[{"publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:41Z","file_id":"4761","file_size":5813685,"checksum":"53d905e0180e23ef3e813b969ffed4e1","file_name":"IST-2016-603-v1+1_liquidError_web.pdf","relation":"main_file","access_level":"open_access","creator":"system","content_type":"application/pdf","date_created":"2018-12-12T10:09:37Z"}],"intvolume":" 32","language":[{"iso":"eng"}],"month":"07","day":"01","ddc":["000"],"article_number":"68","file_date_updated":"2020-07-14T12:45:41Z","quality_controlled":"1","scopus_import":1,"date_updated":"2023-02-23T10:44:18Z","doi":"10.1145/2461912.2461991","author":[{"full_name":"Bojsen-Hansen, Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","first_name":"Morten","last_name":"Bojsen-Hansen","orcid":"0000-0002-4417-3224"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546"}],"pubrep_id":"603","date_published":"2013-07-01T00:00:00Z","year":"2013","has_accepted_license":"1","_id":"2468","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":32,"citation":{"ama":"Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 2013;32(4). doi: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.","ista":"Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68.","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.","ieee":"M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.","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"},"issue":"4","status":"public","oa":1,"publist_id":"4434","oa_version":"Submitted Version","date_created":"2018-12-11T11:57:50Z","publisher":"ACM","title":"Liquid surface tracking with error compensation","department":[{"_id":"ChWo"}],"publication":"ACM Transactions on Graphics","abstract":[{"lang":"eng","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."}]},{"file_date_updated":"2020-07-14T12:45:41Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2021-01-12T06:57:40Z","doi":"10.1016/j.cub.2013.06.019","author":[{"last_name":"Maître","orcid":"0000-0002-3688-1474","first_name":"Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","full_name":"Maître, Jean-Léon"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"date_published":"2013-07-22T00:00:00Z","quality_controlled":"1","scopus_import":1,"license":"https://creativecommons.org/licenses/by/4.0/","file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2019-01-24T15:40:22Z","content_type":"application/pdf","file_id":"5881","date_updated":"2020-07-14T12:45:41Z","file_name":"2013_CurrentBiology_Maitre.pdf","checksum":"6a424b2f007b41d4955a9135793b2162","file_size":247320}],"publication_status":"published","intvolume":" 23","ddc":["570"],"day":"22","pmid":1,"month":"07","language":[{"iso":"eng"}],"publisher":"Cell Press","publication":"Current Biology","title":"Three functions of cadherins in cell adhesion","department":[{"_id":"CaHe"}],"publist_id":"4433","date_created":"2018-12-11T11:57:51Z","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":23,"page":"R626 - R633","year":"2013","has_accepted_license":"1","_id":"2469","issue":"14","external_id":{"pmid":["23885883"]},"oa":1,"status":"public","citation":{"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.","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.","ista":"Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion. Current Biology. 23(14), 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.","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.","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"}},{"date_updated":"2021-01-12T06:57:40Z","doi":"10.4153/CMB-2011-177-4","date_published":"2013-08-31T00:00:00Z","author":[{"orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Timothy Browning"}],"extern":1,"quality_controlled":0,"abstract":[{"lang":"eng","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."}],"publisher":"Unknown","title":"The Lang-Weil estimate for cubic hypersurfaces","publication":"Canadian Mathematical Bulletin","publist_id":"7657","date_created":"2018-12-11T11:45:25Z","day":"31","issue":"3","status":"public","acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","month":"08","citation":{"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.","ista":"Browning TD. 2013. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. 56(3), 500–502.","short":"T.D. Browning, Canadian Mathematical Bulletin 56 (2013) 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","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","ieee":"T. D. Browning, “The Lang-Weil estimate for cubic hypersurfaces,” Canadian Mathematical Bulletin, vol. 56, no. 3. Unknown, pp. 500–502, 2013.","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."},"type":"journal_article","page":"500 - 502","volume":56,"publication_status":"published","year":"2013","_id":"247","intvolume":" 56"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:45:41Z","article_number":"e70050","scopus_import":1,"quality_controlled":"1","author":[{"first_name":"Milada","last_name":"Čovanová","full_name":"Čovanová, Milada"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"last_name":"Rychtář","first_name":"Jan","full_name":"Rychtář, Jan"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"}],"date_published":"2013-07-23T00:00:00Z","pubrep_id":"413","date_updated":"2021-01-12T06:57:40Z","doi":"10.1371/journal.pone.0070050","intvolume":" 8","publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:41Z","file_id":"4681","file_name":"IST-2016-413-v1+1_journal.pone.0070050.pdf","checksum":"2d47ef47616ef4de1d517d146548184e","file_size":2294955,"creator":"system","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:08:21Z","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"month":"07","day":"23","ddc":["570"],"oa_version":"Published Version","date_created":"2018-12-11T11:57:51Z","publist_id":"4432","title":"Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells","department":[{"_id":"JiFr"}],"publication":"PLoS One","publisher":"Public Library of Science","abstract":[{"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.","lang":"eng"}],"_id":"2470","has_accepted_license":"1","year":"2013","volume":8,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013).","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.","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","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","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.","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."},"status":"public","oa":1,"issue":"7"},{"issue":"7","oa":1,"status":"public","citation":{"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","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.","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.","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.","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"},"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":8,"has_accepted_license":"1","year":"2013","_id":"2471","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"}],"publisher":"Public Library of Science","title":"Mechanism of protein kinetic stabilization by engineered disulfide crosslinks","department":[{"_id":"HaJa"}],"publication":"PLoS One","publist_id":"4430","oa_version":"Published Version","date_created":"2018-12-11T11:57:51Z","day":"30","ddc":["570"],"language":[{"iso":"eng"}],"month":"07","publication_status":"published","file":[{"file_size":1323666,"file_name":"IST-2016-414-v1+1_journal.pone.0070013.pdf","checksum":"c0c96cc76ed7ef0d036a31a7e33c9a37","date_updated":"2020-07-14T12:45:41Z","file_id":"5124","content_type":"application/pdf","date_created":"2018-12-12T10:15:07Z","relation":"main_file","access_level":"open_access","creator":"system"}],"intvolume":" 8","doi":"10.1371/journal.pone.0070013","date_updated":"2021-01-12T06:57:41Z","date_published":"2013-07-30T00:00:00Z","pubrep_id":"414","author":[{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero","first_name":"Inmaculada"},{"last_name":"Ariza","first_name":"Antonio","full_name":"Ariza, Antonio"},{"last_name":"Wilson","first_name":"Keith","full_name":"Wilson, Keith"},{"first_name":"Michael","last_name":"Skjøt","full_name":"Skjøt, Michael"},{"last_name":"Vind","first_name":"Jesper","full_name":"Vind, Jesper"},{"first_name":"Leonardo","last_name":"De Maria","full_name":"De Maria, Leonardo"},{"full_name":"Skov, Lars","last_name":"Skov","first_name":"Lars"},{"full_name":"Sánchez Ruiz, Jose","last_name":"Sánchez Ruiz","first_name":"Jose"}],"quality_controlled":"1","scopus_import":1,"article_number":"e70013","file_date_updated":"2020-07-14T12:45:41Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"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"}],"ec_funded":1,"date_created":"2018-12-11T11:57:52Z","oa_version":"Published Version","publist_id":"4431","publication":"PLoS One","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"title":"Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development","publisher":"Public Library of Science","citation":{"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","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.","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.","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).","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.","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.","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"},"status":"public","oa":1,"issue":"7","_id":"2472","has_accepted_license":"1","year":"2013","volume":8,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","scopus_import":1,"quality_controlled":"1","author":[{"full_name":"Cazzonelli, Christopher","last_name":"Cazzonelli","first_name":"Christopher"},{"last_name":"Vanstraelen","first_name":"Marleen","full_name":"Vanstraelen, Marleen"},{"first_name":"Sibu","last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yin, Kuide","first_name":"Kuide","last_name":"Yin"},{"first_name":"Ashley","last_name":"Carron Arthur","full_name":"Carron Arthur, Ashley"},{"full_name":"Nisar, Nazia","last_name":"Nisar","first_name":"Nazia"},{"first_name":"Gauri","last_name":"Tarle","full_name":"Tarle, Gauri"},{"last_name":"Cuttriss","first_name":"Abby","full_name":"Cuttriss, Abby"},{"full_name":"Searle, Iain","first_name":"Iain","last_name":"Searle"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mathesius, Ulrike","last_name":"Mathesius","first_name":"Ulrike"},{"last_name":"Masle","first_name":"Josette","full_name":"Masle, Josette"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Pogson, Barry","first_name":"Barry","last_name":"Pogson"}],"date_published":"2013-07-29T00:00:00Z","pubrep_id":"393","date_updated":"2021-01-12T06:57:41Z","doi":"10.1371/journal.pone.0070069","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:45:41Z","article_number":"e70069","month":"07","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"},{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7"}],"ddc":["580","570"],"day":"29","intvolume":" 8","file":[{"access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T10:16:34Z","content_type":"application/pdf","file_id":"5222","date_updated":"2020-07-14T12:45:41Z","checksum":"3be71828b6c2ba9c90eb7056e3f7f57a","file_name":"IST-2015-393-v1+1_journal.pone.0070069.pdf","file_size":9003465}],"publication_status":"published"},{"citation":{"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","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.","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","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.","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.","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"},"status":"public","oa":1,"issue":"8","_id":"2473","has_accepted_license":"1","year":"2013","page":"75 - 89","volume":87,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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."}],"oa_version":"Submitted Version","date_created":"2018-12-11T11:57:52Z","ec_funded":1,"publist_id":"4428","title":"Genetic hitch-hiking in spatially extended populations","department":[{"_id":"NiBa"}],"publication":"Theoretical Population Biology","publisher":"Elsevier","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"month":"01","day":"03","ddc":["570"],"intvolume":" 87","publication_status":"published","file":[{"file_size":1706282,"file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","checksum":"4274ec1f433b838a7d5b941cc9684ca7","date_updated":"2020-07-14T12:45:41Z","file_id":"5376","content_type":"application/pdf","date_created":"2018-12-12T10:18:54Z","relation":"main_file","creator":"system","access_level":"open_access"}],"scopus_import":1,"quality_controlled":"1","pubrep_id":"118","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"date_published":"2013-01-03T00:00:00Z","date_updated":"2021-01-12T06:57:42Z","doi":"10.1016/j.tpb.2012.12.001","file_date_updated":"2020-07-14T12:45:41Z"},{"date_created":"2018-12-11T11:57:54Z","publist_id":"4423","title":"Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling","publication":"PNAS","publisher":"National Academy of Sciences","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"}],"extern":1,"quality_controlled":0,"date_published":"2013-01-08T00:00:00Z","author":[{"full_name":"Budreck, Elaine C","last_name":"Budreck","first_name":"Elaine"},{"last_name":"Kwon","first_name":"Oh","full_name":"Kwon, Oh-Bin"},{"last_name":"Jung","first_name":"Jung","full_name":"Jung, Jung-Hoon"},{"first_name":"Stéphane","last_name":"Baudouin","full_name":"Baudouin, Stéphane J"},{"last_name":"Thommen","first_name":"Albert","full_name":"Thommen, Albert"},{"full_name":"Kim, Hye-Sun","first_name":"Hye","last_name":"Kim"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"last_name":"Harada","orcid":"0000-0001-7429-7896","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harumi Harada"},{"last_name":"Tabuchi","first_name":"Katsuhiko","full_name":"Tabuchi, Katsuhiko"},{"first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Ryuichi Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Scheiffele, Peter","last_name":"Scheiffele","first_name":"Peter"},{"full_name":"Kim, Joung-Hun","last_name":"Kim","first_name":"Joung"}],"doi":"10.1073/pnas.1214718110","date_updated":"2021-01-12T06:57:43Z","_id":"2478","intvolume":" 110","publication_status":"published","year":"2013","page":"725 - 730","volume":110,"type":"journal_article","citation":{"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","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.","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.","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.","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.","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.","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"},"month":"01","status":"public","day":"08","issue":"2"},{"page":"1030 - 1078","volume":108,"type":"journal_article","_id":"250","intvolume":" 108","main_file_link":[{"url":"https://arxiv.org/abs/1210.4010","open_access":"1"}],"publication_status":"published","year":"2013","oa":1,"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.","status":"public","day":"29","issue":"4","citation":{"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","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.","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.","short":"R. De La Bretèche, T.D. Browning, Proceedings of the London Mathematical Society 108 (2013) 1030–1078.","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.","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.","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"},"month":"11","title":"Density of Châtelet surfaces failing the Hasse principle","publication":"Proceedings of the London Mathematical Society","publisher":"Oxford University Press","date_created":"2018-12-11T11:45:26Z","publist_id":"7652","author":[{"first_name":"Régis","last_name":"De La Bretèche","full_name":"de la Bretèche, Régis"},{"full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning"}],"date_published":"2013-11-29T00:00:00Z","date_updated":"2021-01-12T06:57:51Z","doi":"10.1112/plms/pdt060","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,"quality_controlled":0},{"month":"05","citation":{"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","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.","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.","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.","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.","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"},"issue":"1","day":"14","status":"public","year":"2013","publication_status":"published","intvolume":" 26","_id":"251","type":"journal_article","volume":26,"page":"25 - 44","extern":1,"quality_controlled":0,"abstract":[{"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].","lang":"eng"}],"doi":"10.5802/jtnb.857","date_updated":"2021-01-12T06:57:55Z","date_published":"2013-05-14T00:00:00Z","author":[{"full_name":"de la Bretèche, Régis","first_name":"Régis","last_name":"De La Bretèche"},{"full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning"}],"publist_id":"7651","date_created":"2018-12-11T11:45:26Z","publisher":"Universite de Bordeaux I","publication":"Journal de Theorie des Nombres de Bordeaux","title":"Counter examples to the Hasse principle among certain coflasque tori"},{"doi":"10.1109/TPAMI.2013.140","date_updated":"2021-01-12T06:57:58Z","date_published":"2013-07-30T00:00:00Z","author":[{"last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"full_name":"Nickisch, Hannes","last_name":"Nickisch","first_name":"Hannes"},{"last_name":"Harmeling","first_name":"Stefan","full_name":"Harmeling, Stefan"}],"quality_controlled":"1","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"}],"scopus_import":1,"publisher":"IEEE","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","department":[{"_id":"ChLa"}],"title":"Attribute-based classification for zero-shot learning of object categories","publist_id":"4385","date_created":"2018-12-11T11:58:08Z","oa_version":"None","issue":"3","day":"30","status":"public","month":"07","language":[{"iso":"eng"}],"citation":{"short":"C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2013) 453–465.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":36,"page":"453 - 465","year":"2013","publication_status":"published","intvolume":" 36","_id":"2516"},{"file_date_updated":"2020-07-14T12:45:42Z","conference":{"start_date":"2013-07-08","location":"Riga, Latvia","end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming"},"article_processing_charge":"No","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-39212-2_3","date_updated":"2020-08-11T10:09:47Z","date_published":"2013-07-01T00:00:00Z","author":[{"first_name":"Shaull","last_name":"Almagor","full_name":"Almagor, Shaull"},{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi","last_name":"Boker","first_name":"Udi"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"quality_controlled":"1","scopus_import":1,"file":[{"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2020-05-15T11:16:12Z","content_type":"application/pdf","date_updated":"2020-07-14T12:45:42Z","file_id":"7860","file_name":"2013_ICALP_Almagor.pdf","checksum":"85afbf6c18a2c7e377c52c9410e2d824","file_size":363031}],"publication_status":"published","intvolume":" 7966","ddc":["000"],"day":"01","month":"07","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"language":[{"iso":"eng"}],"publisher":"Springer","department":[{"_id":"ToHe"}],"title":"Formalizing and reasoning about quality","publist_id":"4384","ec_funded":1,"date_created":"2018-12-11T11:58:08Z","oa_version":"Submitted Version","series_title":"Lecture Notes in Computer Science","abstract":[{"lang":"eng","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":7966,"page":"15 - 27","has_accepted_license":"1","year":"2013","_id":"2517","issue":"Part 2","status":"public","oa":1,"acknowledgement":"ERC Grant QUALITY. ","citation":{"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.","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.","short":"S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27.","ista":"Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality. 7966(Part 2), 15–27.","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.","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"}},{"author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"}],"date_published":"2013-07-01T00:00:00Z","doi":"10.1007/978-3-642-39206-1_53","related_material":{"record":[{"status":"public","relation":"later_version","id":"2271"}]},"alternative_title":["LNCS"],"date_updated":"2023-02-23T10:35:42Z","scopus_import":1,"quality_controlled":"1","conference":{"name":"ICALP: Automata, Languages and Programming","end_date":"2013-07-12","location":"Riga, Latvia","start_date":"2013-07-08"},"day":"01","month":"07","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1207.7213","open_access":"1"}],"intvolume":" 7965","publication_status":"published","arxiv":1,"abstract":[{"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.","lang":"eng"}],"department":[{"_id":"VlKo"}],"title":"The power of linear programming for finite-valued CSPs: A constructive characterization","publisher":"Springer","date_created":"2018-12-11T11:58:08Z","oa_version":"Preprint","publist_id":"4383","status":"public","oa":1,"issue":"1","external_id":{"arxiv":["1207.7213"]},"citation":{"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","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.","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.","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.","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.","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"},"volume":7965,"page":"625 - 636","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"2518","year":"2013"},{"page":"527 - 536","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2520","year":"2013","has_accepted_license":"1","oa":1,"status":"public","citation":{"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.","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.","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.","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.","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.","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."},"publication_identifier":{"isbn":["9780974903996"]},"department":[{"_id":"ChLa"}],"title":"The supervised IBP: Neighbourhood preserving infinite latent feature models","publication":"Proceedings of the 29th conference uncertainty in Artificial Intelligence","publisher":"AUAI Press","oa_version":"Submitted Version","date_created":"2018-12-11T11:58:09Z","publist_id":"4381","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."}],"publication_status":"published","file":[{"relation":"main_file","creator":"system","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:15:16Z","file_id":"5134","date_updated":"2020-07-14T12:45:42Z","file_size":1117100,"file_name":"IST-2013-137-v1+1_QuaShaKnoGha13.pdf","checksum":"325f20c4b926bd74d39006b97df572bd"}],"day":"11","ddc":["000"],"language":[{"iso":"eng"}],"month":"07","file_date_updated":"2020-07-14T12:45:42Z","conference":{"name":"UAI: Uncertainty in Artificial Intelligence","end_date":"2013-07-15","location":"Bellevue, WA, United States","start_date":"2013-07-11"},"pubrep_id":"137","date_published":"2013-07-11T00:00:00Z","author":[{"full_name":"Quadrianto, Novi","last_name":"Quadrianto","first_name":"Novi"},{"full_name":"Sharmanska, Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia","orcid":"0000-0003-0192-9308","last_name":"Sharmanska"},{"first_name":"David","last_name":"Knowles","full_name":"Knowles, David"},{"full_name":"Ghahramani, Zoubin","first_name":"Zoubin","last_name":"Ghahramani"}],"date_updated":"2023-02-23T10:46:36Z","scopus_import":1,"quality_controlled":"1"},{"status":"public","issue":"1","day":"06","citation":{"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.","chicago":"Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” Mathematika. Unknown, 2013. https://doi.org/10.1112/S0025579313000132.","short":"T.D. Browning, Mathematika 60 (2013) 101–107.","ista":"Browning TD. 2013. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 60(1), 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.","ama":"Browning TD. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 2013;60(1):101-107. doi:10.1112/S0025579313000132"},"month":"09","volume":60,"page":"101 - 107","type":"journal_article","_id":"253","intvolume":" 60","year":"2013","publication_status":"published","date_published":"2013-09-06T00:00:00Z","author":[{"first_name":"Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1112/S0025579313000132","date_updated":"2021-01-12T06:58:03Z","quality_controlled":0,"extern":1,"publication":"Mathematika","title":"Counting rational points on cubic hypersurfaces: Corrigendum","publisher":"Unknown","date_created":"2018-12-11T11:45:27Z","publist_id":"7649"},{"publisher":"Wiley-Blackwell","title":"Evaluation of glutamate concentration transient in the synaptic cleft of the rat calyx of Held","publication":"Journal of Physiology","publist_id":"4207","date_created":"2018-12-11T11:59:05Z","doi":"10.1113/jphysiol.2012.241398","date_updated":"2021-01-12T06:59:04Z","date_published":"2013-01-01T00:00:00Z","author":[{"full_name":"Budisantoso, Timotheus","first_name":"Timotheus","last_name":"Budisantoso"},{"id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harumi Harada","last_name":"Harada","orcid":"0000-0001-7429-7896","first_name":"Harumi"},{"first_name":"Naomi","last_name":"Kamasawa","full_name":"Kamasawa, Naomi"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Matsui, Ko","first_name":"Ko","last_name":"Matsui"}],"quality_controlled":0,"extern":1,"abstract":[{"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.","lang":"eng"}],"type":"journal_article","page":"219 - 239","volume":591,"publication_status":"published","year":"2013","intvolume":" 591","_id":"2690","day":"01","issue":"1","status":"public","month":"01","citation":{"short":"T. Budisantoso, H. Harada, N. Kamasawa, Y. Fukazawa, R. Shigemoto, K. Matsui, Journal of Physiology 591 (2013) 219–239.","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.","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.","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","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","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.","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."}},{"publisher":"Society for Neuroscience","publication":"Journal of Neuroscience","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","publist_id":"4206","date_created":"2018-12-11T11:59:05Z","date_updated":"2021-01-12T06:59:05Z","doi":"10.1523/JNEUROSCI.2921-12.2013","date_published":"2013-02-20T00:00:00Z","author":[{"full_name":"Indriati, Dwi Wahyu","last_name":"Indriati","first_name":"Dwi"},{"first_name":"Naomi","last_name":"Kamasawa","full_name":"Kamasawa, Naomi"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"},{"full_name":"Meredith, Andrea L","last_name":"Meredith","first_name":"Andrea"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto"}],"extern":1,"quality_controlled":0,"abstract":[{"lang":"eng","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."}],"type":"journal_article","volume":33,"page":"3668 - 3678","year":"2013","publication_status":"published","_id":"2691","intvolume":" 33","issue":"8","day":"20","status":"public","month":"02","citation":{"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.","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.","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.","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.","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"}},{"day":"01","status":"public","month":"03","citation":{"short":"A. Dobi, S. Sartori, D. Busti, H. Van Der Putten, N. Singewald, R. Shigemoto, F. Ferraguti, Neuropharmacology 66 (2013) 274–289.","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.","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.","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","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","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.","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."},"type":"journal_article","page":"274 - 289","volume":66,"publication_status":"published","year":"2013","_id":"2692","intvolume":" 66","date_updated":"2021-01-12T06:59:05Z","doi":"10.1016/j.neuropharm.2012.05.025","date_published":"2013-03-01T00:00:00Z","author":[{"first_name":"Alice","last_name":"Dobi","full_name":"Dobi, Alice"},{"full_name":"Sartori, Simone B","last_name":"Sartori","first_name":"Simone"},{"full_name":"Busti, Daniela","first_name":"Daniela","last_name":"Busti"},{"first_name":"Herman","last_name":"Van Der Putten","full_name":"Van Der Putten, Herman V"},{"full_name":"Singewald, Nicolas","last_name":"Singewald","first_name":"Nicolas"},{"full_name":"Ryuichi Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"full_name":"Ferraguti, Francesco","first_name":"Francesco","last_name":"Ferraguti"}],"extern":1,"quality_controlled":0,"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."}],"publisher":"Elsevier","title":"Neural substrates for the distinct effects of presynaptic group III metabotropic glutamate receptors on extinction of contextual fear conditioning in mice","publication":"Neuropharmacology","publist_id":"4205","date_created":"2018-12-11T11:59:06Z"},{"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."}],"extern":1,"quality_controlled":0,"author":[{"full_name":"Booker, Sam A","first_name":"Sam","last_name":"Booker"},{"last_name":"Gross","first_name":"Anna","full_name":"Gross, Anna"},{"full_name":"Althof, Daniel","first_name":"Daniel","last_name":"Althof"},{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto"},{"full_name":"Bettler, Bernhard","first_name":"Bernhard","last_name":"Bettler"},{"full_name":"Frotscher, Michael","last_name":"Frotscher","first_name":"Michael"},{"last_name":"Hearing","first_name":"Matthew","full_name":"Hearing, Matthew C"},{"full_name":"Wickman, Kevin D","last_name":"Wickman","first_name":"Kevin"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"last_name":"Kulik","first_name":"Ákos","full_name":"Kulik, Ákos"},{"full_name":"Vida, Imre","first_name":"Imre","last_name":"Vida"}],"date_published":"2013-05-01T00:00:00Z","doi":"10.1523/JNEUROSCI.1186-12.2013","date_updated":"2021-01-12T06:59:05Z","date_created":"2018-12-11T11:59:06Z","publist_id":"4204","publication":"Journal of Neuroscience","title":"Differential GABAB-receptor-mediated effects in perisomatic- and dendrite-targeting parvalbumin interneurons","publisher":"Society for Neuroscience","citation":{"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","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.","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.","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.","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.","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"},"month":"05","status":"public","issue":"18","day":"01","intvolume":" 33","_id":"2693","year":"2013","publication_status":"published","volume":33,"page":"7961 - 7974","type":"journal_article"},{"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."}],"quality_controlled":0,"extern":1,"date_published":"2013-10-01T00:00:00Z","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"László Erdös","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László"},{"last_name":"Knowles","first_name":"Antti","full_name":"Knowles, Antti"},{"last_name":"Yau","first_name":"Horng","full_name":"Yau, Horng-Tzer"},{"last_name":"Yin","first_name":"Jun","full_name":"Yin, Jun"}],"doi":"10.1007/s00220-013-1773-3","date_updated":"2021-01-12T06:59:07Z","date_created":"2018-12-11T11:59:07Z","publist_id":"4199","publication":"Communications in Mathematical Physics","title":"Delocalization and diffusion profile for random band matrices","publisher":"Springer","citation":{"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","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.","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.","short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Communications in Mathematical Physics 323 (2013) 367–416.","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.","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.","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"},"month":"10","status":"public","oa":1,"issue":"1","day":"01","_id":"2697","intvolume":" 323","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.5669"}],"year":"2013","publication_status":"published","volume":323,"page":"367 - 416","type":"journal_article"}]