"day":"20","month":"02","page":"3668 - 3678","quality_controlled":0,"citation":{"chicago":"Indriati, Dwi, Naomi Kamasawa, Ko Matsui, Andrea Meredith, Masahiko Watanabe, and Ryuichi Shigemoto. “Quantitative Localization of Cav2.1 (P/Q-Type) Voltage-Dependent Calcium Channels in Purkinje Cells: Somatodendritic Gradient and Distinct Somatic Coclustering with Calcium-Activated Potassium Channels.” Journal of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.2921-12.2013.","short":"D. Indriati, N. Kamasawa, K. Matsui, A. Meredith, M. Watanabe, R. Shigemoto, Journal of Neuroscience 33 (2013) 3668–3678.","mla":"Indriati, Dwi, et al. “Quantitative Localization of Cav2.1 (P/Q-Type) Voltage-Dependent Calcium Channels in Purkinje Cells: Somatodendritic Gradient and Distinct Somatic Coclustering with Calcium-Activated Potassium Channels.” Journal of Neuroscience, vol. 33, no. 8, Society for Neuroscience, 2013, pp. 3668–78, doi:10.1523/JNEUROSCI.2921-12.2013.","apa":"Indriati, D., Kamasawa, N., Matsui, K., Meredith, A., Watanabe, M., & Shigemoto, R. (2013). Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2921-12.2013","ieee":"D. Indriati, N. Kamasawa, K. Matsui, A. Meredith, M. Watanabe, and R. Shigemoto, “Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels,” Journal of Neuroscience, vol. 33, no. 8. Society for Neuroscience, pp. 3668–3678, 2013.","ista":"Indriati D, Kamasawa N, Matsui K, Meredith A, Watanabe M, Shigemoto R. 2013. Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels. Journal of Neuroscience. 33(8), 3668–3678.","ama":"Indriati D, Kamasawa N, Matsui K, Meredith A, Watanabe M, Shigemoto R. Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels. Journal of Neuroscience. 2013;33(8):3668-3678. doi:10.1523/JNEUROSCI.2921-12.2013"},"publication":"Journal of Neuroscience","doi":"10.1523/JNEUROSCI.2921-12.2013","date_published":"2013-02-20T00:00:00Z","type":"journal_article","extern":1,"issue":"8","publist_id":"4206","abstract":[{"text":"P/Q-type voltage-dependent calcium channels play key roles in transmitter release, integration of dendritic signals, generation of dendritic spikes, and gene expression. High intracellular calcium concentration transient produced by these channels is restricted to tens to hundreds of nanometers from the channels. Therefore, precise localization of these channels along the plasma membrane was long sought to decipher how each neuronal cell function is controlled. Here, we analyzed the distribution of Cav2.1 subunit of the P/Q-type channel using highly sensitive SDS-digested freeze-fracture replica labeling in the rat cerebellar Purkinje cells. The labeling efficiency was such that the number of immunogold particles in each parallel fiber active zone was comparable to that of functional channels calculated from previous reports. Two distinct patterns of Cav2.1 distribution, scattered and clustered, were found in Purkinje cells. The scattered Cav2.1 had a somatodendritic gradient with the density of immunogold particles increasing 2.5-fold from soma to distal dendrites. The other population with 74-fold higher density than the scattered particles was found within clusters of intramembrane particles on the P-face of soma and primary dendrites. Both populations of Cav2.1 were found as early as P3 and increased in the second postnatal week to a mature level. Using double immunogold labeling, we found that virtually all of the Cav2.1 clusters were colocalized with two types of calcium-activated potassium channels, BK and SK2, with the nearest neighbor distance of 40∼nm. Calcium nanodomain created by the opening of Cav2.1 channels likely activates the two channels that limit the extent of depolarization.","lang":"eng"}],"intvolume":" 33","publisher":"Society for Neuroscience","publication_status":"published","title":"Quantitative localization of Cav2.1 (P/Q-Type) voltage-dependent calcium channels in Purkinje cells: Somatodendritic gradient and distinct somatic coclustering with calcium-activated potassium channels","status":"public","year":"2013","_id":"2691","volume":33,"date_created":"2018-12-11T11:59:05Z","date_updated":"2021-01-12T06:59:05Z","author":[{"full_name":"Indriati, Dwi Wahyu","first_name":"Dwi","last_name":"Indriati"},{"full_name":"Kamasawa, Naomi","last_name":"Kamasawa","first_name":"Naomi"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"},{"last_name":"Meredith","first_name":"Andrea","full_name":"Meredith, Andrea L"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"full_name":"Ryuichi Shigemoto","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}]},{"quality_controlled":0,"page":"219 - 239","publication":"Journal of Physiology","citation":{"ama":"Budisantoso T, Harada H, Kamasawa N, Fukazawa Y, Shigemoto R, Matsui K. Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held. Journal of Physiology. 2013;591(1):219-239. doi:10.1113/jphysiol.2012.241398","ieee":"T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, and K. Matsui, “Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held,” Journal of Physiology, vol. 591, no. 1. Wiley-Blackwell, pp. 219–239, 2013.","apa":"Budisantoso, T., Harada, H., Kamasawa, N., Fukazawa, Y., Shigemoto, R., & Matsui, K. (2013). Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2012.241398","ista":"Budisantoso T, Harada H, Kamasawa N, Fukazawa Y, Shigemoto R, Matsui K. 2013. Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held. Journal of Physiology. 591(1), 219–239.","short":"T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, K. Matsui, Journal of Physiology 591 (2013) 219–239.","mla":"Budisantoso, Timotheus, et al. “Evaluation of Glutamate Concentration Transient in the Synaptic Cleft of the Rat Calyx of Held.” Journal of Physiology, vol. 591, no. 1, Wiley-Blackwell, 2013, pp. 219–39, doi:10.1113/jphysiol.2012.241398.","chicago":"Budisantoso, Timotheus, Harumi Harada, Naomi Kamasawa, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Evaluation of Glutamate Concentration Transient in the Synaptic Cleft of the Rat Calyx of Held.” Journal of Physiology. Wiley-Blackwell, 2013. https://doi.org/10.1113/jphysiol.2012.241398."},"date_published":"2013-01-01T00:00:00Z","doi":"10.1113/jphysiol.2012.241398","day":"01","month":"01","publication_status":"published","status":"public","title":"Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held","publisher":"Wiley-Blackwell","intvolume":" 591","_id":"2690","year":"2013","date_created":"2018-12-11T11:59:05Z","date_updated":"2021-01-12T06:59:04Z","volume":591,"author":[{"last_name":"Budisantoso","first_name":"Timotheus","full_name":"Budisantoso, Timotheus"},{"last_name":"Harada","first_name":"Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harumi Harada"},{"full_name":"Kamasawa, Naomi","last_name":"Kamasawa","first_name":"Naomi"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Ryuichi Shigemoto"},{"last_name":"Matsui","first_name":"Ko","full_name":"Matsui, Ko"}],"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"Establishing the spatiotemporal concentration profile of neurotransmitter following synaptic vesicular release is essential for our understanding of inter-neuronal communication. Such profile is a determinant of synaptic strength, short-term plasticity and inter-synaptic crosstalk. Synaptically released glutamate has been suggested to reach a few millimolar in concentration and last for <1 ms. The synaptic cleft is often conceived as a single concentration compartment, whereas a huge gradient likely exists. Modelling studies have attempted to describe this gradient, but two key parameters, the number of glutamate in a vesicle (NGlu) and its diffusion coefficient (DGlu) in the extracellular space, remained unresolved. To determine this profile, the rat calyx of Held synapse at postnatal day 12-16 was studied where diffusion of glutamate occurs two-dimensionally and where quantification of AMPA receptor distribution on individual postsynaptic specialization on medial nucleus of the trapezoid body principal cells is possible using SDS-digested freeze-fracture replica labelling. To assess the performance of these receptors as glutamate sensors, a kinetic model of the receptors was constructed from outside-out patch recordings. From here, we simulated synaptic responses and compared them with the EPSC recordings. Combinations of NGlu and DGlu with an optimum of 7000 and 0.3 μm2 ms-1 reproduced the data, suggesting slow diffusion. Further simulations showed that a single vesicle does not saturate the synaptic receptors, and that glutamate spillover does not affect the conductance amplitude at this synapse. Using the estimated profile, we also evaluated how the number of multiple vesicle releases at individual active zones affects the amplitude of postsynaptic signals."}],"issue":"1","publist_id":"4207"},{"quality_controlled":0,"page":"7961 - 7974","publication":"Journal of Neuroscience","citation":{"ieee":"S. Booker et al., “Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons,” Journal of Neuroscience, vol. 33, no. 18. Society for Neuroscience, pp. 7961–7974, 2013.","apa":"Booker, S., Gross, A., Althof, D., Shigemoto, R., Bettler, B., Frotscher, M., … Vida, I. (2013). Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1186-12.2013","ista":"Booker S, Gross A, Althof D, Shigemoto R, Bettler B, Frotscher M, Hearing M, Wickman K, Watanabe M, Kulik Á, Vida I. 2013. Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience. 33(18), 7961–7974.","ama":"Booker S, Gross A, Althof D, et al. Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons. Journal of Neuroscience. 2013;33(18):7961-7974. doi:10.1523/JNEUROSCI.1186-12.2013","chicago":"Booker, Sam, Anna Gross, Daniel Althof, Ryuichi Shigemoto, Bernhard Bettler, Michael Frotscher, Matthew Hearing, et al. “Differential GABAB-Receptor-Mediated Effects in Perisomatic- and Dendrite-Targeting Parvalbumin Interneurons.” Journal of Neuroscience. Society for Neuroscience, 2013. https://doi.org/10.1523/JNEUROSCI.1186-12.2013.","short":"S. Booker, A. Gross, D. Althof, R. Shigemoto, B. Bettler, M. Frotscher, M. Hearing, K. Wickman, M. Watanabe, Á. Kulik, I. Vida, Journal of Neuroscience 33 (2013) 7961–7974.","mla":"Booker, Sam, et al. “Differential GABAB-Receptor-Mediated Effects in Perisomatic- and Dendrite-Targeting Parvalbumin Interneurons.” Journal of Neuroscience, vol. 33, no. 18, Society for Neuroscience, 2013, pp. 7961–74, doi:10.1523/JNEUROSCI.1186-12.2013."},"date_published":"2013-05-01T00:00:00Z","doi":"10.1523/JNEUROSCI.1186-12.2013","month":"05","day":"01","publication_status":"published","status":"public","title":"Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons","intvolume":" 33","publisher":"Society for Neuroscience","year":"2013","_id":"2693","date_updated":"2021-01-12T06:59:05Z","date_created":"2018-12-11T11:59:06Z","volume":33,"author":[{"first_name":"Sam","last_name":"Booker","full_name":"Booker, Sam A"},{"last_name":"Gross","first_name":"Anna","full_name":"Gross, Anna"},{"first_name":"Daniel","last_name":"Althof","full_name":"Althof, Daniel"},{"full_name":"Ryuichi Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"first_name":"Bernhard","last_name":"Bettler","full_name":"Bettler, Bernhard"},{"full_name":"Frotscher, Michael","last_name":"Frotscher","first_name":"Michael"},{"full_name":"Hearing, Matthew C","last_name":"Hearing","first_name":"Matthew"},{"full_name":"Wickman, Kevin D","first_name":"Kevin","last_name":"Wickman"},{"full_name":"Watanabe, Masahiko","last_name":"Watanabe","first_name":"Masahiko"},{"full_name":"Kulik, Ákos","first_name":"Ákos","last_name":"Kulik"},{"last_name":"Vida","first_name":"Imre","full_name":"Vida, Imre"}],"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"Inhibitory parvalbumin-containing interneurons (PVIs) control neuronal discharge and support the generation of theta- and gammafrequency oscillations in cortical networks. Fast GABAergic input onto PVIs is crucial for their synchronization and oscillatory entrainment, but the role of metabotropic GABAB receptors (GABABRs) in mediating slow presynaptic and postsynaptic inhibition remains unknown. In this study, we have combined high-resolution immunoelectron microscopy, whole-cell patch-clamp recording, and computational modeling to investigate the subcellular distribution and effects of GABABRs and their postsynaptic effector Kir3 channels in rat hippocampal PVIs. Pre-embedding immunogold labeling revealed that the receptors and channels localize at high levels to the extrasynaptic membrane of parvalbumin-immunoreactive dendrites. Immunoreactivity forGABABRs was also present at lower levels on PVI axon terminals. Whole-cell recordings further showed that synaptically released GABA in response to extracellular stimulation evokes large GABABR-mediated slow IPSCs in perisomatic-targeting (PT) PVIs, but only small or no currents in dendrite-targeting (DT) PVIs. In contrast, paired recordings demonstrated that GABABR activation results in presynaptic inhibition at the output synapses of both PT and DT PVIs, but more strongly in the latter. Finally, computational analysis indicated that GABAB IPSCs can phasically modulate the discharge of PT interneurons at theta frequencies. In summary, our results show that GABABRs differentially mediate slow presynaptic and postsynaptic inhibition in PVIs and can contribute to the dynamic modulation of their activity during oscillations. Furthermore, these data provide evidence for a compartment-specific molecular divergence of hippocampal PVI subtypes, suggesting that activation of GABABRs may shift the balance between perisomatic and dendritic inhibition."}],"issue":"18","publist_id":"4204"},{"language":[{"iso":"eng"}],"doi":"10.4171/JEMS/416","date_published":"2013-10-16T00:00:00Z","quality_controlled":"1","page":"2093 - 2113","publication":"Journal of the European Mathematical Society","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1105.0506"}],"citation":{"ama":"Erdös L, Fournais S, Solovej J. Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. 2013;15(6):2093-2113. doi:10.4171/JEMS/416","ieee":"L. Erdös, S. Fournais, and J. Solovej, “Stability and semiclassics in self-generated fields,” Journal of the European Mathematical Society, vol. 15, no. 6. European Mathematical Society, pp. 2093–2113, 2013.","apa":"Erdös, L., Fournais, S., & Solovej, J. (2013). Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/416","ista":"Erdös L, Fournais S, Solovej J. 2013. Stability and semiclassics in self-generated fields. Journal of the European Mathematical Society. 15(6), 2093–2113.","short":"L. Erdös, S. Fournais, J. Solovej, Journal of the European Mathematical Society 15 (2013) 2093–2113.","mla":"Erdös, László, et al. “Stability and Semiclassics in Self-Generated Fields.” Journal of the European Mathematical Society, vol. 15, no. 6, European Mathematical Society, 2013, pp. 2093–113, doi:10.4171/JEMS/416.","chicago":"Erdös, László, Søren Fournais, and Jan Solovej. “Stability and Semiclassics in Self-Generated Fields.” Journal of the European Mathematical Society. European Mathematical Society, 2013. https://doi.org/10.4171/JEMS/416."},"external_id":{"arxiv":["1105.0506"]},"oa":1,"month":"10","day":"16","date_created":"2018-12-11T11:59:07Z","date_updated":"2021-01-12T06:59:07Z","volume":15,"oa_version":"Preprint","author":[{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"last_name":"Fournais","first_name":"Søren","full_name":"Fournais, Søren"},{"full_name":"Solovej, Jan","first_name":"Jan","last_name":"Solovej"}],"publication_status":"published","title":"Stability and semiclassics in self-generated fields","status":"public","department":[{"_id":"LaEr"}],"publisher":"European Mathematical Society","intvolume":" 15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2698","year":"2013","abstract":[{"text":"We consider non-interacting particles subject to a fixed external potential V and a self-generated magnetic field B. The total energy includes the field energy β∫B2 and we minimize over all particle states and magnetic fields. In the case of spin-1/2 particles this minimization leads to the coupled Maxwell-Pauli system. The parameter β tunes the coupling strength between the field and the particles and it effectively determines the strength of the field. We investigate the stability and the semiclassical asymptotics, h→0, of the total ground state energy E(β,h,V). The relevant parameter measuring the field strength in the semiclassical limit is κ=βh. We are not able to give the exact leading order semiclassical asymptotics uniformly in κ or even for fixed κ. We do however give upper and lower bounds on E with almost matching dependence on κ. In the simultaneous limit h→0 and κ→∞ we show that the standard non-magnetic Weyl asymptotics holds. The same result also holds for the spinless case, i.e. where the Pauli operator is replaced by the Schrödinger operator.","lang":"eng"}],"issue":"6","publist_id":"4198","type":"journal_article"},{"type":"journal_article","issue":"1","publist_id":"4199","abstract":[{"lang":"eng","text":"We consider Hermitian and symmetric random band matrices H = (h xy ) in d⩾1 d ⩾ 1 dimensions. The matrix entries h xy , indexed by x,y∈(Z/LZ)d x , y ∈ ( Z / L Z ) d , are independent, centred random variables with variances sxy=E|hxy|2 s x y = E | h x y | 2 . We assume that s xy is negligible if |x − y| exceeds the band width W. In one dimension we prove that the eigenvectors of H are delocalized if W≫L4/5 W ≫ L 4 / 5 . We also show that the magnitude of the matrix entries |Gxy|2 | G x y | 2 of the resolvent G=G(z)=(H−z)−1 G = G ( z ) = ( H - z ) - 1 is self-averaging and we compute E|Gxy|2 E | G x y | 2 . We show that, as L→∞ L → ∞ and W≫L4/5 W ≫ L 4 / 5 , the behaviour of E|Gxy|2 E | G x y | 2 is governed by a diffusion operator whose diffusion constant we compute. Similar results are obtained in higher dimensions."}],"extern":1,"_id":"2697","year":"2013","publisher":"Springer","intvolume":" 323","publication_status":"published","title":"Delocalization and diffusion profile for random band matrices","status":"public","author":[{"full_name":"László Erdös","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng-Tzer"},{"last_name":"Yin","first_name":"Jun","full_name":"Yin, Jun"}],"volume":323,"date_updated":"2021-01-12T06:59:07Z","date_created":"2018-12-11T11:59:07Z","month":"10","day":"01","citation":{"short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Communications in Mathematical Physics 323 (2013) 367–416.","mla":"Erdös, László, et al. “Delocalization and Diffusion Profile for Random Band Matrices.” Communications in Mathematical Physics, vol. 323, no. 1, Springer, 2013, pp. 367–416, doi:10.1007/s00220-013-1773-3.","chicago":"Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Delocalization and Diffusion Profile for Random Band Matrices.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-013-1773-3.","ama":"Erdös L, Knowles A, Yau H, Yin J. Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. 2013;323(1):367-416. doi:10.1007/s00220-013-1773-3","apa":"Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-013-1773-3","ieee":"L. Erdös, A. Knowles, H. Yau, and J. Yin, “Delocalization and diffusion profile for random band matrices,” Communications in Mathematical Physics, vol. 323, no. 1. Springer, pp. 367–416, 2013.","ista":"Erdös L, Knowles A, Yau H, Yin J. 2013. Delocalization and diffusion profile for random band matrices. Communications in Mathematical Physics. 323(1), 367–416."},"main_file_link":[{"url":"http://arxiv.org/abs/1205.5669","open_access":"1"}],"oa":1,"publication":"Communications in Mathematical Physics","page":"367 - 416","quality_controlled":0,"date_published":"2013-10-01T00:00:00Z","doi":"10.1007/s00220-013-1773-3"},{"month":"07","language":[{"iso":"eng"}],"doi":"10.1145/2463372.2463568","conference":{"name":"GECCO: Genetic and evolutionary computation conference","end_date":"2013-07-10","start_date":"2013-07-06","location":"Amsterdam, Netherlands"},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","oa":1,"ec_funded":1,"publist_id":"4174","file_date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-11T11:59:14Z","date_updated":"2021-01-12T06:59:15Z","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"}],"publisher":"ACM","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","year":"2013","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","page":"1573 - 1580","citation":{"chicago":"Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM, 2013. https://doi.org/10.1145/2463372.2463568.","short":"N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.","mla":"Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80, doi:10.1145/2463372.2463568.","apa":"Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics help us understand evolutionary computation? In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463568","ieee":"N. H. Barton and T. Paixao, “Can quantitative and population genetics help us understand evolutionary computation?,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 1573–1580.","ista":"Barton NH, Paixao T. 2013. Can quantitative and population genetics help us understand evolutionary computation? Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 1573–1580.","ama":"Barton NH, Paixao T. Can quantitative and population genetics help us understand evolutionary computation? In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568"},"publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","abstract":[{"text":"Even though both population and quantitative genetics, and evolutionary computation, deal with the same questions, they have developed largely independently of each other. I review key results from each field, emphasising those that apply independently of the (usually unknown) relation between genotype and phenotype. The infinitesimal model provides a simple framework for predicting the response of complex traits to selection, which in biology has proved remarkably successful. This allows one to choose the schedule of population sizes and selection intensities that will maximise the response to selection, given that the total number of individuals realised, C = ∑t Nt, is constrained. This argument shows that for an additive trait (i.e., determined by the sum of effects of the genes), the optimum population size and the maximum possible response (i.e., the total change in trait mean) are both proportional to √C.","lang":"eng"}],"type":"conference","file":[{"checksum":"9d9be9090ce5c20766e0eb076ace5b98","date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-12T10:15:38Z","file_id":"5159","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":475844,"access_level":"open_access","file_name":"IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf"}],"oa_version":"Submitted Version","pubrep_id":"564","status":"public","ddc":["570"],"title":"Can quantitative and population genetics help us understand evolutionary computation?","_id":"2718","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_processing_charge":"No","day":"01","scopus_import":1,"date_published":"2013-10-01T00:00:00Z","citation":{"mla":"Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536.","short":"H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.","chicago":"Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics. Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536.","ama":"Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540. doi:10.1534/genetics.113.153536","ista":"Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.","ieee":"H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195, no. 2. Genetics Society of America, pp. 527–540, 2013.","apa":"Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.153536"},"publication":"Genetics","page":"527-540","issue":"2","abstract":[{"text":"Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal mutations is <10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2720","intvolume":" 195","status":"public","title":"Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila","month":"10","doi":"10.1534/genetics.113.153536","language":[{"iso":"eng"}],"external_id":{"pmid":["23934880"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","ec_funded":1,"publist_id":"4172","author":[{"full_name":"Long, Hongan","last_name":"Long","first_name":"Hongan"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"},{"first_name":"Ricardo","last_name":"Azevedo","full_name":"Azevedo, Ricardo"},{"last_name":"Zufall","first_name":"Rebecca","full_name":"Zufall, Rebecca"}],"volume":195,"date_updated":"2021-01-12T06:59:16Z","date_created":"2018-12-11T11:59:15Z","pmid":1,"year":"2013","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Genetics Society of America","publication_status":"published"},{"scopus_import":1,"month":"07","day":"01","quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"page":"845 - 852","publication":"Proceedings of the 15th annual conference on Genetic and evolutionary computation","citation":{"apa":"Paixao, T., & Barton, N. H. (2013). A variance decomposition approach to the analysis of genetic algorithms. In Proceedings of the 15th annual conference on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands: ACM. https://doi.org/10.1145/2463372.2463470","ieee":"T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.","ista":"Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis of genetic algorithms. Proceedings of the 15th annual conference on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation conference, 845–852.","ama":"Paixao T, Barton NH. A variance decomposition approach to the analysis of genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470","chicago":"Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.","short":"T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.","mla":"Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470."},"language":[{"iso":"eng"}],"conference":{"name":"GECCO: Genetic and evolutionary computation conference","end_date":"2013-07-10","start_date":"2013-07-06","location":"Amsterdam, Netherlands"},"doi":"10.1145/2463372.2463470","date_published":"2013-07-01T00:00:00Z","type":"conference","abstract":[{"text":"Prediction of the evolutionary process is a long standing problem both in the theory of evolutionary biology and evolutionary computation (EC). It has long been realized that heritable variation is crucial to both the response to selection and the success of genetic algorithms. However, not all variation contributes in the same way to the response. Quantitative genetics has developed a large body of work trying to estimate and understand how different components of the variance in fitness in the population contribute to the response to selection. We illustrate how to apply some concepts of quantitative genetics to the analysis of genetic algorithms. In particular, we derive estimates for the short term prediction of the response to selection and we use variance decomposition to gain insight on local aspects of the landscape. Finally, we propose a new population based genetic algorithm that uses these methods to improve its operation.","lang":"eng"}],"ec_funded":1,"publist_id":"4173","publication_status":"published","title":"A variance decomposition approach to the analysis of genetic algorithms","status":"public","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"ACM","year":"2013","_id":"2719","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:59:15Z","date_updated":"2021-01-12T06:59:15Z","oa_version":"None","author":[{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}]},{"publisher":"Springer","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2013","volume":152,"date_created":"2018-12-11T11:59:34Z","date_updated":"2021-01-12T06:59:41Z","author":[{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Farrell, Brendan","first_name":"Brendan","last_name":"Farrell"}],"publist_id":"4107","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.0031"}],"oa":1,"external_id":{"arxiv":["1207.0031"]},"language":[{"iso":"eng"}],"doi":"10.1007/s10955-013-0807-8","month":"07","intvolume":" 152","title":"Local eigenvalue density for general MANOVA matrices","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2782","oa_version":"Preprint","type":"journal_article","issue":"6","abstract":[{"text":"We consider random n×n matrices of the form (XX*+YY*)^{-1/2}YY*(XX*+YY*)^{-1/2}, where X and Y have independent entries with zero mean and variance one. These matrices are the natural generalization of the Gaussian case, which are known as MANOVA matrices and which have joint eigenvalue density given by the third classical ensemble, the Jacobi ensemble. We show that, away from the spectral edge, the eigenvalue density converges to the limiting density of the Jacobi ensemble even on the shortest possible scales of order 1/n (up to log n factors). This result is the analogue of the local Wigner semicircle law and the local Marchenko-Pastur law for general MANOVA matrices.","lang":"eng"}],"page":"1003 - 1032","citation":{"mla":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” Journal of Statistical Physics, vol. 152, no. 6, Springer, 2013, pp. 1003–32, doi:10.1007/s10955-013-0807-8.","short":"L. Erdös, B. Farrell, Journal of Statistical Physics 152 (2013) 1003–1032.","chicago":"Erdös, László, and Brendan Farrell. “Local Eigenvalue Density for General MANOVA Matrices.” Journal of Statistical Physics. Springer, 2013. https://doi.org/10.1007/s10955-013-0807-8.","ama":"Erdös L, Farrell B. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 2013;152(6):1003-1032. doi:10.1007/s10955-013-0807-8","ista":"Erdös L, Farrell B. 2013. Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. 152(6), 1003–1032.","ieee":"L. Erdös and B. Farrell, “Local eigenvalue density for general MANOVA matrices,” Journal of Statistical Physics, vol. 152, no. 6. Springer, pp. 1003–1032, 2013.","apa":"Erdös, L., & Farrell, B. (2013). Local eigenvalue density for general MANOVA matrices. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-013-0807-8"},"publication":"Journal of Statistical Physics","date_published":"2013-07-18T00:00:00Z","scopus_import":1,"day":"18"},{"volume":41,"date_updated":"2021-01-12T06:59:41Z","date_created":"2018-12-11T11:59:34Z","author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"László Erdös"},{"full_name":"Knowles, Antti","last_name":"Knowles","first_name":"Antti"},{"last_name":"Yau","first_name":"Horng","full_name":"Yau, Horng-Tzer"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"intvolume":" 41","publisher":"Institute of Mathematical Statistics","publication_status":"published","title":"Spectral statistics of Erdős-Rényi graphs I: Local semicircle law","status":"public","year":"2013","_id":"2781","extern":1,"issue":"3 B","publist_id":"4109","abstract":[{"text":"We consider the ensemble of adjacency matrices of Erdős-Rényi random graphs, that is, graphs on N vertices where every edge is chosen independently and with probability p = p(N). We rescale the matrix so that its bulk eigenvalues are of order one. We prove that, as long as pN→∞(with a speed at least logarithmic in N), the density of eigenvalues of the Erdős-Rényi ensemble is given by the Wigner semicircle law for spectral windows of length larger than N-1 (up to logarithmic corrections). As a consequence, all eigenvectors are proved to be completely delocalized in the sense that the ℓ∞-norms of the ℓ2-normalized eigenvectors are at most of order N-1/2 with a very high probability. The estimates in this paper will be used in the companion paper [Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues (2011) Preprint] to prove the universality of eigenvalue distributions both in the bulk and at the spectral edges under the further restriction that pN »N2/3.","lang":"eng"}],"type":"journal_article","date_published":"2013-05-01T00:00:00Z","doi":"10.1214/11-AOP734","page":"2279 - 2375","quality_controlled":0,"main_file_link":[{"url":"http://arxiv.org/abs/1103.1919","open_access":"1"}],"citation":{"ieee":"L. Erdös, A. Knowles, H. Yau, and J. Yin, “Spectral statistics of Erdős-Rényi graphs I: Local semicircle law,” Annals of Probability, vol. 41, no. 3 B. Institute of Mathematical Statistics, pp. 2279–2375, 2013.","apa":"Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/11-AOP734","ista":"Erdös L, Knowles A, Yau H, Yin J. 2013. Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. 41(3 B), 2279–2375.","ama":"Erdös L, Knowles A, Yau H, Yin J. Spectral statistics of Erdős-Rényi graphs I: Local semicircle law. Annals of Probability. 2013;41(3 B):2279-2375. doi:10.1214/11-AOP734","chicago":"Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Spectral Statistics of Erdős-Rényi Graphs I: Local Semicircle Law.” Annals of Probability. Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/11-AOP734.","short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Annals of Probability 41 (2013) 2279–2375.","mla":"Erdös, László, et al. “Spectral Statistics of Erdős-Rényi Graphs I: Local Semicircle Law.” Annals of Probability, vol. 41, no. 3 B, Institute of Mathematical Statistics, 2013, pp. 2279–375, doi:10.1214/11-AOP734."},"oa":1,"publication":"Annals of Probability","month":"05","day":"01"},{"publist_id":"4110","issue":"8","abstract":[{"lang":"eng","text":"We consider a general class of random matrices whose entries are centred random variables, independent up to a symmetry constraint. We establish precise high-probability bounds on the averages of arbitrary monomials in the resolvent matrix entries. Our results generalize the previous results of Erdős et al. (Ann Probab, arXiv:1103.1919, 2013; Commun Math Phys, arXiv:1103.3869, 2013; J Combin 1(2):15-85, 2011) which constituted a key step in the proof of the local semicircle law with optimal error bound in mean-field random matrix models. Our bounds apply to random band matrices and improve previous estimates from order 2 to order 4 in the cases relevant to applications. In particular, they lead to a proof of the diffusion approximation for the magnitude of the resolvent of random band matrices. This, in turn, implies new delocalization bounds on the eigenvectors. The applications are presented in a separate paper (Erdős et al., arXiv:1205.5669, 2013)."}],"extern":1,"type":"journal_article","author":[{"full_name":"László Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"first_name":"Antti","last_name":"Knowles","full_name":"Knowles, Antti"},{"first_name":"Horng","last_name":"Yau","full_name":"Yau, Horng-Tzer"}],"volume":14,"date_created":"2018-12-11T11:59:33Z","date_updated":"2021-01-12T06:59:40Z","year":"2013","_id":"2780","intvolume":" 14","publisher":"Birkhäuser","title":"Averaging fluctuations in resolvents of random band matrices","status":"public","publication_status":"published","day":"01","month":"12","date_published":"2013-12-01T00:00:00Z","doi":"10.1007/s00023-013-0235-y","oa":1,"citation":{"mla":"Erdös, László, et al. “Averaging Fluctuations in Resolvents of Random Band Matrices.” Annales Henri Poincare, vol. 14, no. 8, Birkhäuser, 2013, pp. 1837–926, doi:10.1007/s00023-013-0235-y.","short":"L. Erdös, A. Knowles, H. Yau, Annales Henri Poincare 14 (2013) 1837–1926.","chicago":"Erdös, László, Antti Knowles, and Horng Yau. “Averaging Fluctuations in Resolvents of Random Band Matrices.” Annales Henri Poincare. Birkhäuser, 2013. https://doi.org/10.1007/s00023-013-0235-y.","ama":"Erdös L, Knowles A, Yau H. Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. 2013;14(8):1837-1926. doi:10.1007/s00023-013-0235-y","ista":"Erdös L, Knowles A, Yau H. 2013. Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. 14(8), 1837–1926.","apa":"Erdös, L., Knowles, A., & Yau, H. (2013). Averaging fluctuations in resolvents of random band matrices. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-013-0235-y","ieee":"L. Erdös, A. Knowles, and H. Yau, “Averaging fluctuations in resolvents of random band matrices,” Annales Henri Poincare, vol. 14, no. 8. Birkhäuser, pp. 1837–1926, 2013."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.5664"}],"publication":"Annales Henri Poincare","page":"1837 - 1926","quality_controlled":0},{"scopus_import":1,"day":"01","has_accepted_license":"1","publication":"45th Annual ACM Symposium on theory of computing","citation":{"ama":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. Extending continuous maps: Polynomiality and undecidability. In: 45th Annual ACM Symposium on Theory of Computing. ACM; 2013:595-604. doi:10.1145/2488608.2488683","ista":"Čadek M, Krcál M, Matoušek J, Vokřínek L, Wagner U. 2013. Extending continuous maps: Polynomiality and undecidability. 45th Annual ACM Symposium on theory of computing. STOC: Symposium on the Theory of Computing, 595–604.","apa":"Čadek, M., Krcál, M., Matoušek, J., Vokřínek, L., & Wagner, U. (2013). Extending continuous maps: Polynomiality and undecidability. In 45th Annual ACM Symposium on theory of computing (pp. 595–604). Palo Alto, CA, United States: ACM. https://doi.org/10.1145/2488608.2488683","ieee":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, and U. Wagner, “Extending continuous maps: Polynomiality and undecidability,” in 45th Annual ACM Symposium on theory of computing, Palo Alto, CA, United States, 2013, pp. 595–604.","mla":"Čadek, Martin, et al. “Extending Continuous Maps: Polynomiality and Undecidability.” 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604, doi:10.1145/2488608.2488683.","short":"M. Čadek, M. Krcál, J. Matoušek, L. Vokřínek, U. Wagner, in:, 45th Annual ACM Symposium on Theory of Computing, ACM, 2013, pp. 595–604.","chicago":"Čadek, Martin, Marek Krcál, Jiří Matoušek, Lukáš Vokřínek, and Uli Wagner. “Extending Continuous Maps: Polynomiality and Undecidability.” In 45th Annual ACM Symposium on Theory of Computing, 595–604. ACM, 2013. https://doi.org/10.1145/2488608.2488683."},"page":"595 - 604","date_published":"2013-06-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"We consider several basic problems of algebraic topology, with connections to combinatorial and geometric questions, from the point of view of computational complexity. The extension problem asks, given topological spaces X; Y , a subspace A ⊆ X, and a (continuous) map f : A → Y , whether f can be extended to a map X → Y . For computational purposes, we assume that X and Y are represented as finite simplicial complexes, A is a subcomplex of X, and f is given as a simplicial map. In this generality the problem is undecidable, as follows from Novikov's result from the 1950s on uncomputability of the fundamental group π1(Y ). We thus study the problem under the assumption that, for some k ≥ 2, Y is (k - 1)-connected; informally, this means that Y has \\no holes up to dimension k-1" (a basic example of such a Y is the sphere Sk). We prove that, on the one hand, this problem is still undecidable for dimX = 2k. On the other hand, for every fixed k ≥ 2, we obtain an algorithm that solves the extension problem in polynomial time assuming Y (k - 1)-connected and dimX ≤ 2k - 1. For dimX ≤ 2k - 2, the algorithm also provides a classification of all extensions up to homotopy (continuous deformation). This relies on results of our SODA 2012 paper, and the main new ingredient is a machinery of objects with polynomial-time homology, which is a polynomial-time analog of objects with effective homology developed earlier by Sergeraert et al. We also consider the computation of the higher homotopy groups πk(Y ), k ≥ 2, for a 1-connected Y . Their computability was established by Brown in 1957; we show that πk(Y ) can be computed in polynomial time for every fixed k ≥ 2. On the other hand, Anick proved in 1989 that computing πk(Y ) is #P-hard if k is a part of input, where Y is a cell complex with certain rather compact encoding. We strengthen his result to #P-hardness for Y given as a simplicial complex. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2807","title":"Extending continuous maps: Polynomiality and undecidability","ddc":["510"],"status":"public","pubrep_id":"533","file":[{"file_id":"5081","relation":"main_file","checksum":"06c2ce5c1135fbc1f71ca15eeb242dcf","date_updated":"2020-07-14T12:45:48Z","date_created":"2018-12-12T10:14:29Z","access_level":"open_access","file_name":"IST-2016-533-v1+1_Extending_continuous_maps_polynomiality_and_undecidability.pdf","creator":"system","file_size":447945,"content_type":"application/pdf"}],"oa_version":"Submitted Version","month":"06","oa":1,"quality_controlled":"1","conference":{"end_date":"2013-06-04","start_date":"2013-06-01","location":"Palo Alto, CA, United States","name":"STOC: Symposium on the Theory of Computing"},"doi":"10.1145/2488608.2488683","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:48Z","publist_id":"4078","year":"2013","publication_status":"published","publisher":"ACM","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"author":[{"full_name":"Čadek, Martin","last_name":"Čadek","first_name":"Martin"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","first_name":"Marek","full_name":"Krcál, Marek"},{"last_name":"Matoušek","first_name":"Jiří","full_name":"Matoušek, Jiří"},{"full_name":"Vokřínek, Lukáš","last_name":"Vokřínek","first_name":"Lukáš"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"date_updated":"2021-01-12T06:59:51Z","date_created":"2018-12-11T11:59:42Z"},{"_id":"2808","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 162","title":"The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs."}],"citation":{"ama":"Landberg K, Pederson E, Viaene T, et al. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. 2013;162(3):1406-1419. doi:10.1104/pp.113.214023","ieee":"K. Landberg et al., “The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain,” Plant Physiology, vol. 162, no. 3. American Society of Plant Biologists, pp. 1406–1419, 2013.","apa":"Landberg, K., Pederson, E., Viaene, T., Bozorg, B., Friml, J., Jönsson, H., … Sundberg, E. (2013). The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.113.214023","ista":"Landberg K, Pederson E, Viaene T, Bozorg B, Friml J, Jönsson H, Thelander M, Sundberg E. 2013. The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain. Plant Physiology. 162(3), 1406–1419.","short":"K. Landberg, E. Pederson, T. Viaene, B. Bozorg, J. Friml, H. Jönsson, M. Thelander, E. Sundberg, Plant Physiology 162 (2013) 1406–1419.","mla":"Landberg, Katarina, et al. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” Plant Physiology, vol. 162, no. 3, American Society of Plant Biologists, 2013, pp. 1406–19, doi:10.1104/pp.113.214023.","chicago":"Landberg, Katarina, Eric Pederson, Tom Viaene, Behruz Bozorg, Jiří Friml, Henrik Jönsson, Mattias Thelander, and Eva Sundberg. “The Moss Physcomitrella Patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain.” Plant Physiology. American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.214023."},"publication":"Plant Physiology","page":"1406 - 1419","date_published":"2013-07-03T00:00:00Z","scopus_import":1,"day":"03","pmid":1,"year":"2013","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","publication_status":"published","author":[{"last_name":"Landberg","first_name":"Katarina","full_name":"Landberg, Katarina"},{"full_name":"Pederson, Eric","last_name":"Pederson","first_name":"Eric"},{"full_name":"Viaene, Tom","first_name":"Tom","last_name":"Viaene"},{"full_name":"Bozorg, Behruz","last_name":"Bozorg","first_name":"Behruz"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Henrik","last_name":"Jönsson","full_name":"Jönsson, Henrik"},{"full_name":"Thelander, Mattias","first_name":"Mattias","last_name":"Thelander"},{"full_name":"Sundberg, Eva","first_name":"Eva","last_name":"Sundberg"}],"volume":162,"date_updated":"2021-01-12T06:59:51Z","date_created":"2018-12-11T11:59:42Z","publist_id":"4079","external_id":{"pmid":["23669745"]},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3707547/","open_access":"1"}],"quality_controlled":"1","doi":"10.1104/pp.113.214023","language":[{"iso":"eng"}],"month":"07"},{"_id":"2806","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Institute of Physics","intvolume":" 84","department":[{"_id":"BjHo"}],"title":"High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects","status":"public","publication_status":"published","author":[{"last_name":"Avila","first_name":"Kerstin","full_name":"Avila, Kerstin"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"oa_version":"None","volume":84,"date_updated":"2021-01-12T06:59:50Z","date_created":"2018-12-11T11:59:42Z","type":"journal_article","article_number":"065106","publist_id":"4081","issue":"6","abstract":[{"lang":"eng","text":"A novel Taylor-Couette system has been constructed for investigations of transitional as well as high Reynolds number turbulent flows in very large aspect ratios. The flexibility of the setup enables studies of a variety of problems regarding hydrodynamic instabilities and turbulence in rotating flows. The inner and outer cylinders and the top and bottom endplates can be rotated independently with rotation rates of up to 30 Hz, thereby covering five orders of magnitude in Reynolds numbers (Re = 101-106). The radius ratio can be easily changed, the highest realized one is η = 0.98 corresponding to an aspect ratio of 260 gap width in the vertical and 300 in the azimuthal direction. For η < 0.98 the aspect ratio can be dynamically changed during measurements and complete transparency in the radial direction over the full length of the cylinders is provided by the usage of a precision glass inner cylinder. The temperatures of both cylinders are controlled independently. Overall this apparatus combines an unmatched variety in geometry, rotation rates, and temperatures, which is provided by a sophisticated high-precision bearing system. Possible applications are accurate studies of the onset of turbulence and spatio-temporal intermittent flow patterns in very large domains, transport processes of turbulence at high Re, the stability of Keplerian flows for different boundary conditions, and studies of baroclinic instabilities."}],"citation":{"short":"K. Avila, B. Hof, Review of Scientific Instruments 84 (2013).","mla":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” Review of Scientific Instruments, vol. 84, no. 6, 065106, American Institute of Physics, 2013, doi:10.1063/1.4807704.","chicago":"Avila, Kerstin, and Björn Hof. “High-Precision Taylor-Couette Experiment to Study Subcritical Transitions and the Role of Boundary Conditions and Size Effects.” Review of Scientific Instruments. American Institute of Physics, 2013. https://doi.org/10.1063/1.4807704.","ama":"Avila K, Hof B. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. 2013;84(6). doi:10.1063/1.4807704","apa":"Avila, K., & Hof, B. (2013). High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. American Institute of Physics. https://doi.org/10.1063/1.4807704","ieee":"K. Avila and B. Hof, “High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects,” Review of Scientific Instruments, vol. 84, no. 6. American Institute of Physics, 2013.","ista":"Avila K, Hof B. 2013. High-precision Taylor-Couette experiment to study subcritical transitions and the role of boundary conditions and size effects. Review of Scientific Instruments. 84(6), 065106."},"publication":"Review of Scientific Instruments","quality_controlled":"1","doi":"10.1063/1.4807704","date_published":"2013-06-06T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"06","month":"06"},{"_id":"2805","year":"2013","title":"Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow","status":"public","publication_status":"published","publisher":"Cambridge University Press","intvolume":" 723","author":[{"full_name":"Holzner, Markus","last_name":"Holzner","first_name":"Markus"},{"first_name":"Baofang","last_name":"Song","full_name":"Song, Baofang"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Björn Hof"}],"date_created":"2018-12-11T11:59:41Z","date_updated":"2021-01-12T06:59:50Z","volume":723,"type":"journal_article","abstract":[{"lang":"eng","text":"Transition in shear flows is characterized by localized turbulent regions embedded in the surrounding laminar flow. These so-called turbulent spots or puffs are observed in a variety of shear flows and in certain Reynolds-number regimes, and they are advected by the flow while keeping their characteristic length. We show here for the case of pipe flow that this seemingly passive advection of turbulent puffs involves continuous entrainment and relaminarization of laminar and turbulent fluid across strongly convoluted interfaces. Surprisingly, interface areas are almost two orders of magnitude larger than the pipe cross-section, while local entrainment velocities are much smaller than the mean speed. Even though these velocities were shown to be small and proportional to the Kolmogorov velocity scale (in agreement with a prediction by Corrsin) in a flow without mean shear before, we find that, in pipe flow, local entrainment velocities are about an order of magnitude smaller than this scale. The Lagrangian method used to study the dynamics of the laminar-turbulent interfaces allows accurate determination of the leading and trailing edge speeds. However, to resolve the highly complex interface dynamics requires much higher numerical resolutions than for ordinary turbulent flows. This method also reveals that the volume flux across the leading edge has the same radial dependence but the opposite sign as that across the trailing edge, and it is this symmetry that is responsible for the puff shape remaining constant."}],"publist_id":"4084","extern":1,"publication":"Journal of Fluid Mechanics","citation":{"chicago":"Holzner, Markus, Baofang Song, Marc Avila, and Björn Hof. “Lagrangian Approach to Laminar-Turbulent Interfaces in Transitional Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2013. https://doi.org/10.1017/jfm.2013.127.","short":"M. Holzner, B. Song, M. Avila, B. Hof, Journal of Fluid Mechanics 723 (2013) 140–162.","mla":"Holzner, Markus, et al. “Lagrangian Approach to Laminar-Turbulent Interfaces in Transitional Pipe Flow.” Journal of Fluid Mechanics, vol. 723, Cambridge University Press, 2013, pp. 140–62, doi:10.1017/jfm.2013.127.","apa":"Holzner, M., Song, B., Avila, M., & Hof, B. (2013). Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2013.127","ieee":"M. Holzner, B. Song, M. Avila, and B. Hof, “Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow,” Journal of Fluid Mechanics, vol. 723. Cambridge University Press, pp. 140–162, 2013.","ista":"Holzner M, Song B, Avila M, Hof B. 2013. Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. 723, 140–162.","ama":"Holzner M, Song B, Avila M, Hof B. Lagrangian approach to laminar-turbulent interfaces in transitional pipe flow. Journal of Fluid Mechanics. 2013;723:140-162. doi:10.1017/jfm.2013.127"},"quality_controlled":0,"page":"140 - 162","date_published":"2013-05-01T00:00:00Z","doi":"10.1017/jfm.2013.127","day":"01","month":"05"},{"date_published":"2013-06-27T00:00:00Z","citation":{"chicago":"Vos, Marjon de, Frank Poelwijk, Nico Battich, Joseph Ndika, and Sander Tans. “Environmental Dependence of Genetic Constraint.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003580.","mla":"de Vos, Marjon, et al. “Environmental Dependence of Genetic Constraint.” PLoS Genetics, vol. 9, no. 6, e1003580, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003580.","short":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, S. Tans, PLoS Genetics 9 (2013).","ista":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. 2013. Environmental dependence of genetic constraint. PLoS Genetics. 9(6), e1003580.","apa":"de Vos, M., Poelwijk, F., Battich, N., Ndika, J., & Tans, S. (2013). Environmental dependence of genetic constraint. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003580","ieee":"M. de Vos, F. Poelwijk, N. Battich, J. Ndika, and S. Tans, “Environmental dependence of genetic constraint,” PLoS Genetics, vol. 9, no. 6. Public Library of Science, 2013.","ama":"de Vos M, Poelwijk F, Battich N, Ndika J, Tans S. Environmental dependence of genetic constraint. PLoS Genetics. 2013;9(6). doi:10.1371/journal.pgen.1003580"},"publication":"PLoS Genetics","has_accepted_license":"1","day":"27","scopus_import":1,"pubrep_id":"412","oa_version":"Published Version","file":[{"checksum":"7a4736dd80496d29ff6908b6f2329b4e","date_updated":"2020-07-14T12:45:48Z","date_created":"2018-12-12T10:08:51Z","relation":"main_file","file_id":"4713","file_size":474655,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-412-v1+1_journal.pgen.1003580.pdf"}],"_id":"2810","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","title":"Environmental dependence of genetic constraint","ddc":["570"],"status":"public","issue":"6","abstract":[{"lang":"eng","text":"The epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. Here we investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We have systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how the interactions can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and affects the interpretation of phylogenetic data."}],"type":"journal_article","doi":"10.1371/journal.pgen.1003580","language":[{"iso":"eng"}],"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,"quality_controlled":"1","month":"06","author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","last_name":"De Vos","first_name":"Marjon","full_name":"De Vos, Marjon"},{"first_name":"Frank","last_name":"Poelwijk","full_name":"Poelwijk, Frank"},{"first_name":"Nico","last_name":"Battich","full_name":"Battich, Nico"},{"full_name":"Ndika, Joseph","first_name":"Joseph","last_name":"Ndika"},{"last_name":"Tans","first_name":"Sander","full_name":"Tans, Sander"}],"volume":9,"date_updated":"2021-01-12T06:59:52Z","date_created":"2018-12-11T11:59:43Z","year":"2013","department":[{"_id":"ToBo"}],"publisher":"Public Library of Science","publication_status":"published","publist_id":"4075","file_date_updated":"2020-07-14T12:45:48Z","article_number":"e1003580"},{"type":"journal_article","abstract":[{"text":"We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing "reset" action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies. We also discuss the memory requirement for deterministic strategies and extensions of our results to other models, such as pushdown systems and timed systems.","lang":"eng"}],"issue":"2","title":"The complexity of coverage","status":"public","intvolume":" 24","_id":"2814","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":1,"day":"01","page":"165 - 185","publication":"International Journal of Foundations of Computer Science","citation":{"ama":"Chatterjee K, Alfaro L, Majumdar R. The complexity of coverage. International Journal of Foundations of Computer Science. 2013;24(2):165-185. doi:10.1142/S0129054113400066","ista":"Chatterjee K, Alfaro L, Majumdar R. 2013. The complexity of coverage. International Journal of Foundations of Computer Science. 24(2), 165–185.","ieee":"K. Chatterjee, L. Alfaro, and R. Majumdar, “The complexity of coverage,” International Journal of Foundations of Computer Science, vol. 24, no. 2. World Scientific Publishing, pp. 165–185, 2013.","apa":"Chatterjee, K., Alfaro, L., & Majumdar, R. (2013). The complexity of coverage. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054113400066","mla":"Chatterjee, Krishnendu, et al. “The Complexity of Coverage.” International Journal of Foundations of Computer Science, vol. 24, no. 2, World Scientific Publishing, 2013, pp. 165–85, doi:10.1142/S0129054113400066.","short":"K. Chatterjee, L. Alfaro, R. Majumdar, International Journal of Foundations of Computer Science 24 (2013) 165–185.","chicago":"Chatterjee, Krishnendu, Luca Alfaro, and Ritankar Majumdar. “The Complexity of Coverage.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2013. https://doi.org/10.1142/S0129054113400066."},"date_published":"2013-02-01T00:00:00Z","publist_id":"4070","ec_funded":1,"publication_status":"published","publisher":"World Scientific Publishing","department":[{"_id":"KrCh"}],"year":"2013","date_created":"2018-12-11T11:59:44Z","date_updated":"2021-01-12T06:59:54Z","volume":24,"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Alfaro","first_name":"Luca","full_name":"Alfaro, Luca"},{"full_name":"Majumdar, Ritankar","last_name":"Majumdar","first_name":"Ritankar"}],"month":"02","quality_controlled":"1","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/0804.4525"}],"external_id":{"arxiv":["0804.4525"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1142/S0129054113400066"},{"title":"Nature of laminar-turbulence intermittency in shear flows","status":"public","intvolume":" 87","_id":"2811","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers.","lang":"eng"}],"issue":"6","publication":"Physical Review E","citation":{"chicago":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” Physical Review E. American Institute of Physics, 2013. https://doi.org/10.1103/PhysRevE.87.063012.","mla":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” Physical Review E, vol. 87, no. 6, 063012, American Institute of Physics, 2013, doi:10.1103/PhysRevE.87.063012.","short":"M. Avila, B. Hof, Physical Review E 87 (2013).","ista":"Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 063012.","ieee":"M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear flows,” Physical Review E, vol. 87, no. 6. American Institute of Physics, 2013.","apa":"Avila, M., & Hof, B. (2013). Nature of laminar-turbulence intermittency in shear flows. Physical Review E. American Institute of Physics. https://doi.org/10.1103/PhysRevE.87.063012","ama":"Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 2013;87(6). doi:10.1103/PhysRevE.87.063012"},"date_published":"2013-06-18T00:00:00Z","scopus_import":1,"day":"18","publication_status":"published","publisher":"American Institute of Physics","department":[{"_id":"BjHo"}],"year":"2013","date_updated":"2021-01-12T06:59:53Z","date_created":"2018-12-11T11:59:43Z","volume":87,"author":[{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"article_number":"063012","ec_funded":1,"publist_id":"4074","quality_controlled":"1","project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"}],"external_id":{"arxiv":["1306.5890"]},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1306.5890","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.87.063012","month":"06"},{"abstract":[{"lang":"eng","text":"Turbulence is ubiquitous in nature, yet even for the case of ordinary Newtonian fluids like water, our understanding of this phenomenon is limited. Many liquids of practical importance are more complicated (e.g., blood, polymer melts, paints), however; they exhibit elastic as well as viscous characteristics, and the relation between stress and strain is nonlinear. We demonstrate here for a model system of such complex fluids that at high shear rates, turbulence is not simply modified as previously believed but is suppressed and replaced by a different type of disordered motion, elasto-inertial turbulence. Elasto-inertial turbulence is found to occur at much lower Reynolds numbers than Newtonian turbulence, and the dynamical properties differ significantly. The friction scaling observed coincides with the so-called "maximum drag reduction" asymptote, which is exhibited by a wide range of viscoelastic fluids."}],"issue":"26","type":"journal_article","oa_version":"Submitted Version","_id":"2813","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Elasto-inertial turbulence","intvolume":" 110","day":"25","scopus_import":1,"date_published":"2013-06-25T00:00:00Z","publication":"PNAS","citation":{"chicago":"Samanta, Devranjan, Yves Dubief, Markus Holzner, Christof Schäfer, Alexander Morozov, Christian Wagner, and Björn Hof. “Elasto-Inertial Turbulence.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1219666110.","short":"D. Samanta, Y. Dubief, M. Holzner, C. Schäfer, A. Morozov, C. Wagner, B. Hof, PNAS 110 (2013) 10557–10562.","mla":"Samanta, Devranjan, et al. “Elasto-Inertial Turbulence.” PNAS, vol. 110, no. 26, National Academy of Sciences, 2013, pp. 10557–62, doi:10.1073/pnas.1219666110.","ieee":"D. Samanta et al., “Elasto-inertial turbulence,” PNAS, vol. 110, no. 26. National Academy of Sciences, pp. 10557–10562, 2013.","apa":"Samanta, D., Dubief, Y., Holzner, M., Schäfer, C., Morozov, A., Wagner, C., & Hof, B. (2013). Elasto-inertial turbulence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1219666110","ista":"Samanta D, Dubief Y, Holzner M, Schäfer C, Morozov A, Wagner C, Hof B. 2013. Elasto-inertial turbulence. PNAS. 110(26), 10557–10562.","ama":"Samanta D, Dubief Y, Holzner M, et al. Elasto-inertial turbulence. PNAS. 2013;110(26):10557-10562. doi:10.1073/pnas.1219666110"},"page":"10557 - 10562","publist_id":"4073","author":[{"last_name":"Samanta","first_name":"Devranjan","full_name":"Samanta, Devranjan"},{"full_name":"Dubief, Yves","first_name":"Yves","last_name":"Dubief"},{"full_name":"Holzner, Markus","last_name":"Holzner","first_name":"Markus"},{"full_name":"Schäfer, Christof","first_name":"Christof","last_name":"Schäfer"},{"full_name":"Morozov, Alexander","first_name":"Alexander","last_name":"Morozov"},{"last_name":"Wagner","first_name":"Christian","full_name":"Wagner, Christian"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"date_updated":"2021-01-12T06:59:54Z","date_created":"2018-12-11T11:59:44Z","volume":110,"year":"2013","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"BjHo"}],"month":"06","doi":"10.1073/pnas.1219666110","language":[{"iso":"eng"}],"external_id":{"pmid":["23757498"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696777/"}],"quality_controlled":"1"},{"scopus_import":1,"month":"06","day":"01","publication":"Proceedings of the 29th annual symposium on Computational Geometry","oa":1,"main_file_link":[{"url":"http://hal.archives-ouvertes.fr/hal-00833791/","open_access":"1"}],"citation":{"ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. In: Proceedings of the 29th Annual Symposium on Computational Geometry. ACM; 2013:117-125. doi:10.1145/2462356.2462373","ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2013. Homological reconstruction and simplification in R3. Proceedings of the 29th annual symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 117–125.","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” in Proceedings of the 29th annual symposium on Computational Geometry, Rio de Janeiro, Brazil, 2013, pp. 117–125.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2013). Homological reconstruction and simplification in R3. In Proceedings of the 29th annual symposium on Computational Geometry (pp. 117–125). Rio de Janeiro, Brazil: ACM. https://doi.org/10.1145/2462356.2462373","mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–25, doi:10.1145/2462356.2462373.","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, in:, Proceedings of the 29th Annual Symposium on Computational Geometry, ACM, 2013, pp. 117–125.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” In Proceedings of the 29th Annual Symposium on Computational Geometry, 117–25. ACM, 2013. https://doi.org/10.1145/2462356.2462373."},"quality_controlled":"1","page":"117 - 125","conference":{"location":"Rio de Janeiro, Brazil","start_date":"2013-06-17","end_date":"2013-06-20","name":"SoCG: Symposium on Computational Geometry"},"doi":"10.1145/2462356.2462373","date_published":"2013-06-01T00:00:00Z","language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K, L) can be realized as the homology H* (X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in ℝ3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.","lang":"eng"}],"publist_id":"4072","acknowledgement":"Some of the authors were partially supported by the GIGA ANR grant (contract ANR-09-BLAN-0331-01) and the European project CG-Learning (contract 255827).","_id":"2812","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","status":"public","title":"Homological reconstruction and simplification in R3","publication_status":"published","publisher":"ACM","department":[{"_id":"HeEd"}],"author":[{"first_name":"Dominique","last_name":"Attali","full_name":"Attali, Dominique"},{"orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","last_name":"Bauer","first_name":"Ulrich","full_name":"Bauer, Ulrich"},{"last_name":"Devillers","first_name":"Olivier","full_name":"Devillers, Olivier"},{"first_name":"Marc","last_name":"Glisse","full_name":"Glisse, Marc"},{"full_name":"Lieutier, André","first_name":"André","last_name":"Lieutier"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"1805"}]},"date_updated":"2023-02-23T10:15:15Z","date_created":"2018-12-11T11:59:44Z","oa_version":"Submitted Version"},{"intvolume":" 334","ddc":["000"],"title":"Density games","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2817","file":[{"creator":"system","content_type":"application/pdf","file_size":834604,"access_level":"open_access","file_name":"IST-2016-400-v1+1_1-s2.0-S0022519313002609-main.pdf","checksum":"3c29059ab03a4b8f97a07646b817ddbb","date_created":"2018-12-12T10:14:54Z","date_updated":"2020-07-14T12:45:49Z","file_id":"5110","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"400","type":"journal_article","abstract":[{"text":"The basic idea of evolutionary game theory is that payoff determines reproductive rate. Successful individuals have a higher payoff and produce more offspring. But in evolutionary and ecological situations there is not only reproductive rate but also carrying capacity. Individuals may differ in their exposure to density limiting effects. Here we explore an alternative approach to evolutionary game theory by assuming that the payoff from the game determines the carrying capacity of individual phenotypes. Successful strategies are less affected by density limitation (crowding) and reach higher equilibrium abundance. We demonstrate similarities and differences between our framework and the standard replicator equation. Our equation is defined on the positive orthant, instead of the simplex, but has the same equilibrium points as the replicator equation. Linear stability analysis produces the classical conditions for asymptotic stability of pure strategies, but the stability properties of internal equilibria can differ in the two frameworks. For example, in a two-strategy game with an internal equilibrium that is always stable under the replicator equation, the corresponding equilibrium can be unstable in the new framework resulting in a limit cycle.","lang":"eng"}],"page":"26 - 34","citation":{"mla":"Novak, Sebastian, et al. “Density Games.” Journal of Theoretical Biology, vol. 334, Elsevier, 2013, pp. 26–34, doi:10.1016/j.jtbi.2013.05.029.","short":"S. Novak, K. Chatterjee, M. Nowak, Journal of Theoretical Biology 334 (2013) 26–34.","chicago":"Novak, Sebastian, Krishnendu Chatterjee, and Martin Nowak. “Density Games.” Journal of Theoretical Biology. Elsevier, 2013. https://doi.org/10.1016/j.jtbi.2013.05.029.","ama":"Novak S, Chatterjee K, Nowak M. Density games. Journal of Theoretical Biology. 2013;334:26-34. doi:10.1016/j.jtbi.2013.05.029","ista":"Novak S, Chatterjee K, Nowak M. 2013. Density games. Journal of Theoretical Biology. 334, 26–34.","apa":"Novak, S., Chatterjee, K., & Nowak, M. (2013). Density games. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2013.05.029","ieee":"S. Novak, K. Chatterjee, and M. Nowak, “Density games,” Journal of Theoretical Biology, vol. 334. Elsevier, pp. 26–34, 2013."},"publication":"Journal of Theoretical Biology","date_published":"2013-10-07T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"07","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"publisher":"Elsevier","publication_status":"published","year":"2013","volume":334,"date_updated":"2021-01-12T06:59:55Z","date_created":"2018-12-11T11:59:45Z","author":[{"last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"ec_funded":1,"publist_id":"3984","file_date_updated":"2020-07-14T12:45:49Z","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"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":"10.1016/j.jtbi.2013.05.029","month":"10"},{"publist_id":"3982","ec_funded":1,"year":"2013","acknowledgement":"This work has been financially supported in part by the European Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract # 270180 (NOP-TILUS); 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); and the Microsoft faculty fellows award","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}],"date_created":"2018-12-11T11:59:46Z","date_updated":"2021-01-12T06:59:56Z","volume":1,"month":"04","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1212.6556"}],"oa":1,"quality_controlled":"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","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"HSCC: Hybrid Systems - Computation and Control","location":"Philadelphia, PA USA","start_date":"2013-04-08","end_date":"2013-04-11"},"doi":"10.1145/2461328.2461370","language":[{"iso":"eng"}],"type":"conference","abstract":[{"lang":"eng","text":"We introduce quantatitive timed refinement metrics and quantitative timed simulation functions, incorporating zenoness checks, for timed systems. These functions assign positive real numbers between zero and infinity which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximum timing mismatch that can arise, (2) the "steady-state" maximum timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation functions to within any desired degree of accuracy. In order to compute the values of the quantitative simulation functions, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives for player 1, and then use these algorithms to compute the values of the quantitative timed simulation functions. "}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2819","title":"Quantitative timed simulation functions and refinement metrics for real-time systems","status":"public","intvolume":" 1","oa_version":"Preprint","scopus_import":1,"day":"01","publication":"Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control","citation":{"ama":"Chatterjee K, Prabhu V. Quantitative timed simulation functions and refinement metrics for real-time systems. In: Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. Vol 1. Springer; 2013:273-282. doi:10.1145/2461328.2461370","ieee":"K. Chatterjee and V. Prabhu, “Quantitative timed simulation functions and refinement metrics for real-time systems,” in Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Philadelphia, PA USA, 2013, vol. 1, pp. 273–282.","apa":"Chatterjee, K., & Prabhu, V. (2013). Quantitative timed simulation functions and refinement metrics for real-time systems. In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control (Vol. 1, pp. 273–282). Philadelphia, PA USA: Springer. https://doi.org/10.1145/2461328.2461370","ista":"Chatterjee K, Prabhu V. 2013. Quantitative timed simulation functions and refinement metrics for real-time systems. Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control vol. 1, 273–282.","short":"K. Chatterjee, V. Prabhu, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, Springer, 2013, pp. 273–282.","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, vol. 1, Springer, 2013, pp. 273–82, doi:10.1145/2461328.2461370.","chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Timed Simulation Functions and Refinement Metrics for Real-Time Systems.” In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, 1:273–82. Springer, 2013. https://doi.org/10.1145/2461328.2461370."},"page":"273 - 282","date_published":"2013-04-01T00:00:00Z"},{"abstract":[{"text":"Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus.","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Preprint","_id":"2818","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Learning quadratic receptive fields from neural responses to natural stimuli","intvolume":" 25","day":"01","scopus_import":1,"date_published":"2013-07-01T00:00:00Z","publication":"Neural Computation","citation":{"mla":"Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463.","short":"K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.","chicago":"Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation. MIT Press , 2013. https://doi.org/10.1162/NECO_a_00463.","ama":"Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 2013;25(7):1661-1692. doi:10.1162/NECO_a_00463","ista":"Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692.","ieee":"K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” Neural Computation, vol. 25, no. 7. MIT Press , pp. 1661–1692, 2013.","apa":"Rajan, K., Marre, O., & Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. MIT Press . https://doi.org/10.1162/NECO_a_00463"},"page":"1661 - 1692","publist_id":"3983","author":[{"full_name":"Rajan, Kanaka","last_name":"Rajan","first_name":"Kanaka"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:59:56Z","date_created":"2018-12-11T11:59:45Z","volume":25,"year":"2013","publication_status":"published","publisher":"MIT Press ","department":[{"_id":"GaTk"}],"month":"07","doi":"10.1162/NECO_a_00463","language":[{"iso":"eng"}],"external_id":{"arxiv":["1209.0121"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.0121"}],"quality_controlled":"1"},{"oa_version":"Submitted Version","_id":"2826","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Mutations in SCO2 are associated with autosomal-dominant high-grade myopia","intvolume":" 92","abstract":[{"text":"Myopia, or near-sightedness, is an ocular refractive error of unfocused image quality in front of the retinal plane. Individuals with high-grade myopia (dioptric power greater than -6.00) are predisposed to ocular morbidities such as glaucoma, retinal detachment, and myopic maculopathy. Nonsyndromic, high-grade myopia is highly heritable, and to date multiple gene loci have been reported. We performed exome sequencing in 4 individuals from an 11-member family of European descent from the United States. Affected individuals had a mean dioptric spherical equivalent of -22.00 sphere. A premature stop codon mutation c.157C>T (p.Gln53*) cosegregating with disease was discovered within SCO2 that maps to chromosome 22q13.33. Subsequent analyses identified three additional mutations in three highly myopic unrelated individuals (c.341G>A, c.418G>A, and c.776C>T). To determine differential gene expression in a developmental mouse model, we induced myopia by applying a -15.00D lens over one eye. Messenger RNA levels of SCO2 were significantly downregulated in myopic mouse retinae. Immunohistochemistry in mouse eyes confirmed SCO2 protein localization in retina, retinal pigment epithelium, and sclera. SCO2 encodes for a copper homeostasis protein influential in mitochondrial cytochrome c oxidase activity. Copper deficiencies have been linked with photoreceptor loss and myopia with increased scleral wall elasticity. Retinal thinning has been reported with an SC02 variant. Human mutation identification with support from an induced myopic animal provides biological insights of myopic development.","lang":"eng"}],"issue":"5","type":"journal_article","date_published":"2013-05-02T00:00:00Z","publication":"American Journal of Human Genetics","citation":{"chicago":"Tran Viet, Khanh, Caldwell Powell, Veluchamy Barathi, Thomas Klemm, Sebastian Maurer Stroh, Vachiranee Limviphuvadh, Vincent Soler, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal of Human Genetics. Cell Press, 2013. https://doi.org/10.1016/j.ajhg.2013.04.005.","short":"K. Tran Viet, C. Powell, V. Barathi, T. Klemm, S. Maurer Stroh, V. Limviphuvadh, V. Soler, C. Ho, T. Yanovitch, G. Schneider, Y. Li, E. Nading, R. Metlapally, S. Saw, L. Goh, S. Rozen, T. Young, American Journal of Human Genetics 92 (2013) 820–826.","mla":"Tran Viet, Khanh, et al. “Mutations in SCO2 Are Associated with Autosomal-Dominant High-Grade Myopia.” American Journal of Human Genetics, vol. 92, no. 5, Cell Press, 2013, pp. 820–26, doi:10.1016/j.ajhg.2013.04.005.","ieee":"K. Tran Viet et al., “Mutations in SCO2 are associated with autosomal-dominant high-grade myopia,” American Journal of Human Genetics, vol. 92, no. 5. Cell Press, pp. 820–826, 2013.","apa":"Tran Viet, K., Powell, C., Barathi, V., Klemm, T., Maurer Stroh, S., Limviphuvadh, V., … Young, T. (2013). Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. Cell Press. https://doi.org/10.1016/j.ajhg.2013.04.005","ista":"Tran Viet K, Powell C, Barathi V, Klemm T, Maurer Stroh S, Limviphuvadh V, Soler V, Ho C, Yanovitch T, Schneider G, Li Y, Nading E, Metlapally R, Saw S, Goh L, Rozen S, Young T. 2013. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. 92(5), 820–826.","ama":"Tran Viet K, Powell C, Barathi V, et al. Mutations in SCO2 are associated with autosomal-dominant high-grade myopia. American Journal of Human Genetics. 2013;92(5):820-826. doi:10.1016/j.ajhg.2013.04.005"},"page":"820 - 826","day":"02","scopus_import":1,"author":[{"last_name":"Tran Viet","first_name":"Khanh","full_name":"Tran Viet, Khanh"},{"full_name":"Powell, Caldwell","last_name":"Powell","first_name":"Caldwell"},{"first_name":"Veluchamy","last_name":"Barathi","full_name":"Barathi, Veluchamy"},{"last_name":"Klemm","first_name":"Thomas","full_name":"Klemm, Thomas"},{"full_name":"Maurer Stroh, Sebastian","last_name":"Maurer Stroh","first_name":"Sebastian"},{"full_name":"Limviphuvadh, Vachiranee","last_name":"Limviphuvadh","first_name":"Vachiranee"},{"last_name":"Soler","first_name":"Vincent","full_name":"Soler, Vincent"},{"last_name":"Ho","first_name":"Candice","full_name":"Ho, Candice"},{"full_name":"Yanovitch, Tammy","last_name":"Yanovitch","first_name":"Tammy"},{"first_name":"Georg","last_name":"Schneider","id":"329095A0-F248-11E8-B48F-1D18A9856A87","full_name":"Schneider, Georg"},{"last_name":"Li","first_name":"Yi","full_name":"Li, Yi"},{"last_name":"Nading","first_name":"Erica","full_name":"Nading, Erica"},{"last_name":"Metlapally","first_name":"Ravikanth","full_name":"Metlapally, Ravikanth"},{"full_name":"Saw, Seang","last_name":"Saw","first_name":"Seang"},{"last_name":"Goh","first_name":"Liang","full_name":"Goh, Liang"},{"full_name":"Rozen, Steve","last_name":"Rozen","first_name":"Steve"},{"first_name":"Terri","last_name":"Young","full_name":"Young, Terri"}],"date_created":"2018-12-11T11:59:48Z","date_updated":"2021-01-12T06:59:59Z","volume":92,"year":"2013","pmid":1,"publication_status":"published","department":[{"_id":"MD"}],"publisher":"Cell Press","publist_id":"3974","doi":"10.1016/j.ajhg.2013.04.005","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644634/"}],"external_id":{"pmid":["23643385"]},"oa":1,"quality_controlled":"1","month":"05"},{"day":"30","scopus_import":1,"date_published":"2013-04-30T00:00:00Z","page":"E1695 - E1704","citation":{"apa":"Topp, C., Iyer Pascuzzi, A., Anderson, J., Lee, C., Zurek, P., Symonova, O., … Benfey, P. (2013). 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1304354110","ieee":"C. Topp et al., “3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture,” PNAS, vol. 110, no. 18. National Academy of Sciences, pp. E1695–E1704, 2013.","ista":"Topp C, Iyer Pascuzzi A, Anderson J, Lee C, Zurek P, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore B, Harer J, Edelsbrunner H, Mitchell Olds T, Weitz J, Benfey P. 2013. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 110(18), E1695–E1704.","ama":"Topp C, Iyer Pascuzzi A, Anderson J, et al. 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS. 2013;110(18):E1695-E1704. doi:10.1073/pnas.1304354110","chicago":"Topp, Christopher, Anjali Iyer Pascuzzi, Jill Anderson, Cheng Lee, Paul Zurek, Olga Symonova, Ying Zheng, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1304354110.","short":"C. Topp, A. Iyer Pascuzzi, J. Anderson, C. Lee, P. Zurek, O. Symonova, Y. Zheng, A. Bucksch, Y. Mileyko, T. Galkovskyi, B. Moore, J. Harer, H. Edelsbrunner, T. Mitchell Olds, J. Weitz, P. Benfey, PNAS 110 (2013) E1695–E1704.","mla":"Topp, Christopher, et al. “3D Phenotyping and Quantitative Trait Locus Mapping Identify Core Regions of the Rice Genome Controlling Root Architecture.” PNAS, vol. 110, no. 18, National Academy of Sciences, 2013, pp. E1695–704, doi:10.1073/pnas.1304354110."},"publication":"PNAS","issue":"18","abstract":[{"text":"Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala x Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r2 = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 110","status":"public","title":"3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2822","month":"04","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1304354110","quality_controlled":"1","external_id":{"pmid":["25673779"]},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378147/","open_access":"1"}],"publist_id":"3979","volume":110,"date_updated":"2021-01-12T06:59:58Z","date_created":"2018-12-11T11:59:47Z","author":[{"first_name":"Christopher","last_name":"Topp","full_name":"Topp, Christopher"},{"full_name":"Iyer Pascuzzi, Anjali","last_name":"Iyer Pascuzzi","first_name":"Anjali"},{"full_name":"Anderson, Jill","first_name":"Jill","last_name":"Anderson"},{"last_name":"Lee","first_name":"Cheng","full_name":"Lee, Cheng"},{"last_name":"Zurek","first_name":"Paul","full_name":"Zurek, Paul"},{"full_name":"Symonova, Olga","last_name":"Symonova","first_name":"Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zheng","first_name":"Ying","full_name":"Zheng, Ying"},{"last_name":"Bucksch","first_name":"Alexander","full_name":"Bucksch, Alexander"},{"first_name":"Yuriy","last_name":"Mileyko","full_name":"Mileyko, Yuriy"},{"last_name":"Galkovskyi","first_name":"Taras","full_name":"Galkovskyi, Taras"},{"full_name":"Moore, Brad","last_name":"Moore","first_name":"Brad"},{"full_name":"Harer, John","last_name":"Harer","first_name":"John"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Mitchell Olds, Thomas","first_name":"Thomas","last_name":"Mitchell Olds"},{"full_name":"Weitz, Joshua","last_name":"Weitz","first_name":"Joshua"},{"last_name":"Benfey","first_name":"Philip","full_name":"Benfey, Philip"}],"department":[{"_id":"MaJö"},{"_id":"HeEd"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2013"},{"month":"04","quality_controlled":"1","external_id":{"pmid":["23524662"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634696/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1105/tpc.113.110353","publist_id":"3980","publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"year":"2013","pmid":1,"date_updated":"2021-01-12T06:59:57Z","date_created":"2018-12-11T11:59:46Z","volume":25,"author":[{"first_name":"Estelle","last_name":"Remy","full_name":"Remy, Estelle"},{"last_name":"Cabrito","first_name":"Tânia","full_name":"Cabrito, Tânia"},{"full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Baster"},{"last_name":"Batista","first_name":"Rita","full_name":"Batista, Rita"},{"last_name":"Teixeira","first_name":"Miguel","full_name":"Teixeira, Miguel"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"},{"first_name":"Isabel","last_name":"Sá Correia","full_name":"Sá Correia, Isabel"},{"first_name":"Paula","last_name":"Duque","full_name":"Duque, Paula"}],"scopus_import":1,"day":"24","page":"901 - 926","publication":"Plant Cell","citation":{"chicago":"Remy, Estelle, Tânia Cabrito, Pawel Baster, Rita Batista, Miguel Teixeira, Jiří Friml, Isabel Sá Correia, and Paula Duque. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.110353.","short":"E. Remy, T. Cabrito, P. Baster, R. Batista, M. Teixeira, J. Friml, I. Sá Correia, P. Duque, Plant Cell 25 (2013) 901–926.","mla":"Remy, Estelle, et al. “A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis.” Plant Cell, vol. 25, no. 3, American Society of Plant Biologists, 2013, pp. 901–26, doi:10.1105/tpc.113.110353.","ieee":"E. Remy et al., “A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis,” Plant Cell, vol. 25, no. 3. American Society of Plant Biologists, pp. 901–926, 2013.","apa":"Remy, E., Cabrito, T., Baster, P., Batista, R., Teixeira, M., Friml, J., … Duque, P. (2013). A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.113.110353","ista":"Remy E, Cabrito T, Baster P, Batista R, Teixeira M, Friml J, Sá Correia I, Duque P. 2013. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. 25(3), 901–926.","ama":"Remy E, Cabrito T, Baster P, et al. A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis. Plant Cell. 2013;25(3):901-926. doi:10.1105/tpc.113.110353"},"date_published":"2013-04-24T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells."}],"issue":"3","title":"A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis","status":"public","intvolume":" 25","_id":"2821","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version"},{"publist_id":"3972","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","year":"2013","pmid":1,"date_updated":"2021-01-12T06:59:59Z","date_created":"2018-12-11T11:59:48Z","volume":110,"author":[{"first_name":"Yunlong","last_name":"Du","full_name":"Du, Yunlong"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"last_name":"Beck","first_name":"Martina","full_name":"Beck, Martina"},{"full_name":"Himschoot, Ellie","last_name":"Himschoot","first_name":"Ellie"},{"id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","first_name":"Hongjiang","last_name":"Li","full_name":"Li, Hongjiang"},{"full_name":"Robatzek, Silke","first_name":"Silke","last_name":"Robatzek"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"month":"05","quality_controlled":"1","project":[{"_id":"2574781E-B435-11E9-9278-68D0E5697425","name":"Koerber Prize 2010"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651428/"}],"oa":1,"external_id":{"pmid":["23613581"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1220205110","type":"journal_article","abstract":[{"text":"Removal of cargos from the cell surface via endocytosis is an efficient mechanism to regulate activities of plasma membrane (PM)-resident proteins, such as receptors or transporters. Salicylic acid (SA) is an important plant hormone that is traditionally associated with pathogen defense. Here, we describe an unanticipated effect of SA on subcellular endocytic cycling of proteins. Both exogenous treatments and endogenously enhanced SA levels repressed endocytosis of different PM proteins. The SA effect on endocytosis did not involve transcription or known components of the SA signaling pathway for transcriptional regulation. SA likely targets an endocytic mechanism that involves the coat protein clathrin, because SA interfered with the clathrin incidence at the PM and clathrin-deficient mutants were less sensitive to the impact of SA on the auxin distribution and root bending during the gravitropic response. By contrast, SA did not affect the ligand-induced endocytosis of the FLAGELLIN SENSING2 (FLS2) receptor during pathogen responses. Our data suggest that the established SA impact on transcription in plant immunity and the nontranscriptional effect of SA on clathrin-mediated endocytosis are independent mechanisms by which SA regulates distinct aspects of plant physiology.","lang":"eng"}],"issue":"19","title":"Salicylic acid interferes with clathrin-mediated endocytic protein trafficking","status":"public","intvolume":" 110","_id":"2827","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"day":"07","page":"7946 - 7951","publication":"PNAS","citation":{"chicago":"Du, Yunlong, Ricardo Tejos, Martina Beck, Ellie Himschoot, Hongjiang Li, Silke Robatzek, Steffen Vanneste, and Jiří Friml. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic Protein Trafficking.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1220205110.","short":"Y. Du, R. Tejos, M. Beck, E. Himschoot, H. Li, S. Robatzek, S. Vanneste, J. Friml, PNAS 110 (2013) 7946–7951.","mla":"Du, Yunlong, et al. “Salicylic Acid Interferes with Clathrin-Mediated Endocytic Protein Trafficking.” PNAS, vol. 110, no. 19, National Academy of Sciences, 2013, pp. 7946–51, doi:10.1073/pnas.1220205110.","apa":"Du, Y., Tejos, R., Beck, M., Himschoot, E., Li, H., Robatzek, S., … Friml, J. (2013). Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1220205110","ieee":"Y. Du et al., “Salicylic acid interferes with clathrin-mediated endocytic protein trafficking,” PNAS, vol. 110, no. 19. National Academy of Sciences, pp. 7946–7951, 2013.","ista":"Du Y, Tejos R, Beck M, Himschoot E, Li H, Robatzek S, Vanneste S, Friml J. 2013. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. 110(19), 7946–7951.","ama":"Du Y, Tejos R, Beck M, et al. Salicylic acid interferes with clathrin-mediated endocytic protein trafficking. PNAS. 2013;110(19):7946-7951. doi:10.1073/pnas.1220205110"},"date_published":"2013-05-07T00:00:00Z"},{"language":[{"iso":"eng"}],"date_published":"2013-05-01T00:00:00Z","doi":"10.1111/j.1442-9993.2012.02404.x","page":"300 - 312","quality_controlled":"1","citation":{"short":"M. Pickup, S. Wilson, D. Freudenberger, N. Nicholls, L. Gould, S. Hnatiuk, J. Delandre, Austral Ecology 38 (2013) 300–312.","mla":"Pickup, Melinda, et al. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology, vol. 38, no. 3, Wiley-Blackwell, 2013, pp. 300–12, doi:10.1111/j.1442-9993.2012.02404.x.","chicago":"Pickup, Melinda, Susie Wilson, David Freudenberger, Nick Nicholls, Lori Gould, Sarah Hnatiuk, and Jeni Delandre. “Post-Fire Recovery of Revegetated Woodland Communities in South-Eastern Australia.” Austral Ecology. Wiley-Blackwell, 2013. https://doi.org/10.1111/j.1442-9993.2012.02404.x.","ama":"Pickup M, Wilson S, Freudenberger D, et al. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 2013;38(3):300-312. doi:10.1111/j.1442-9993.2012.02404.x","apa":"Pickup, M., Wilson, S., Freudenberger, D., Nicholls, N., Gould, L., Hnatiuk, S., & Delandre, J. (2013). Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1442-9993.2012.02404.x","ieee":"M. Pickup et al., “Post-fire recovery of revegetated woodland communities in south-eastern Australia,” Austral Ecology, vol. 38, no. 3. Wiley-Blackwell, pp. 300–312, 2013.","ista":"Pickup M, Wilson S, Freudenberger D, Nicholls N, Gould L, Hnatiuk S, Delandre J. 2013. Post-fire recovery of revegetated woodland communities in south-eastern Australia. Austral Ecology. 38(3), 300–312."},"publication":"Austral Ecology","day":"01","month":"05","scopus_import":1,"oa_version":"None","volume":38,"date_created":"2018-12-11T11:59:47Z","date_updated":"2021-01-12T06:59:58Z","author":[{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda"},{"full_name":"Wilson, Susie","first_name":"Susie","last_name":"Wilson"},{"full_name":"Freudenberger, David","last_name":"Freudenberger","first_name":"David"},{"full_name":"Nicholls, Nick","last_name":"Nicholls","first_name":"Nick"},{"full_name":"Gould, Lori","last_name":"Gould","first_name":"Lori"},{"last_name":"Hnatiuk","first_name":"Sarah","full_name":"Hnatiuk, Sarah"},{"first_name":"Jeni","last_name":"Delandre","full_name":"Delandre, Jeni"}],"intvolume":" 38","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"title":"Post-fire recovery of revegetated woodland communities in south-eastern Australia","publication_status":"published","status":"public","_id":"2823","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3978","issue":"3","abstract":[{"text":"The primary goal of restoration is to create self-sustaining ecological communities that are resilient to periodic disturbance. Currently, little is known about how restored communities respond to disturbance events such as fire and how this response compares to remnant vegetation. Following the 2003 fires in south-eastern Australia we examined the post-fire response of revegetation plantings and compared this to remnant vegetation. Ten burnt and 10 unburnt (control) sites were assessed for each of three types of vegetation (direct seeding revegetation, revegetation using nursery seedlings (tubestock) and remnant woodland). Sixty sampling sites were surveyed 6months after fire to quantify the initial survival of mid- and overstorey plant species in each type of vegetation. Three and 5years after fire all sites were resurveyed to assess vegetation structure, species diversity and vigour, as well as indicators of soil function. Overall, revegetation showed high (>60%) post-fire survival, but this varied among species depending on regeneration strategy (obligate seeder or resprouter). The native ground cover, mid- and overstorey in both types of plantings showed rapid recovery of vegetation structure and cover within 3years of fire. This recovery was similar to the burnt remnant woodlands. Non-native (exotic) ground cover initially increased after fire, but was no different in burnt and unburnt sites 5years after fire. Fire had no effect on species richness, but burnt direct seeding sites had reduced species diversity (Simpson's Diversity Index) while diversity was higher in burnt remnant woodlands. Indices of soil function in all types of vegetation had recovered to levels found in unburnt sites 5years after fire. These results indicate that even young revegetation (stands <10years old) showed substantial recovery from disturbance by fire. This suggests that revegetation can provide an important basis for restoring woodland communities in the fire-prone Australian environment.","lang":"eng"}],"type":"journal_article"},{"scopus_import":1,"day":"24","month":"04","quality_controlled":"1","page":"83-119","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication":"Information and Computation","citation":{"ama":"Chatterjee K, Prabhu V. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. 2013;228-229:83-119. doi:10.1016/j.ic.2013.04.003","apa":"Chatterjee, K., & Prabhu, V. (2013). Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2013.04.003","ieee":"K. Chatterjee and V. Prabhu, “Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems,” Information and Computation, vol. 228–229. Elsevier, pp. 83–119, 2013.","ista":"Chatterjee K, Prabhu V. 2013. Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems. Information and Computation. 228–229, 83–119.","short":"K. Chatterjee, V. Prabhu, Information and Computation 228–229 (2013) 83–119.","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information and Computation, vol. 228–229, Elsevier, 2013, pp. 83–119, doi:10.1016/j.ic.2013.04.003.","chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Synthesis of Memory-Efficient, Clock-Memory Free, and Non-Zeno Safety Controllers for Timed Systems.” Information and Computation. Elsevier, 2013. https://doi.org/10.1016/j.ic.2013.04.003."},"language":[{"iso":"eng"}],"doi":"10.1016/j.ic.2013.04.003","date_published":"2013-04-24T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study synthesis of controllers for real-time systems, where the objective is to stay in a given safe set. The problem is solved by obtaining winning strategies in the setting of concurrent two player timed automaton games with safety objectives. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a Zeno run. We construct winning strategies for the controller which require access only to (1) the system clocks (thus, controllers which require their own internal infinitely precise clocks are not necessary), and (2) a logarithmic (in the number of clocks) number of memory bits (i.e. a linear number of memory states). Precisely, we show that for safety objectives, a memory of size (3 + lg (| C | + 1)) bits suffices for winning controller strategies, where C is the set of clocks of the timed automaton game, significantly improving the previous known exponential memory states bound. We also settle the open question of whether winning region-based strategies require memory for safety objectives by showing with an example the necessity of memory for such strategies to win for safety objectives. Finally, we show that the decision problem of determining if there exists a receptive player-1 winning strategy for safety objectives is EXPTIME-complete over timed automaton games."}],"publist_id":"3977","ec_funded":1,"publication_status":"published","title":"Synthesis of memory-efficient, clock-memory free, and non-Zeno safety controllers for timed systems","status":"public","publisher":"Elsevier","department":[{"_id":"KrCh"}],"_id":"2824","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:59:47Z","date_updated":"2021-01-12T06:59:58Z","volume":"228-229","oa_version":"None","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Prabhu","first_name":"Vinayak","full_name":"Prabhu, Vinayak"}]},{"month":"05","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"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.pgen.1003540","article_number":"e1003540","ec_funded":1,"publist_id":"3967","file_date_updated":"2020-07-14T12:45:50Z","department":[{"_id":"JiFr"}],"publisher":"Public Library of Science","publication_status":"published","year":"2013","volume":9,"date_created":"2018-12-11T11:59:50Z","date_updated":"2021-01-12T07:00:03Z","author":[{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"first_name":"Saeko","last_name":"Kitakura","full_name":"Kitakura, Saeko"},{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"},{"first_name":"Tomohiro","last_name":"Uemura","full_name":"Uemura, Tomohiro"},{"full_name":"Feraru, Mugurel","first_name":"Mugurel","last_name":"Feraru"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"},{"last_name":"Kakimoto","first_name":"Tatsuo","full_name":"Kakimoto, Tatsuo"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}],"scopus_import":1,"has_accepted_license":"1","day":"05","citation":{"mla":"Tanaka, Hirokazu, et al. “Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics, vol. 9, no. 5, e1003540, Public Library of Science, 2013, doi:10.1371/journal.pgen.1003540.","short":"H. Tanaka, S. Kitakura, H. Rakusová, T. Uemura, M. Feraru, R. De Rycke, S. Robert, T. Kakimoto, J. Friml, PLoS Genetics 9 (2013).","chicago":"Tanaka, Hirokazu, Saeko Kitakura, Hana Rakusová, Tomohiro Uemura, Mugurel Feraru, Riet De Rycke, Stéphanie Robert, Tatsuo Kakimoto, and Jiří Friml. “Cell Polarity and Patterning by PIN Trafficking through Early Endosomal Compartments in Arabidopsis Thaliana.” PLoS Genetics. Public Library of Science, 2013. https://doi.org/10.1371/journal.pgen.1003540.","ama":"Tanaka H, Kitakura S, Rakusová H, et al. Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 2013;9(5). doi:10.1371/journal.pgen.1003540","ista":"Tanaka H, Kitakura S, Rakusová H, Uemura T, Feraru M, De Rycke R, Robert S, Kakimoto T, Friml J. 2013. Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. 9(5), e1003540.","apa":"Tanaka, H., Kitakura, S., Rakusová, H., Uemura, T., Feraru, M., De Rycke, R., … Friml, J. (2013). Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1003540","ieee":"H. Tanaka et al., “Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana,” PLoS Genetics, vol. 9, no. 5. Public Library of Science, 2013."},"publication":"PLoS Genetics","date_published":"2013-05-05T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and mediate intercellular polar transport of the plant hormone auxin that is crucial for a multitude of developmental processes in plants. PIN localization is under extensive control by environmental or developmental cues, but mechanisms regulating PIN localization are not fully understood. Here we show that early endosomal components ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively required for polar PIN localization, for their dynamic repolarization, and consequently for auxin activity gradient formation and auxin-related developmental processes including embryonic patterning, organogenesis, and vasculature venation patterning. These results show that early endosomal trafficking is crucial for cell polarity and auxin-dependent regulation of plant architecture."}],"intvolume":" 9","title":"Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana","ddc":["570"],"status":"public","_id":"2832","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"4957","relation":"main_file","date_created":"2018-12-12T10:12:39Z","date_updated":"2020-07-14T12:45:50Z","checksum":"050237d6c53e8d1601b26808ee1dd6d8","file_name":"IST-2016-411-v1+1_journal.pgen.1003540.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":3813091}],"pubrep_id":"411"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2828","title":"The complexity of conservative valued CSPs","status":"public","intvolume":" 60","abstract":[{"text":"We study the complexity of valued constraint satisfaction problems (VCSPs) parametrized 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 minimize the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well understood, see Raghavendra [2008]. However, there is no characterization of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimization perspective. We 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 [2003, 2011] and recently by Barto [2011]. 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. [2006] for languages over Boolean domains, by Deineko et al. [2008] for {0, 1}-valued languages (a.k.a Max-CSP), and by Takhanov [2010a] for {0, ∞}-valued languages containing all finite-valued unary cost functions (a.k.a. Min-Cost-Hom). We 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 multimor-phisms), then any instance can be solved in polynomial time (via a new algorithm developed in this article), 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 are significantly harder than the Boolean cases. The polynomial-time algorithm we present for the tractable cases is a generalization of the submodular minimization problem and a result of Cohen et al. [2008]. Our results generalize previous results by Takhanov [2010a] and (a subset of results) by Cohen et al. [2006] and Deineko et al. [2008]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [2008], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.","lang":"eng"}],"issue":"2","type":"journal_article","date_published":"2013-04-02T00:00:00Z","publication":"Journal of the ACM","citation":{"chicago":"Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” Journal of the ACM. ACM, 2013. https://doi.org/10.1145/2450142.2450146.","short":"V. Kolmogorov, S. Živný, Journal of the ACM 60 (2013).","mla":"Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs.” Journal of the ACM, vol. 60, no. 2, 10, ACM, 2013, doi:10.1145/2450142.2450146.","ieee":"V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,” Journal of the ACM, vol. 60, no. 2. ACM, 2013.","apa":"Kolmogorov, V., & Živný, S. (2013). The complexity of conservative valued CSPs. Journal of the ACM. ACM. https://doi.org/10.1145/2450142.2450146","ista":"Kolmogorov V, Živný S. 2013. The complexity of conservative valued CSPs. Journal of the ACM. 60(2), 10.","ama":"Kolmogorov V, Živný S. The complexity of conservative valued CSPs. Journal of the ACM. 2013;60(2). doi:10.1145/2450142.2450146"},"day":"02","scopus_import":1,"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"full_name":"Živný, Stanislav","first_name":"Stanislav","last_name":"Živný"}],"date_created":"2018-12-11T11:59:48Z","date_updated":"2021-01-12T07:00:00Z","volume":60,"year":"2013","publication_status":"published","publisher":"ACM","department":[{"_id":"VlKo"}],"publist_id":"3971","article_number":"10","doi":"10.1145/2450142.2450146","language":[{"iso":"eng"}],"external_id":{"arxiv":["1110.2809"]},"main_file_link":[{"url":"http://arxiv.org/abs/1110.2809","open_access":"1"}],"oa":1,"quality_controlled":"1","month":"04"},{"date_published":"2013-05-13T00:00:00Z","publication":"Physical Review Letters","citation":{"chicago":"Shi, Liang, Marc Avila, and Björn Hof. “Scale Invariance at the Onset of Turbulence in Couette Flow.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.204502.","mla":"Shi, Liang, et al. “Scale Invariance at the Onset of Turbulence in Couette Flow.” Physical Review Letters, vol. 110, no. 20, 204502, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.204502.","short":"L. Shi, M. Avila, B. Hof, Physical Review Letters 110 (2013).","ista":"Shi L, Avila M, Hof B. 2013. Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. 110(20), 204502.","apa":"Shi, L., Avila, M., & Hof, B. (2013). Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.204502","ieee":"L. Shi, M. Avila, and B. Hof, “Scale invariance at the onset of turbulence in couette flow,” Physical Review Letters, vol. 110, no. 20. American Physical Society, 2013.","ama":"Shi L, Avila M, Hof B. Scale invariance at the onset of turbulence in couette flow. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.204502"},"day":"13","scopus_import":1,"oa_version":"Preprint","title":"Scale invariance at the onset of turbulence in couette flow","status":"public","intvolume":" 110","_id":"2829","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Laminar-turbulent intermittency is intrinsic to the transitional regime of a wide range of fluid flows including pipe, channel, boundary layer, and Couette flow. In the latter turbulent spots can grow and form continuous stripes, yet in the stripe-normal direction they remain interspersed by laminar fluid. We carry out direct numerical simulations in a long narrow domain and observe that individual turbulent stripes are transient. In agreement with recent observations in pipe flow, we find that turbulence becomes sustained at a distinct critical point once the spatial proliferation outweighs the inherent decaying process. By resolving the asymptotic size distributions close to criticality we can for the first time demonstrate scale invariance at the onset of turbulence.","lang":"eng"}],"issue":"20","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.110.204502","quality_controlled":"1","project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"_id":"2511D90C-B435-11E9-9278-68D0E5697425","grant_number":"SFB 963 TP A8","name":"Astrophysical instability of currents and turbulences"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1304.5446","open_access":"1"}],"external_id":{"arxiv":["1304.5446"]},"month":"05","date_updated":"2021-01-12T07:00:00Z","date_created":"2018-12-11T11:59:49Z","volume":110,"author":[{"id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang","last_name":"Shi","full_name":"Shi, Liang"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"year":"2013","publist_id":"3970","ec_funded":1,"article_number":"204502"},{"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.110.224502","project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1212.0230"]},"main_file_link":[{"url":"http://arxiv.org/abs/1212.0230","open_access":"1"}],"month":"05","volume":110,"date_updated":"2021-01-12T07:00:05Z","date_created":"2018-12-11T11:59:50Z","author":[{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"},{"last_name":"Mellibovsky","first_name":"Fernando","full_name":"Mellibovsky, Fernando"},{"full_name":"Roland, Nicolas","last_name":"Roland","first_name":"Nicolas"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","year":"2013","publist_id":"3965","ec_funded":1,"article_number":"224502","date_published":"2013-05-29T00:00:00Z","citation":{"ama":"Avila M, Mellibovsky F, Roland N, Hof B. Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. 2013;110(22). doi:10.1103/PhysRevLett.110.224502","apa":"Avila, M., Mellibovsky, F., Roland, N., & Hof, B. (2013). Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.224502","ieee":"M. Avila, F. Mellibovsky, N. Roland, and B. Hof, “Streamwise-localized solutions at the onset of turbulence in pipe flow,” Physical Review Letters, vol. 110, no. 22. American Physical Society, 2013.","ista":"Avila M, Mellibovsky F, Roland N, Hof B. 2013. Streamwise-localized solutions at the onset of turbulence in pipe flow. Physical Review Letters. 110(22), 224502.","short":"M. Avila, F. Mellibovsky, N. Roland, B. Hof, Physical Review Letters 110 (2013).","mla":"Avila, Marc, et al. “Streamwise-Localized Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters, vol. 110, no. 22, 224502, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.224502.","chicago":"Avila, Marc, Fernando Mellibovsky, Nicolas Roland, and Björn Hof. “Streamwise-Localized Solutions at the Onset of Turbulence in Pipe Flow.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.224502."},"publication":"Physical Review Letters","day":"29","scopus_import":1,"oa_version":"Preprint","intvolume":" 110","status":"public","title":"Streamwise-localized solutions at the onset of turbulence in pipe flow","_id":"2834","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"22","abstract":[{"lang":"eng","text":"Although the equations governing fluid flow are well known, there are no analytical expressions that describe the complexity of turbulent motion. A recent proposition is that in analogy to low dimensional chaotic systems, turbulence is organized around unstable solutions of the governing equations which provide the building blocks of the disordered dynamics. We report the discovery of periodic solutions which just like intermittent turbulence are spatially localized and show that turbulent transients arise from one such solution branch."}],"type":"journal_article"},{"type":"journal_article","abstract":[{"lang":"eng","text":"During development, mechanical forces cause changes in size, shape, number, position, and gene expression of cells. They are therefore integral to any morphogenetic processes. Force generation by actin-myosin networks and force transmission through adhesive complexes are two self-organizing phenomena driving tissue morphogenesis. Coordination and integration of forces by long-range force transmission and mechanosensing of cells within tissues produce large-scale tissue shape changes. Extrinsic mechanical forces also control tissue patterning by modulating cell fate specification and differentiation. Thus, the interplay between tissue mechanics and biochemical signaling orchestrates tissue morphogenesis and patterning in development."}],"issue":"5","publist_id":"3966","title":"Forces in tissue morphogenesis and patterning","publication_status":"published","status":"public","department":[{"_id":"CaHe"}],"publisher":"Cell Press","intvolume":" 153","_id":"2833","acknowledgement":"C.-P.H. is supported by the Institute of Science and Technology Austria and grants from the Deutsche Forschungsgemeinschaft (DFG) and Fonds zur Förderung der wissenschaftlichen Forschung (FWF).","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:00:04Z","date_created":"2018-12-11T11:59:50Z","volume":153,"oa_version":"None","author":[{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"full_name":"Bellaïche, Yohanns","first_name":"Yohanns","last_name":"Bellaïche"}],"scopus_import":1,"day":"23","month":"05","quality_controlled":"1","page":"948 - 962","publication":"Cell","citation":{"mla":"Heisenberg, Carl-Philipp J., and Yohanns Bellaïche. “Forces in Tissue Morphogenesis and Patterning.” Cell, vol. 153, no. 5, Cell Press, 2013, pp. 948–62, doi:10.1016/j.cell.2013.05.008.","short":"C.-P.J. Heisenberg, Y. Bellaïche, Cell 153 (2013) 948–962.","chicago":"Heisenberg, Carl-Philipp J, and Yohanns Bellaïche. “Forces in Tissue Morphogenesis and Patterning.” Cell. Cell Press, 2013. https://doi.org/10.1016/j.cell.2013.05.008.","ama":"Heisenberg C-PJ, Bellaïche Y. Forces in tissue morphogenesis and patterning. Cell. 2013;153(5):948-962. doi:10.1016/j.cell.2013.05.008","ista":"Heisenberg C-PJ, Bellaïche Y. 2013. Forces in tissue morphogenesis and patterning. Cell. 153(5), 948–962.","ieee":"C.-P. J. Heisenberg and Y. Bellaïche, “Forces in tissue morphogenesis and patterning,” Cell, vol. 153, no. 5. Cell Press, pp. 948–962, 2013.","apa":"Heisenberg, C.-P. J., & Bellaïche, Y. (2013). Forces in tissue morphogenesis and patterning. Cell. Cell Press. https://doi.org/10.1016/j.cell.2013.05.008"},"language":[{"iso":"eng"}],"date_published":"2013-05-23T00:00:00Z","doi":"10.1016/j.cell.2013.05.008"},{"scopus_import":1,"month":"05","day":"23","publication":"Immunity","citation":{"chicago":"Moussion, Christine, and Michael K Sixt. “A Conduit to Amplify Innate Immunity.” Immunity. Cell Press, 2013. https://doi.org/10.1016/j.immuni.2013.05.005.","short":"C. Moussion, M.K. Sixt, Immunity 38 (2013) 853–854.","mla":"Moussion, Christine, and Michael K. Sixt. “A Conduit to Amplify Innate Immunity.” Immunity, vol. 38, no. 5, Cell Press, 2013, pp. 853–54, doi:10.1016/j.immuni.2013.05.005.","apa":"Moussion, C., & Sixt, M. K. (2013). A conduit to amplify innate immunity. Immunity. Cell Press. https://doi.org/10.1016/j.immuni.2013.05.005","ieee":"C. Moussion and M. K. Sixt, “A conduit to amplify innate immunity,” Immunity, vol. 38, no. 5. Cell Press, pp. 853–854, 2013.","ista":"Moussion C, Sixt MK. 2013. A conduit to amplify innate immunity. Immunity. 38(5), 853–854.","ama":"Moussion C, Sixt MK. A conduit to amplify innate immunity. Immunity. 2013;38(5):853-854. doi:10.1016/j.immuni.2013.05.005"},"quality_controlled":"1","page":"853 - 854","doi":"10.1016/j.immuni.2013.05.005","date_published":"2013-05-23T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"3969","issue":"5","_id":"2830","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","title":"A conduit to amplify innate immunity","status":"public","publication_status":"published","intvolume":" 38","department":[{"_id":"MiSi"}],"publisher":"Cell Press","author":[{"full_name":"Moussion, Christine","last_name":"Moussion","first_name":"Christine","id":"3356F664-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"date_created":"2018-12-11T11:59:49Z","date_updated":"2021-01-12T07:00:01Z","volume":38,"oa_version":"None"},{"citation":{"short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 105–119.","mla":"Barton, Nicholas H., et al. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology, vol. 87, no. 1, Elsevier, 2013, pp. 105–19, doi:10.1016/j.tpb.2013.03.001.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Inference in Two Dimensions: Allele Frequencies versus Lengths of Shared Sequence Blocks.” Theoretical Population Biology. Elsevier, 2013. https://doi.org/10.1016/j.tpb.2013.03.001.","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 2013;87(1):105-119. doi:10.1016/j.tpb.2013.03.001","apa":"Barton, N. H., Etheridge, A., Kelleher, J., & Véber, A. (2013). Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2013.03.001","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks,” Theoretical Population Biology, vol. 87, no. 1. Elsevier, pp. 105–119, 2013.","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks. Theoretical Population Biology. 87(1), 105–119."},"publication":"Theoretical Population Biology","page":"105 - 119","date_published":"2013-08-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","_id":"2842","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 87","ddc":["570"],"status":"public","title":"Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks","pubrep_id":"558","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5288","checksum":"9bf9d9a6fd03dd9df50906891f393bf8","date_created":"2018-12-12T10:17:33Z","date_updated":"2020-07-14T12:45:50Z","access_level":"open_access","file_name":"IST-2016-558-v1+1_inference_revised3101NB.pdf","file_size":1554712,"content_type":"application/pdf","creator":"system"},{"file_id":"5289","relation":"main_file","checksum":"2bceddb76edacd0cd5fad73051e2a928","date_created":"2018-12-12T10:17:34Z","date_updated":"2020-07-14T12:45:50Z","access_level":"open_access","file_name":"IST-2016-558-v1+2_inference_revised3101NBApp.pdf","creator":"system","file_size":822964,"content_type":"application/pdf"}],"type":"journal_article","issue":"1","abstract":[{"text":"We outline two approaches to inference of neighbourhood size, N, and dispersal rate, σ2, based on either allele frequencies or on the lengths of sequence blocks that are shared between genomes. Over intermediate timescales (10-100 generations, say), populations that live in two dimensions approach a quasi-equilibrium that is independent of both their local structure and their deeper history. Over such scales, the standardised covariance of allele frequencies (i.e. pairwise FS T) falls with the logarithm of distance, and depends only on neighbourhood size, N, and a 'local scale', κ; the rate of gene flow, σ2, cannot be inferred. We show how spatial correlations can be accounted for, assuming a Gaussian distribution of allele frequencies, giving maximum likelihood estimates of N and κ. Alternatively, inferences can be based on the distribution of the lengths of sequence that are identical between blocks of genomes: long blocks (>0.1 cM, say) tell us about intermediate timescales, over which we assume a quasi-equilibrium. For large neighbourhood size, the distribution of long blocks is given directly by the classical Wright-Malécot formula; this relationship can be used to infer both N and σ2. With small neighbourhood size, there is an appreciable chance that recombinant lineages will coalesce back before escaping into the distant past. For this case, we show that if genomes are sampled from some distance apart, then the distribution of lengths of blocks that are identical in state is geometric, with a mean that depends on N and σ2.","lang":"eng"}],"oa":1,"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.1016/j.tpb.2013.03.001","language":[{"iso":"eng"}],"month":"08","year":"2013","department":[{"_id":"NiBa"}],"publisher":"Elsevier","publication_status":"published","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"}],"volume":87,"date_updated":"2021-01-12T07:00:09Z","date_created":"2018-12-11T11:59:53Z","ec_funded":1,"publist_id":"3953","file_date_updated":"2020-07-14T12:45:50Z"},{"title":"Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome","status":"public","ddc":["570"],"intvolume":" 8","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2838","file":[{"relation":"main_file","file_id":"5160","date_updated":"2020-07-14T12:45:50Z","date_created":"2018-12-12T10:15:38Z","checksum":"512733b21419574a45f10cabef3d7f81","file_name":"IST-2016-407-v1+1_journal.pone.0054285.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4795977,"creator":"system"}],"oa_version":"Published Version","pubrep_id":"407","type":"journal_article","abstract":[{"text":"Individuals with Down syndrome (DS) present important motor deficits that derive from altered motor development of infants and young children. DYRK1A, a candidate gene for DS abnormalities has been implicated in motor function due to its expression in motor nuclei in the adult brain, and its overexpression in DS mouse models leads to hyperactivity and altered motor learning. However, its precise role in the adult motor system, or its possible involvement in postnatal locomotor development has not yet been clarified. During the postnatal period we observed time-specific expression of Dyrk1A in discrete subsets of brainstem nuclei and spinal cord motor neurons. Interestingly, we describe for the first time the presence of Dyrk1A in the presynaptic terminal of the neuromuscular junctions and its axonal transport from the facial nucleus, suggesting a function for Dyrk1A in these structures. Relevant to DS, Dyrk1A overexpression in transgenic mice (TgDyrk1A) produces motor developmental alterations possibly contributing to DS motor phenotypes and modifies the numbers of motor cholinergic neurons, suggesting that the kinase may have a role in the development of the brainstem and spinal cord motor system.","lang":"eng"}],"issue":"1","publication":"PLoS One","citation":{"chicago":"Arquè Fuste, Gloria, Anna Casanovas, and Mara Dierssen. “Dyrk1A Is Dynamically Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0054285.","mla":"Arquè Fuste, Gloria, et al. “Dyrk1A Is Dynamically Expressed on Subsets of Motor Neurons and in the Neuromuscular Junction: Possible Role in Down Syndrome.” PLoS One, vol. 8, no. 1, e54285, Public Library of Science, 2013, doi:10.1371/journal.pone.0054285.","short":"G. Arquè Fuste, A. Casanovas, M. Dierssen, PLoS One 8 (2013).","ista":"Arquè Fuste G, Casanovas A, Dierssen M. 2013. Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. 8(1), e54285.","apa":"Arquè Fuste, G., Casanovas, A., & Dierssen, M. (2013). Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0054285","ieee":"G. Arquè Fuste, A. Casanovas, and M. Dierssen, “Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome,” PLoS One, vol. 8, no. 1. Public Library of Science, 2013.","ama":"Arquè Fuste G, Casanovas A, Dierssen M. Dyrk1A is dynamically expressed on subsets of motor neurons and in the neuromuscular junction: Possible role in Down syndrome. PLoS One. 2013;8(1). doi:10.1371/journal.pone.0054285"},"date_published":"2013-01-16T00:00:00Z","scopus_import":1,"day":"16","has_accepted_license":"1","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"SiHi"}],"year":"2013","date_created":"2018-12-11T11:59:52Z","date_updated":"2021-01-12T07:00:07Z","volume":8,"author":[{"full_name":"Arquè Fuste, Gloria","first_name":"Gloria","last_name":"Arquè Fuste","id":"3CF33908-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Casanovas, Anna","last_name":"Casanovas","first_name":"Anna"},{"last_name":"Dierssen","first_name":"Mara","full_name":"Dierssen, Mara"}],"article_number":"e54285","file_date_updated":"2020-07-14T12:45:50Z","publist_id":"3960","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.pone.0054285","month":"01"},{"title":"Interstitial dendritic cell guidance by haptotactic chemokine gradients","status":"public","intvolume":" 339","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2839","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Directional guidance of cells via gradients of chemokines is considered crucial for embryonic development, cancer dissemination, and immune responses. Nevertheless, the concept still lacks direct experimental confirmation in vivo. Here, we identify endogenous gradients of the chemokine CCL21 within mouse skin and show that they guide dendritic cells toward lymphatic vessels. Quantitative imaging reveals depots of CCL21 within lymphatic endothelial cells and steeply decaying gradients within the perilymphatic interstitium. These gradients match the migratory patterns of the dendritic cells, which directionally approach vessels from a distance of up to 90-micrometers. Interstitial CCL21 is immobilized to heparan sulfates, and its experimental delocalization or swamping the endogenous gradients abolishes directed migration. These findings functionally establish the concept of haptotaxis, directed migration along immobilized gradients, in tissues.","lang":"eng"}],"issue":"6117","article_type":"original","page":"328 - 332","publication":"Science","citation":{"ama":"Weber M, Hauschild R, Schwarz J, et al. Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. 2013;339(6117):328-332. doi:10.1126/science.1228456","ista":"Weber M, Hauschild R, Schwarz J, Moussion C, de Vries I, Legler D, Luther S, Bollenbach MT, Sixt MK. 2013. Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. 339(6117), 328–332.","ieee":"M. Weber et al., “Interstitial dendritic cell guidance by haptotactic chemokine gradients,” Science, vol. 339, no. 6117. American Association for the Advancement of Science, pp. 328–332, 2013.","apa":"Weber, M., Hauschild, R., Schwarz, J., Moussion, C., de Vries, I., Legler, D., … Sixt, M. K. (2013). Interstitial dendritic cell guidance by haptotactic chemokine gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1228456","mla":"Weber, Michele, et al. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.” Science, vol. 339, no. 6117, American Association for the Advancement of Science, 2013, pp. 328–32, doi:10.1126/science.1228456.","short":"M. Weber, R. Hauschild, J. Schwarz, C. Moussion, I. de Vries, D. Legler, S. Luther, M.T. Bollenbach, M.K. Sixt, Science 339 (2013) 328–332.","chicago":"Weber, Michele, Robert Hauschild, Jan Schwarz, Christine Moussion, Ingrid de Vries, Daniel Legler, Sanjiv Luther, Mark Tobias Bollenbach, and Michael K Sixt. “Interstitial Dendritic Cell Guidance by Haptotactic Chemokine Gradients.” Science. American Association for the Advancement of Science, 2013. https://doi.org/10.1126/science.1228456."},"date_published":"2013-01-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"No","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"MiSi"},{"_id":"Bio"}],"acknowledgement":"We thank M. Frank for technical assistance and S. Cremer, P. Schmalhorst, and E. Kiermaier for critical reading of the manuscript. This work was supported by a Humboldt Foundation postdoctoral fellowship (to M.W.), the German Research Foundation (Si1323 1,2 to M.S.), the Human Frontier Science Program (HFSP RGP0058/2011 to M.S.), the European Research Council (ERC StG 281556 to M.S.), and the Swiss National Science Foundation (31003A 127474 to D.F.L., 130488 to S.A.L.).","year":"2013","date_updated":"2022-06-10T10:21:40Z","date_created":"2018-12-11T11:59:52Z","volume":339,"author":[{"id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Weber","full_name":"Weber, Michele"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"full_name":"Schwarz, Jan","first_name":"Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"id":"3356F664-F248-11E8-B48F-1D18A9856A87","last_name":"Moussion","first_name":"Christine","full_name":"Moussion, Christine"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"full_name":"Legler, Daniel","first_name":"Daniel","last_name":"Legler"},{"first_name":"Sanjiv","last_name":"Luther","full_name":"Luther, Sanjiv"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"publist_id":"3959","ec_funded":1,"quality_controlled":"1","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7"},{"name":"Cell migration in complex environments: from in vivo experiments to theoretical models","grant_number":"RGP0058/2011","_id":"25ABD200-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://kops.uni-konstanz.de/bitstream/123456789/26341/2/Weber_263418.pdf"}],"language":[{"iso":"eng"}],"doi":"10.1126/science.1228456","month":"01"},{"publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2013","volume":18,"date_created":"2018-12-11T11:59:51Z","date_updated":"2021-01-12T07:00:06Z","author":[{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"last_name":"Knowles","first_name":"Antti","full_name":"Knowles, Antti"},{"full_name":"Yau, Horng","first_name":"Horng","last_name":"Yau"},{"full_name":"Yin, Jun","last_name":"Yin","first_name":"Jun"}],"publist_id":"3962","file_date_updated":"2020-07-14T12:45:50Z","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":"10.1214/EJP.v18-2473","month":"05","intvolume":" 18","ddc":["530"],"title":"The local semicircle law for a general class of random matrices","status":"public","_id":"2837","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":651497,"creator":"system","access_level":"open_access","file_name":"IST-2016-406-v1+1_2473-13759-1-PB.pdf","checksum":"aac9e52a00cb2f5149dc9e362b5ccf44","date_created":"2018-12-12T10:15:46Z","date_updated":"2020-07-14T12:45:50Z","relation":"main_file","file_id":"5169"}],"pubrep_id":"406","type":"journal_article","issue":"59","abstract":[{"text":"We consider a general class of N × N random matrices whose entries hij are independent up to a symmetry constraint, but not necessarily identically distributed. Our main result is a local semicircle law which improves previous results [17] both in the bulk and at the edge. The error bounds are given in terms of the basic small parameter of the model, maxi,j E|hij|2. As a consequence, we prove the universality of the local n-point correlation functions in the bulk spectrum for a class of matrices whose entries do not have comparable variances, including random band matrices with band width W ≫N1-εn with some εn > 0 and with a negligible mean-field component. In addition, we provide a coherent and pedagogical proof of the local semicircle law, streamlining and strengthening previous arguments from [17, 19, 6].","lang":"eng"}],"page":"1-58","citation":{"ama":"Erdös L, Knowles A, Yau H, Yin J. The local semicircle law for a general class of random matrices. Electronic Journal of Probability. 2013;18(59):1-58. doi:10.1214/EJP.v18-2473","apa":"Erdös, L., Knowles, A., Yau, H., & Yin, J. (2013). The local semicircle law for a general class of random matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v18-2473","ieee":"L. Erdös, A. Knowles, H. Yau, and J. Yin, “The local semicircle law for a general class of random matrices,” Electronic Journal of Probability, vol. 18, no. 59. Institute of Mathematical Statistics, pp. 1–58, 2013.","ista":"Erdös L, Knowles A, Yau H, Yin J. 2013. The local semicircle law for a general class of random matrices. Electronic Journal of Probability. 18(59), 1–58.","short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of Probability 18 (2013) 1–58.","mla":"Erdös, László, et al. “The Local Semicircle Law for a General Class of Random Matrices.” Electronic Journal of Probability, vol. 18, no. 59, Institute of Mathematical Statistics, 2013, pp. 1–58, doi:10.1214/EJP.v18-2473.","chicago":"Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “The Local Semicircle Law for a General Class of Random Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/EJP.v18-2473."},"publication":"Electronic Journal of Probability","date_published":"2013-05-29T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"29"},{"month":"06","doi":"10.1104/pp.113.217018","language":[{"iso":"eng"}],"external_id":{"pmid":["23580592"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668084/"}],"quality_controlled":"1","publist_id":"3964","author":[{"last_name":"Yu","first_name":"Hong","full_name":"Yu, Hong"},{"full_name":"Karampelias, Michael","first_name":"Michael","last_name":"Karampelias"},{"first_name":"Stéphanie","last_name":"Robert","full_name":"Robert, Stéphanie"},{"full_name":"Peer, Wendy","first_name":"Wendy","last_name":"Peer"},{"last_name":"Swarup","first_name":"Ranjan","full_name":"Swarup, Ranjan"},{"full_name":"Ye, Songqing","last_name":"Ye","first_name":"Songqing"},{"full_name":"Ge, Lei","first_name":"Lei","last_name":"Ge"},{"first_name":"Jerry","last_name":"Cohen","full_name":"Cohen, Jerry"},{"last_name":"Murphy","first_name":"Angus","full_name":"Murphy, Angus"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mark","last_name":"Estelle","full_name":"Estelle, Mark"}],"volume":162,"date_updated":"2021-01-12T07:00:05Z","date_created":"2018-12-11T11:59:51Z","pmid":1,"year":"2013","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"publication_status":"published","day":"01","scopus_import":1,"date_published":"2013-06-01T00:00:00Z","citation":{"ama":"Yu H, Karampelias M, Robert S, et al. Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. 2013;162(2):965-976. doi:10.1104/pp.113.217018","apa":"Yu, H., Karampelias, M., Robert, S., Peer, W., Swarup, R., Ye, S., … Estelle, M. (2013). Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.113.217018","ieee":"H. Yu et al., “Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis,” Plant Physiology, vol. 162, no. 2. American Society of Plant Biologists, pp. 965–976, 2013.","ista":"Yu H, Karampelias M, Robert S, Peer W, Swarup R, Ye S, Ge L, Cohen J, Murphy A, Friml J, Estelle M. 2013. Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis. Plant Physiology. 162(2), 965–976.","short":"H. Yu, M. Karampelias, S. Robert, W. Peer, R. Swarup, S. Ye, L. Ge, J. Cohen, A. Murphy, J. Friml, M. Estelle, Plant Physiology 162 (2013) 965–976.","mla":"Yu, Hong, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential for Polar Auxin Transport in Arabidopsis.” Plant Physiology, vol. 162, no. 2, American Society of Plant Biologists, 2013, pp. 965–76, doi:10.1104/pp.113.217018.","chicago":"Yu, Hong, Michael Karampelias, Stéphanie Robert, Wendy Peer, Ranjan Swarup, Songqing Ye, Lei Ge, et al. “Root Ultraviolet B-Sensitive1/Weak Auxin Response3 Is Essential for Polar Auxin Transport in Arabidopsis.” Plant Physiology. American Society of Plant Biologists, 2013. https://doi.org/10.1104/pp.113.217018."},"publication":"Plant Physiology","page":"965 - 976","issue":"2","abstract":[{"lang":"eng","text":"The phytohormone auxin regulates virtually every aspect of plant development. To identify new genes involved in auxin activity, a genetic screen was performed for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen, designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays severe defects in root development. The wxr3 mutant decreases polar auxin transport and results in a disruption of the asymmetric auxin distribution. The levels of the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3 root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1 (RUS1), a member of the conserved Domain of Unknown Function647 protein family found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an essential role in the regulation of polar auxin transport by maintaining the proper level of auxin transporters on the plasma membrane."}],"type":"journal_article","oa_version":"Submitted Version","_id":"2835","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 162","title":"Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis","status":"public"},{"date_published":"2013-07-04T00:00:00Z","citation":{"ieee":"K. Chatterjee and V. Raman, “Assume-guarantee synthesis for digital contract signing,” Formal Aspects of Computing, vol. 26, no. 4. Springer, pp. 825–859, 2013.","apa":"Chatterjee, K., & Raman, V. (2013). Assume-guarantee synthesis for digital contract signing. Formal Aspects of Computing. Springer. https://doi.org/10.1007/s00165-013-0283-6","ista":"Chatterjee K, Raman V. 2013. Assume-guarantee synthesis for digital contract signing. Formal Aspects of Computing. 26(4), 825–859.","ama":"Chatterjee K, Raman V. Assume-guarantee synthesis for digital contract signing. Formal Aspects of Computing. 2013;26(4):825-859. doi:10.1007/s00165-013-0283-6","chicago":"Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis for Digital Contract Signing.” Formal Aspects of Computing. Springer, 2013. https://doi.org/10.1007/s00165-013-0283-6.","short":"K. Chatterjee, V. Raman, Formal Aspects of Computing 26 (2013) 825–859.","mla":"Chatterjee, Krishnendu, and Vishwanath Raman. “Assume-Guarantee Synthesis for Digital Contract Signing.” Formal Aspects of Computing, vol. 26, no. 4, Springer, 2013, pp. 825–59, doi:10.1007/s00165-013-0283-6."},"publication":"Formal Aspects of Computing","page":"825 - 859","day":"04","scopus_import":1,"oa_version":"Preprint","_id":"2836","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 26","status":"public","title":"Assume-guarantee synthesis for digital contract signing","issue":"4","abstract":[{"lang":"eng","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 and the trusted third party as path formulas in linear temporal logic and prove that the satisfaction of these objectives imply fairness; a property required of fair exchange protocols. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of AGS as follows: (a) any solution of AGS is attack-free; no subset of participants can violate the objectives of the other participants; (b) the Asokan-Shoup-Waidner certified mail protocol that has known vulnerabilities is not a solution of AGS; (c) the Kremer-Markowitch non-repudiation protocol is a solution of AGS; and (d) AGS presents a new and symmetric fair non-repudiation protocol that is attack-free. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can both automatically discover vulnerabilities in protocols and generate correct protocols. The solution to AGS can be computed efficiently as the secure equilibrium solution of three-player graph games. "}],"type":"journal_article","doi":"10.1007/s00165-013-0283-6","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1004.2697"}],"oa":1,"external_id":{"arxiv":["1004.2697"]},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","month":"07","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Raman","first_name":"Vishwanath","full_name":"Raman, Vishwanath"}],"volume":26,"date_created":"2018-12-11T11:59:51Z","date_updated":"2021-01-12T07:00:06Z","year":"2013","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"publist_id":"3963"},{"_id":"2840","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Distinct roles of medial and lateral entorhinal cortex in spatial cognition","publisher":"Oxford University Press","department":[{"_id":"JoCs"}],"intvolume":" 23","author":[{"full_name":"Van Cauter, Tiffany","last_name":"Van Cauter","first_name":"Tiffany"},{"full_name":"Camon, Jeremy","first_name":"Jeremy","last_name":"Camon"},{"id":"467FB3D4-F248-11E8-B48F-1D18A9856A87","last_name":"Alvernhe","first_name":"Alice","full_name":"Alvernhe, Alice"},{"full_name":"Elduayen, Coralie","first_name":"Coralie","last_name":"Elduayen"},{"full_name":"Sargolini, Francesca","last_name":"Sargolini","first_name":"Francesca"},{"first_name":"Étienne","last_name":"Save","full_name":"Save, Étienne"}],"date_updated":"2021-01-12T07:00:08Z","date_created":"2018-12-11T11:59:52Z","volume":23,"oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"It is known that the entorhinal cortex plays a crucial role in spatial cognition in rodents. Neuroanatomical and electrophysiological data suggest that there is a functional distinction between 2 subregions within the entorhinal cortex, the medial entorhinal cortex (MEC), and the lateral entorhinal cortex (LEC). Rats with MEC or LEC lesions were trained in 2 navigation tasks requiring allothetic (water maze task) or idiothetic (path integration) information processing and 2-object exploration tasks allowing testing of spatial and nonspatial processing of intramaze objects. MEC lesions mildly affected place navigation in the water maze and produced a path integration deficit. They also altered the processing of spatial information in both exploration tasks while sparing the processing of nonspatial information. LEC lesions did not affect navigation abilities in both the water maze and the path integration tasks. They altered spatial and nonspatial processing in the object exploration task but not in the one-trial recognition task. Overall, these results indicate that the MEC is important for spatial processing and path integration. The LEC has some influence on both spatial and nonspatial processes, suggesting that the 2 kinds of information interact at the level of the EC."}],"publist_id":"3958","issue":"2","publication":"Cerebral Cortex","citation":{"ieee":"T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, and É. Save, “Distinct roles of medial and lateral entorhinal cortex in spatial cognition,” Cerebral Cortex, vol. 23, no. 2. Oxford University Press, pp. 451–459, 2013.","apa":"Van Cauter, T., Camon, J., Alvernhe, A., Elduayen, C., Sargolini, F., & Save, É. (2013). Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhs033","ista":"Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. 2013. Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral Cortex. 23(2), 451–459.","ama":"Van Cauter T, Camon J, Alvernhe A, Elduayen C, Sargolini F, Save É. Distinct roles of medial and lateral entorhinal cortex in spatial cognition. Cerebral Cortex. 2013;23(2):451-459. doi:10.1093/cercor/bhs033","chicago":"Van Cauter, Tiffany, Jeremy Camon, Alice Alvernhe, Coralie Elduayen, Francesca Sargolini, and Étienne Save. “Distinct Roles of Medial and Lateral Entorhinal Cortex in Spatial Cognition.” Cerebral Cortex. Oxford University Press, 2013. https://doi.org/10.1093/cercor/bhs033.","short":"T. Van Cauter, J. Camon, A. Alvernhe, C. Elduayen, F. Sargolini, É. Save, Cerebral Cortex 23 (2013) 451–459.","mla":"Van Cauter, Tiffany, et al. “Distinct Roles of Medial and Lateral Entorhinal Cortex in Spatial Cognition.” Cerebral Cortex, vol. 23, no. 2, Oxford University Press, 2013, pp. 451–59, doi:10.1093/cercor/bhs033."},"quality_controlled":"1","page":"451 - 459","date_published":"2013-02-01T00:00:00Z","doi":"10.1093/cercor/bhs033","language":[{"iso":"eng"}],"scopus_import":1,"month":"02","day":"01"},{"date_created":"2018-12-11T11:59:52Z","date_updated":"2021-01-12T07:00:09Z","oa_version":"None","volume":24,"author":[{"last_name":"Morita","first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi"},{"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"}],"publication_status":"published","status":"public","title":"Holding on and letting go: Cadherin turnover in cell intercalation","intvolume":" 24","publisher":"Cell Press","department":[{"_id":"CaHe"}],"year":"2013","_id":"2841","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In zebrafish early development, blastoderm cells undergo extensive radial intercalations, triggering the spreading of the blastoderm over the yolk cell and thereby initiating embryonic body axis formation. Now reporting in Developmental Cell, Song et al. (2013) demonstrate a critical function for EGF-dependent E-cadherin endocytosis in promoting blastoderm cell intercalations.","lang":"eng"}],"issue":"6","publist_id":"3956","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2013.03.007","date_published":"2013-05-25T00:00:00Z","quality_controlled":"1","page":"567 - 569","publication":"Developmental Cell","citation":{"ama":"Morita H, Heisenberg C-PJ. Holding on and letting go: Cadherin turnover in cell intercalation. Developmental Cell. 2013;24(6):567-569. doi:10.1016/j.devcel.2013.03.007","ista":"Morita H, Heisenberg C-PJ. 2013. Holding on and letting go: Cadherin turnover in cell intercalation. Developmental Cell. 24(6), 567–569.","ieee":"H. Morita and C.-P. J. Heisenberg, “Holding on and letting go: Cadherin turnover in cell intercalation,” Developmental Cell, vol. 24, no. 6. Cell Press, pp. 567–569, 2013.","apa":"Morita, H., & Heisenberg, C.-P. J. (2013). Holding on and letting go: Cadherin turnover in cell intercalation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2013.03.007","mla":"Morita, Hitoshi, and Carl-Philipp J. Heisenberg. “Holding on and Letting Go: Cadherin Turnover in Cell Intercalation.” Developmental Cell, vol. 24, no. 6, Cell Press, 2013, pp. 567–69, doi:10.1016/j.devcel.2013.03.007.","short":"H. Morita, C.-P.J. Heisenberg, Developmental Cell 24 (2013) 567–569.","chicago":"Morita, Hitoshi, and Carl-Philipp J Heisenberg. “Holding on and Letting Go: Cadherin Turnover in Cell Intercalation.” Developmental Cell. Cell Press, 2013. https://doi.org/10.1016/j.devcel.2013.03.007."},"day":"25","month":"05","scopus_import":1},{"file_date_updated":"2020-07-14T12:45:50Z","publist_id":"3948","extern":"1","year":"2013","publication_status":"published","publisher":"Wiley-Blackwell","author":[{"id":"349A6E66-F248-11E8-B48F-1D18A9856A87","last_name":"El Masri","first_name":"Leila","full_name":"El Masri, Leila"},{"last_name":"Schulte","first_name":"Rebecca","full_name":"Schulte, Rebecca"},{"full_name":"Timmermeyer, Nadine","first_name":"Nadine","last_name":"Timmermeyer"},{"full_name":"Thanisch, Stefanie","last_name":"Thanisch","first_name":"Stefanie"},{"first_name":"Lena","last_name":"Crummenerl","full_name":"Crummenerl, Lena"},{"full_name":"Jansen, Gunther","last_name":"Jansen","first_name":"Gunther"},{"full_name":"Michiels, Nico","last_name":"Michiels","first_name":"Nico"},{"full_name":"Schulenburg, Hinrich","last_name":"Schulenburg","first_name":"Hinrich"}],"date_created":"2018-12-11T11:59:54Z","date_updated":"2022-08-25T14:51:57Z","volume":16,"month":"04","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,"quality_controlled":"1","doi":"10.1111/ele.12068","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"The Red Queen hypothesis proposes that coevolving parasites select for outcrossing in the host. Outcrossing relies on males, which often show lower immune investment due to, for example, sexual selection. Here, we demonstrate that such sex differences in immunity interfere with parasite-mediated selection for outcrossing. Two independent coevolution experiments with Caenorhabditis elegans and its microparasite Bacillus thuringiensis produced decreased yet stable frequencies of outcrossing male hosts. A subsequent systematic analysis verified that male C. elegans suffered from a direct selective disadvantage under parasite pressure (i.e. lower resistance, decreased sexual activity, increased escape behaviour), which can reduce outcrossing and thus male frequencies. At the same time, males offered an indirect selective benefit, because male-mediated outcrossing increased offspring resistance, thus favouring male persistence in the evolving populations. As sex differences in immunity are widespread, such interference of opposing selective constraints is likely of central importance during host adaptation to a coevolving parasite.","lang":"eng"}],"issue":"4","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2846","status":"public","ddc":["570"],"title":"Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution","intvolume":" 16","pubrep_id":"404","file":[{"checksum":"aa7db788f7da7d7f102539a249ebce50","date_updated":"2020-07-14T12:45:50Z","date_created":"2018-12-12T10:15:52Z","file_id":"5176","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":763731,"access_level":"open_access","file_name":"IST-2016-404-v1+1_ele12068.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"No","publication":"Ecology Letters","citation":{"chicago":"El Masri, Leila, Rebecca Schulte, Nadine Timmermeyer, Stefanie Thanisch, Lena Crummenerl, Gunther Jansen, Nico Michiels, and Hinrich Schulenburg. “Sex Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing during Host-Parasite Coevolution.” Ecology Letters. Wiley-Blackwell, 2013. https://doi.org/10.1111/ele.12068.","mla":"El Masri, Leila, et al. “Sex Differences in Host Defence Interfere with Parasite-Mediated Selection for Outcrossing during Host-Parasite Coevolution.” Ecology Letters, vol. 16, no. 4, Wiley-Blackwell, 2013, pp. 461–68, doi:10.1111/ele.12068.","short":"L. El Masri, R. Schulte, N. Timmermeyer, S. Thanisch, L. Crummenerl, G. Jansen, N. Michiels, H. Schulenburg, Ecology Letters 16 (2013) 461–468.","ista":"El Masri L, Schulte R, Timmermeyer N, Thanisch S, Crummenerl L, Jansen G, Michiels N, Schulenburg H. 2013. Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. 16(4), 461–468.","apa":"El Masri, L., Schulte, R., Timmermeyer, N., Thanisch, S., Crummenerl, L., Jansen, G., … Schulenburg, H. (2013). Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. Wiley-Blackwell. https://doi.org/10.1111/ele.12068","ieee":"L. El Masri et al., “Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution,” Ecology Letters, vol. 16, no. 4. Wiley-Blackwell, pp. 461–468, 2013.","ama":"El Masri L, Schulte R, Timmermeyer N, et al. Sex differences in host defence interfere with parasite-mediated selection for outcrossing during host-parasite coevolution. Ecology Letters. 2013;16(4):461-468. doi:10.1111/ele.12068"},"page":"461 - 468","date_published":"2013-04-04T00:00:00Z"},{"doi":"10.1016/j.cub.2013.03.064","date_published":"2013-05-06T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Rosquete M, von Wangenheim D, Marhavý P, et al. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. 2013;23(9):817-822. doi:10.1016/j.cub.2013.03.064","apa":"Rosquete, M., von Wangenheim, D., Marhavý, P., Barbez, E., Stelzer, E., Benková, E., … Kleine Vehn, J. (2013). An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.03.064","ieee":"M. Rosquete et al., “An auxin transport mechanism restricts positive orthogravitropism in lateral roots,” Current Biology, vol. 23, no. 9. Cell Press, pp. 817–822, 2013.","ista":"Rosquete M, von Wangenheim D, Marhavý P, Barbez E, Stelzer E, Benková E, Maizel A, Kleine Vehn J. 2013. An auxin transport mechanism restricts positive orthogravitropism in lateral roots. Current Biology. 23(9), 817–822.","short":"M. Rosquete, D. von Wangenheim, P. Marhavý, E. Barbez, E. Stelzer, E. Benková, A. Maizel, J. Kleine Vehn, Current Biology 23 (2013) 817–822.","mla":"Rosquete, Michel, et al. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” Current Biology, vol. 23, no. 9, Cell Press, 2013, pp. 817–22, doi:10.1016/j.cub.2013.03.064.","chicago":"Rosquete, Michel, Daniel von Wangenheim, Peter Marhavý, Elke Barbez, Ernst Stelzer, Eva Benková, Alexis Maizel, and Jürgen Kleine Vehn. “An Auxin Transport Mechanism Restricts Positive Orthogravitropism in Lateral Roots.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.03.064."},"publication":"Current Biology","page":"817 - 822","project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362"}],"quality_controlled":"1","month":"05","day":"06","scopus_import":1,"author":[{"full_name":"Rosquete, Michel","first_name":"Michel","last_name":"Rosquete"},{"full_name":"Von Wangenheim, Daniel","last_name":"Von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marhavy","first_name":"Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavy, Peter"},{"last_name":"Barbez","first_name":"Elke","full_name":"Barbez, Elke"},{"full_name":"Stelzer, Ernst","last_name":"Stelzer","first_name":"Ernst"},{"full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Alexis","last_name":"Maizel","full_name":"Maizel, Alexis"},{"full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen","last_name":"Kleine Vehn"}],"volume":23,"oa_version":"None","date_created":"2018-12-11T11:59:53Z","date_updated":"2021-01-12T07:00:10Z","year":"2013","_id":"2844","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 23","publisher":"Cell Press","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"status":"public","title":"An auxin transport mechanism restricts positive orthogravitropism in lateral roots","publication_status":"published","publist_id":"3950","issue":"9","ec_funded":1,"abstract":[{"lang":"eng","text":"As soon as a seed germinates, plant growth relates to gravity to ensure that the root penetrates the soil and the shoot expands aerially. Whereas mechanisms of positive and negative orthogravitropism of primary roots and shoots are relatively well understood [1-3], lateral organs often show more complex growth behavior [4]. Lateral roots (LRs) seemingly suppress positive gravitropic growth and show a defined gravitropic set-point angle (GSA) that allows radial expansion of the root system (plagiotropism) [3, 4]. Despite its eminent importance for root architecture, it so far remains completely unknown how lateral organs partially suppress positive orthogravitropism. Here we show that the phytohormone auxin steers GSA formation and limits positive orthogravitropism in LR. Low and high auxin levels/signaling lead to radial or axial root systems, respectively. At a cellular level, it is the auxin transport-dependent regulation of asymmetric growth in the elongation zone that determines GSA. Our data suggest that strong repression of PIN4/PIN7 and transient PIN3 expression limit auxin redistribution in young LR columella cells. We conclude that PIN activity, by temporally limiting the asymmetric auxin fluxes in the tip of LRs, induces transient, differential growth responses in the elongation zone and, consequently, controls root architecture."}],"type":"journal_article"},{"scopus_import":1,"day":"21","month":"02","quality_controlled":"1","page":"XV - XIX","publication":"17th IAPR International Conference on Discrete Geometry for Computer Imagery","citation":{"ama":"Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. In: 17th IAPR International Conference on Discrete Geometry for Computer Imagery. Vol 7749. Springer; 2013:XV-XIX. doi:10.1007/978-3-642-37067-0","ista":"Edelsbrunner H, Pausinger F. 2013. Stable length estimates of tube-like shapes. 17th IAPR International Conference on Discrete Geometry for Computer Imagery. DGCI: Discrete Geometry for Computer Imagery, LNCS, vol. 7749, XV–XIX.","apa":"Edelsbrunner, H., & Pausinger, F. (2013). Stable length estimates of tube-like shapes. In 17th IAPR International Conference on Discrete Geometry for Computer Imagery (Vol. 7749, pp. XV–XIX). Seville, Spain: Springer. https://doi.org/10.1007/978-3-642-37067-0","ieee":"H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” in 17th IAPR International Conference on Discrete Geometry for Computer Imagery, Seville, Spain, 2013, vol. 7749, pp. XV–XIX.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” 17th IAPR International Conference on Discrete Geometry for Computer Imagery, vol. 7749, Springer, 2013, pp. XV–XIX, doi:10.1007/978-3-642-37067-0.","short":"H. Edelsbrunner, F. Pausinger, in:, 17th IAPR International Conference on Discrete Geometry for Computer Imagery, Springer, 2013, pp. XV–XIX.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” In 17th IAPR International Conference on Discrete Geometry for Computer Imagery, 7749:XV–XIX. Springer, 2013. https://doi.org/10.1007/978-3-642-37067-0."},"language":[{"iso":"eng"}],"conference":{"name":"DGCI: Discrete Geometry for Computer Imagery","end_date":"2013-03-22","location":"Seville, Spain","start_date":"2013-03-20"},"date_published":"2013-02-21T00:00:00Z","doi":"10.1007/978-3-642-37067-0","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Mathematical objects can be measured unambiguously, but not so objects from our physical world. Even the total length of tubelike shapes has its difficulties. We introduce a combination of geometric, probabilistic, and topological methods to design a stable length estimate for tube-like shapes; that is: one that is insensitive to small shape changes."}],"publist_id":"3952","status":"public","title":"Stable length estimates of tube-like shapes","publication_status":"published","intvolume":" 7749","department":[{"_id":"HeEd"}],"publisher":"Springer","_id":"2843","year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T10:35:00Z","date_created":"2018-12-11T11:59:53Z","volume":7749,"oa_version":"None","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","first_name":"Florian","full_name":"Pausinger, Florian"}],"related_material":{"record":[{"id":"2255","relation":"later_version","status":"public"}]}},{"publist_id":"3949","issue":"6","abstract":[{"text":"At synapses formed between dissociated neurons, about half of all synaptic vesicles are refractory to evoked release, forming the so-called "resting pool." Here, we use optical measurements of vesicular pH to study developmental changes in pool partitioning and vesicle cycling in cultured hippocampal slices. Two-photon imaging of a genetically encoded two-color release sensor (ratio-sypHy) allowed us to perform calibrated measurements at individual Schaffer collateral boutons. Mature boutons released a large fraction of their vesicles during simulated place field activity, and vesicle retrieval rates were 7-fold higher compared to immature boutons. Saturating stimulation mobilized essentially all vesicles at mature synapses. Resting pool formation and a concomitant reduction in evoked release was induced by chronic depolarization but not by acute inhibition of the protein phosphatase calcineurin. We conclude that synapses in CA1 undergo a prominent refinement of vesicle use during early postnatal development that is not recapitulated in dissociated neuronal culture.","lang":"eng"}],"type":"journal_article","oa_version":"None","volume":77,"date_updated":"2021-01-12T07:00:11Z","date_created":"2018-12-11T11:59:54Z","author":[{"full_name":"Rose, Tobias","first_name":"Tobias","last_name":"Rose"},{"full_name":"Schönenberger, Philipp","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","last_name":"Schönenberger","first_name":"Philipp"},{"full_name":"Jezek, Karel","last_name":"Jezek","first_name":"Karel"},{"last_name":"Oertner","first_name":"Thomas","full_name":"Oertner, Thomas"}],"intvolume":" 77","publisher":"Elsevier","department":[{"_id":"JoCs"}],"publication_status":"published","title":"Developmental refinement of vesicle cycling at Schaffer collateral synapses","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2845","year":"2013","day":"20","month":"03","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2013-03-20T00:00:00Z","doi":"10.1016/j.neuron.2013.01.021","page":"1109 - 1121","quality_controlled":"1","citation":{"chicago":"Rose, Tobias, Philipp Schönenberger, Karel Jezek, and Thomas Oertner. “Developmental Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.01.021.","mla":"Rose, Tobias, et al. “Developmental Refinement of Vesicle Cycling at Schaffer Collateral Synapses.” Neuron, vol. 77, no. 6, Elsevier, 2013, pp. 1109–21, doi:10.1016/j.neuron.2013.01.021.","short":"T. Rose, P. Schönenberger, K. Jezek, T. Oertner, Neuron 77 (2013) 1109–1121.","ista":"Rose T, Schönenberger P, Jezek K, Oertner T. 2013. Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. 77(6), 1109–1121.","ieee":"T. Rose, P. Schönenberger, K. Jezek, and T. Oertner, “Developmental refinement of vesicle cycling at Schaffer collateral synapses,” Neuron, vol. 77, no. 6. Elsevier, pp. 1109–1121, 2013.","apa":"Rose, T., Schönenberger, P., Jezek, K., & Oertner, T. (2013). Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.01.021","ama":"Rose T, Schönenberger P, Jezek K, Oertner T. Developmental refinement of vesicle cycling at Schaffer collateral synapses. Neuron. 2013;77(6):1109-1121. doi:10.1016/j.neuron.2013.01.021"},"publication":"Neuron"},{"acknowledgement":"This work was partially supported in part by the NSF grants CCR-0132780, CNS-0720884, CCR-0225610, by the Swiss National Science Foundation, ERC Start Grant Graph Games (Project No. 279307), FWF NFN Grant S11407-N23 (RiSE), and a Microsoft faculty fellows","year":"2013","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Elsevier","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"},{"full_name":"De Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"volume":79,"date_updated":"2021-01-12T07:00:16Z","date_created":"2018-12-11T11:59:57Z","ec_funded":1,"publist_id":"3938","file_date_updated":"2020-07-14T12:45:51Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","doi":"10.1016/j.jcss.2012.12.001","language":[{"iso":"eng"}],"month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2854","intvolume":" 79","title":"Strategy improvement for concurrent reachability and turn based stochastic safety games","ddc":["000"],"status":"public","pubrep_id":"388","oa_version":"Published Version","file":[{"file_name":"IST-2015-388-v1+1_1-s2.0-S0022000012001778-main.pdf","access_level":"open_access","content_type":"application/pdf","file_size":425488,"creator":"system","relation":"main_file","file_id":"5370","date_updated":"2020-07-14T12:45:51Z","date_created":"2018-12-12T10:18:48Z","checksum":"6d3ee12cceb946a0abe69594b6a22409"}],"type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"We consider concurrent games played on graphs. At every round of a game, each player simultaneously and independently selects a move; the moves jointly determine the transition to a successor state. Two basic objectives are the safety objective to stay forever in a given set of states, and its dual, the reachability objective to reach a given set of states. First, we present a simple proof of the fact that in concurrent reachability games, for all ε>0, memoryless ε-optimal strategies exist. A memoryless strategy is independent of the history of plays, and an ε-optimal strategy achieves the objective with probability within ε of the value of the game. In contrast to previous proofs of this fact, our proof is more elementary and more combinatorial. Second, we present a strategy-improvement (a.k.a. policy-iteration) algorithm for concurrent games with reachability objectives. Finally, we present a strategy-improvement algorithm for turn-based stochastic games (where each player selects moves in turns) with safety objectives. Our algorithms yield sequences of player-1 strategies which ensure probabilities of winning that converge monotonically (from below) to the value of the game. © 2012 Elsevier Inc."}],"citation":{"ama":"Chatterjee K, De Alfaro L, Henzinger TA. Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. 2013;79(5):640-657. doi:10.1016/j.jcss.2012.12.001","apa":"Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2013). Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2012.12.001","ieee":"K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Strategy improvement for concurrent reachability and turn based stochastic safety games,” Journal of Computer and System Sciences, vol. 79, no. 5. Elsevier, pp. 640–657, 2013.","ista":"Chatterjee K, De Alfaro L, Henzinger TA. 2013. Strategy improvement for concurrent reachability and turn based stochastic safety games. Journal of Computer and System Sciences. 79(5), 640–657.","short":"K. Chatterjee, L. De Alfaro, T.A. Henzinger, Journal of Computer and System Sciences 79 (2013) 640–657.","mla":"Chatterjee, Krishnendu, et al. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” Journal of Computer and System Sciences, vol. 79, no. 5, Elsevier, 2013, pp. 640–57, doi:10.1016/j.jcss.2012.12.001.","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Strategy Improvement for Concurrent Reachability and Turn Based Stochastic Safety Games.” Journal of Computer and System Sciences. Elsevier, 2013. https://doi.org/10.1016/j.jcss.2012.12.001."},"publication":"Journal of Computer and System Sciences","page":"640 - 657","article_type":"original","date_published":"2013-08-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01"}]