[{"oa":1,"publisher":"Academic Press","author":[{"full_name":"Nam, Phan","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam"},{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M","first_name":"Marcin M"},{"last_name":"Solovej","full_name":"Solovej, Jan","first_name":"Jan"}],"title":"Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations","oa_version":"Submitted Version","doi":"10.1016/j.jfa.2015.12.007","page":"4340 - 4368","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:38Z","corr_author":"1","date_updated":"2025-09-18T11:04:09Z","year":"2016","month":"06","type":"journal_article","ec_funded":1,"main_file_link":[{"url":"http://arxiv.org/abs/1508.07321","open_access":"1"}],"intvolume":"       270","citation":{"apa":"Nam, P., Napiórkowski, M. M., &#38; Solovej, J. (2016). Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. <i>Journal of Functional Analysis</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jfa.2015.12.007\">https://doi.org/10.1016/j.jfa.2015.12.007</a>","ista":"Nam P, Napiórkowski MM, Solovej J. 2016. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 270(11), 4340–4368.","ieee":"P. Nam, M. M. Napiórkowski, and J. Solovej, “Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations,” <i>Journal of Functional Analysis</i>, vol. 270, no. 11. Academic Press, pp. 4340–4368, 2016.","ama":"Nam P, Napiórkowski MM, Solovej J. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. <i>Journal of Functional Analysis</i>. 2016;270(11):4340-4368. doi:<a href=\"https://doi.org/10.1016/j.jfa.2015.12.007\">10.1016/j.jfa.2015.12.007</a>","short":"P. Nam, M.M. Napiórkowski, J. Solovej, Journal of Functional Analysis 270 (2016) 4340–4368.","mla":"Nam, Phan, et al. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” <i>Journal of Functional Analysis</i>, vol. 270, no. 11, Academic Press, 2016, pp. 4340–68, doi:<a href=\"https://doi.org/10.1016/j.jfa.2015.12.007\">10.1016/j.jfa.2015.12.007</a>.","chicago":"Nam, Phan, Marcin M Napiórkowski, and Jan Solovej. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” <i>Journal of Functional Analysis</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.jfa.2015.12.007\">https://doi.org/10.1016/j.jfa.2015.12.007</a>."},"acknowledgement":"We thank Jan Dereziński for several inspiring discussions and useful remarks. We thank the referee for helpful comments. J.P.S. thanks the Erwin Schrödinger Institute for the hospitality during the thematic programme “Quantum many-body systems, random matrices, and disorder”. We gratefully acknowledge the financial supports by the European Union's Seventh Framework Programme under the ERC Advanced Grant ERC-2012-AdG 321029 (J.P.S.) and the REA grant agreement No. 291734 (P.T.N.), as well as the support of the National Science Center (NCN) grant No. 2012/07/N/ST1/03185 and the Austrian Science Fund (FWF) project No. P 27533-N27 (M.N.).","arxiv":1,"status":"public","publist_id":"5626","date_published":"2016-06-01T00:00:00Z","day":"01","external_id":{"arxiv":["1508.07321"],"isi":["000375241700011"]},"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"volume":270,"abstract":[{"lang":"eng","text":"We provide general conditions for which bosonic quadratic Hamiltonians on Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover the case when quantum systems have infinite degrees of freedom and the associated one-body kinetic and paring operators are unbounded. Our sufficient conditions are optimal in the sense that they become necessary when the relevant one-body operators commute."}],"isi":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"_id":"1545","issue":"11","article_processing_charge":"No","publication":"Journal of Functional Analysis","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:55Z","volume":55,"abstract":[{"text":"A range of bright and photostable rhodamines and carbopyronines with absorption maxima in the range of λ=500-630 nm were prepared, and enabled the specific labeling of cytoskeletal filaments using HaloTag technology followed by staining with 1 μm solutions of the dye-ligand conjugates. The synthesis, photophysical parameters, fluorogenic behavior, and structure-property relationships of the new dyes are discussed. Light microscopy with stimulated emission depletion (STED) provided one- and two-color images of living cells with an optical resolution of 40-60 nm.","lang":"eng"}],"date_updated":"2021-01-12T06:47:59Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"extern":"1","language":[{"iso":"eng"}],"issue":"10","month":"03","article_processing_charge":"No","publication":"Angewandte Chemie - International Edition","publication_status":"published","year":"2016","_id":"1059","intvolume":"        55","type":"journal_article","publisher":"Wiley-Blackwell","doi":"10.1002/anie.201511018","status":"public","publist_id":"6330","page":"3290 - 3294","date_published":"2016-03-01T00:00:00Z","day":"01","author":[{"last_name":"Butkevich","full_name":"Butkevich, Alexey","first_name":"Alexey"},{"last_name":"Mitronova","first_name":"Gyuzel","full_name":"Mitronova, Gyuzel"},{"first_name":"Sven","full_name":"Sidenstein, Sven","last_name":"Sidenstein"},{"last_name":"Klocke","full_name":"Klocke, Jessica","first_name":"Jessica"},{"last_name":"Kamin","full_name":"Kamin, Dirk","first_name":"Dirk"},{"full_name":"Meineke, Dirk","first_name":"Dirk","last_name":"Meineke"},{"last_name":"D'Este","full_name":"D'Este, Elisa","first_name":"Elisa"},{"full_name":"Kraemer, Philip","first_name":"Philip","last_name":"Kraemer"},{"first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973"},{"last_name":"Belov","full_name":"Belov, Vladimir","first_name":"Vladimir"},{"first_name":"Stefan","full_name":"Hell, Stefan","last_name":"Hell"}],"title":"Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells","oa_version":"None","citation":{"ista":"Butkevich A, Mitronova G, Sidenstein S, Klocke J, Kamin D, Meineke D, D’Este E, Kraemer P, Danzl JG, Belov V, Hell S. 2016. Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. Angewandte Chemie - International Edition. 55(10), 3290–3294.","apa":"Butkevich, A., Mitronova, G., Sidenstein, S., Klocke, J., Kamin, D., Meineke, D., … Hell, S. (2016). Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/anie.201511018\">https://doi.org/10.1002/anie.201511018</a>","short":"A. Butkevich, G. Mitronova, S. Sidenstein, J. Klocke, D. Kamin, D. Meineke, E. D’Este, P. Kraemer, J.G. Danzl, V. Belov, S. Hell, Angewandte Chemie - International Edition 55 (2016) 3290–3294.","mla":"Butkevich, Alexey, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 10, Wiley-Blackwell, 2016, pp. 3290–94, doi:<a href=\"https://doi.org/10.1002/anie.201511018\">10.1002/anie.201511018</a>.","chicago":"Butkevich, Alexey, Gyuzel Mitronova, Sven Sidenstein, Jessica Klocke, Dirk Kamin, Dirk Meineke, Elisa D’Este, et al. “Fluorescent Rhodamines and Fluorogenic Carbopyronines for Super-Resolution STED Microscopy in Living Cells.” <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell, 2016. <a href=\"https://doi.org/10.1002/anie.201511018\">https://doi.org/10.1002/anie.201511018</a>.","ieee":"A. Butkevich <i>et al.</i>, “Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 10. Wiley-Blackwell, pp. 3290–3294, 2016.","ama":"Butkevich A, Mitronova G, Sidenstein S, et al. Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells. <i>Angewandte Chemie - International Edition</i>. 2016;55(10):3290-3294. doi:<a href=\"https://doi.org/10.1002/anie.201511018\">10.1002/anie.201511018</a>"},"acknowledgement":"We thank Prof. Y. Okada (RIKEN Quantitative Biology Center, Osaka, Japan) for the gift of β-tubulin-Halo plasmid, T. Gilat and Dr. E. Rothermel (MPIBPC, Göttingen, Germany) for cell culture and transfection, M. Pulst, J. Bienert (MPIBPC), Dr. M. John, Dr. H. Frauendorf, and co-workers (Institut für Organische und Biomolekulare Chemie, Georg-August-Universität, Göttingen, Germany) for UV/Vis, NMR, and ESI-MS spectra, Prof. M. L. Bossi (University of Buenos-Aires, Argentina) for measuring fluorescence lifetimes, and Dr. S. Vos and Prof. P. Cramer (MPIBPC) for access to a Tecan microplate reader. S.W.H. acknowledges a grant from the Bundesministerium für Bildung und Forschung (BMBF 513) within the program “Optische Technologien für Biowissenschaften und Gesundheit” (FKZ 13N11066). J.G.D. was supported by funds from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013; REA grant agreement PIEF-GA-2011-299283)."},{"doi":"10.1038/srep26725","status":"public","date_published":"2016-05-25T00:00:00Z","publist_id":"6329","page":"1 - 8","day":"25","author":[{"full_name":"Sidenstein, Sven","first_name":"Sven","last_name":"Sidenstein"},{"last_name":"D'Este","full_name":"D'Este, Elisa","first_name":"Elisa"},{"last_name":"Böhm","first_name":"Marvin","full_name":"Böhm, Marvin"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G","first_name":"Johann G"},{"full_name":"Belov, Vladimir","first_name":"Vladimir","last_name":"Belov"},{"first_name":"Stefan","full_name":"Hell, Stefan","last_name":"Hell"}],"title":"Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses","acknowledgement":"We acknowledge the assistance of I. Herfort with neuron preparation, and of J. Bienert and K. Müller with analyses of the dye 540R derivatives. We thank T. Gilat and E. Rothermel for sample preparation as well as J. Keller, F. Winter (all MPI-BPC) and C.A. Wurm (Abberior Instruments) for helpful discussion, and S.J. Sahl (MPI-BPC) for a critical reading of the manuscript.","oa_version":"None","citation":{"ista":"Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. 2016. Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. Scientific Reports. 6, 1–8.","apa":"Sidenstein, S., D’Este, E., Böhm, M., Danzl, J. G., Belov, V., &#38; Hell, S. (2016). Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep26725\">https://doi.org/10.1038/srep26725</a>","short":"S. Sidenstein, E. D’Este, M. Böhm, J.G. Danzl, V. Belov, S. Hell, Scientific Reports 6 (2016) 1–8.","mla":"Sidenstein, Sven, et al. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization at Synapses.” <i>Scientific Reports</i>, vol. 6, Nature Publishing Group, 2016, pp. 1–8, doi:<a href=\"https://doi.org/10.1038/srep26725\">10.1038/srep26725</a>.","chicago":"Sidenstein, Sven, Elisa D’Este, Marvin Böhm, Johann G Danzl, Vladimir Belov, and Stefan Hell. “Multicolour Multilevel STED Nanoscopy of Actin/Spectrin Organization at Synapses.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep26725\">https://doi.org/10.1038/srep26725</a>.","ieee":"S. Sidenstein, E. D’Este, M. Böhm, J. G. Danzl, V. Belov, and S. Hell, “Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, pp. 1–8, 2016.","ama":"Sidenstein S, D’Este E, Böhm M, Danzl JG, Belov V, Hell S. Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses. <i>Scientific Reports</i>. 2016;6:1-8. doi:<a href=\"https://doi.org/10.1038/srep26725\">10.1038/srep26725</a>"},"intvolume":"         6","publisher":"Nature Publishing Group","type":"journal_article","month":"05","article_processing_charge":"No","publication":"Scientific Reports","publication_status":"published","year":"2016","_id":"1060","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:56Z","volume":6,"abstract":[{"text":"Superresolution fluorescence microscopy of multiple fluorophores still requires development. Here we present simultaneous three-colour stimulated emission depletion (STED) nanoscopy relying on a single STED beam at 620 nm. Toggling the STED beam between two or more power levels (&quot;multilevelSTEDv) optimizes resolution and contrast in all colour channels, which are intrinsically co-aligned and well separated. Three-colour recording is demonstrated by imaging the nanoscale cytoskeletal organization in cultured hippocampal neurons. The down to ∼35 nm resolution identified periodic actin/betaII spectrin lattices along dendrites and spines; however, at presynaptic and postsynaptic sites, these patterns were found to be absent. Both our multicolour scheme and the 620 nm STED line should be attractive for routine STED microscopy applications.","lang":"eng"}],"date_updated":"2021-01-12T06:47:59Z","extern":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}]},{"intvolume":"        58","type":"conference","ec_funded":1,"status":"public","day":"01","article_number":"25","publist_id":"6317","date_published":"2016-08-01T00:00:00Z","citation":{"ama":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. Conditionally optimal algorithms for generalized Büchi Games. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>","ieee":"K. Chatterjee, W. Dvorák, M. Henzinger, and V. Loitzenbauer, “Conditionally optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland, 2016, vol. 58.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Veronika Loitzenbauer. “Conditionally Optimal Algorithms for Generalized Büchi Games,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Conditionally Optimal Algorithms for Generalized Büchi Games</i>. Vol. 58, 25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>.","short":"K. Chatterjee, W. Dvorák, M. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M., &#38; Loitzenbauer, V. (2016). Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>","ista":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. 2016. Conditionally optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 25."},"acknowledgement":"K. C., M. H., and W. D. are partially supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant (279307","department":[{"_id":"KrCh"}],"ddc":["000","004","006"],"abstract":[{"text":"Games on graphs provide the appropriate framework to study several central problems in computer science, such as verification and synthesis of reactive systems. One of the most basic objectives for games on graphs is the liveness (or Büchi) objective that given a target set of vertices requires that some vertex in the target set is visited infinitely often. We study generalized Büchi objectives (i.e., conjunction of liveness objectives), and implications between two generalized Büchi objectives (known as GR(1) objectives), that arise in numerous applications in computer-aided verification. We present improved algorithms and conditional super-linear lower bounds based on widely believed assumptions about the complexity of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider graph games with n vertices, m edges, and generalized Büchi objectives with k conjunctions. First, we present an algorithm with running time O(k*n^2), improving the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm is optimal for dense graphs under (A1). Second, we show that the basic algorithm for the problem is optimal for sparse graphs when the target sets have constant size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1 k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time algorithm for m &gt; n^{1.5}. ","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/3.0/","file_date_updated":"2018-12-12T10:16:02Z","volume":58,"scopus_import":"1","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","publication_status":"published","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"}],"conference":{"location":"Krakow, Poland","name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2016-08-22","end_date":"2016-08-26"},"_id":"1068","pubrep_id":"779","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.4230/LIPIcs.MFCS.2016.25","title":"Conditionally optimal algorithms for generalized Büchi Games","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Dvorák","full_name":"Dvorák, Wolfgang","first_name":"Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"full_name":"Loitzenbauer, Veronika","first_name":"Veronika","last_name":"Loitzenbauer"}],"alternative_title":["LIPIcs"],"oa_version":"Published Version","date_created":"2018-12-11T11:49:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:49:55Z","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"month":"08","has_accepted_license":"1","file":[{"file_size":632786,"content_type":"application/pdf","access_level":"open_access","creator":"system","file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf","date_created":"2018-12-12T10:16:02Z","date_updated":"2018-12-12T10:16:02Z","file_id":"5187","relation":"main_file"}],"year":"2016"},{"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","pubrep_id":"778","oa_version":"Published Version","alternative_title":["LIPIcs"],"author":[{"first_name":"Ventsislav K","full_name":"Chonev, Ventsislav K","last_name":"Chonev","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ouaknine","first_name":"Joël","full_name":"Ouaknine, Joël"},{"last_name":"Worrell","first_name":"James","full_name":"Worrell, James"}],"title":"On the skolem problem for continuous linear dynamical systems","doi":"10.4230/LIPIcs.ICALP.2016.100","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-06-03T11:32:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:59Z","year":"2016","file":[{"file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf","file_id":"5213","relation":"main_file","date_updated":"2018-12-12T10:16:26Z","date_created":"2018-12-12T10:16:26Z","access_level":"open_access","content_type":"application/pdf","file_size":521415,"creator":"system"}],"has_accepted_license":"1","month":"08","ec_funded":1,"type":"conference","intvolume":"        55","acknowledgement":"Ventsislav Chonev is supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307:  Graph Games), and ERC Advanced Grant (267989: QUAREM).","citation":{"ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the skolem problem for continuous linear dynamical systems. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 100.","apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On the skolem problem for continuous linear dynamical systems (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Chonev, Ventsislav K., et al. <i>On the Skolem Problem for Continuous Linear Dynamical Systems</i>. Vol. 55, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>.","ama":"Chonev VK, Ouaknine J, Worrell J. On the skolem problem for continuous linear dynamical systems. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the skolem problem for continuous linear dynamical systems,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55."},"publist_id":"6314","date_published":"2016-08-01T00:00:00Z","article_number":"100","day":"01","status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","volume":55,"file_date_updated":"2018-12-12T10:16:26Z","abstract":[{"lang":"eng","text":"The Continuous Skolem Problem asks whether a real-valued function satisfying a linear differen-\r\ntial equation has a zero in a given interval of real numbers. This is a fundamental reachability\r\nproblem for continuous linear dynamical systems, such as linear hybrid automata and continuous-\r\ntime Markov chains. Decidability of the problem is currently open – indeed decidability is open\r\neven for the sub-problem in which a zero is sought in a bounded interval. In this paper we show\r\ndecidability of the bounded problem subject to Schanuel’s Conjecture, a unifying conjecture in\r\ntranscendental number theory. We furthermore analyse the unbounded problem in terms of the\r\nfrequencies of the differential equation, that is, the imaginary parts of the characteristic roots.\r\nWe show that the unbounded problem can be reduced to the bounded problem if there is at most\r\none rationally linearly independent frequency, or if there are two rationally linearly independent\r\nfrequencies and all characteristic roots are simple. We complete the picture by showing that de-\r\ncidability of the unbounded problem in the case of two (or more) rationally linearly independent\r\nfrequencies would entail a major new effectiveness result in Diophantine approximation, namely\r\ncomputability of the Diophantine-approximation types of all real algebraic numbers."}],"department":[{"_id":"KrCh"}],"ddc":["004","006"],"_id":"1069","conference":{"name":"ICALP: Automata, Languages and Programming","location":"Rome, Italy","end_date":"2016-07-15","start_date":"2016-07-12"},"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"publication_status":"published","article_processing_charge":"No"},{"month":"01","file":[{"file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf","relation":"main_file","file_id":"4714","date_updated":"2018-12-12T10:08:52Z","date_created":"2018-12-12T10:08:52Z","access_level":"open_access","content_type":"application/pdf","file_size":546133,"creator":"system"}],"has_accepted_license":"1","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:59Z","date_updated":"2025-06-03T11:18:54Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.4230/LIPIcs.ICALP.2016.98","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"title":"Computation tree logic for synchronization properties","oa_version":"Published Version","alternative_title":["LIPIcs"],"pubrep_id":"812","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"No","publication_status":"published","conference":{"location":"Rome, Italy","name":"ICALP: Automata, Languages and Programming","end_date":"2016-07-15","start_date":"2016-07-12"},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"_id":"1070","ddc":["005"],"department":[{"_id":"KrCh"}],"volume":55,"file_date_updated":"2018-12-12T10:08:52Z","abstract":[{"lang":"eng","text":"We present a logic that extends CTL (Computation Tree Logic) with operators that express synchronization properties. A property is synchronized in a system if it holds in all paths of a certain length. The new logic is obtained by using the same path quantifiers and temporal operators as in CTL, but allowing a different order of the quantifiers. This small syntactic variation induces a logic that can express non-regular properties for which known extensions of MSO with equality of path length are undecidable. We show that our variant of CTL is decidable and that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We analogously consider quantifier exchange in extensions of CTL, and we present operators defined using basic operators of CTL* that express the occurrence of infinitely many synchronization points. We show that the model-checking problem remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide if the Next operator is allowed in the logics, thus the classical bisimulation quotient can be used for state-space reduction before model checking. "}],"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publist_id":"6313","date_published":"2016-01-01T00:00:00Z","day":"01","article_number":"98","citation":{"ista":"Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.","apa":"Chatterjee, K., &#38; Doyen, L. (2016). Computation tree logic for synchronization properties (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>","short":"K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Computation Tree Logic for Synchronization Properties</i>. Vol. 55, 98, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Computation Tree Logic for Synchronization Properties,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>.","ieee":"K. Chatterjee and L. Doyen, “Computation tree logic for synchronization properties,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55.","ama":"Chatterjee K, Doyen L. Computation tree logic for synchronization properties. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>"},"acknowledgement":"This research was partially supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003, and European project Cassting (FP7-601148).\r\n\r\nWe thank Stefan Göller and anonymous reviewers for their insightful\r\ncomments and suggestions.\r\n","intvolume":"        55","type":"conference","ec_funded":1},{"publication_identifier":{"issn":["0003-0503"]},"year":"2016","month":"03","date_created":"2022-02-08T09:55:09Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-02-08T10:44:06Z","title":"Study of vortex states and dynamics in mesoscopic superconducting samples with MFM","author":[{"id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896","last_name":"Polshyn","full_name":"Polshyn, Hryhoriy","first_name":"Hryhoriy"},{"last_name":"Naibert","full_name":"Naibert, Tyler","first_name":"Tyler"},{"last_name":"Chua","first_name":"Victor","full_name":"Chua, Victor"},{"full_name":"Budakian, Raffi","first_name":"Raffi","last_name":"Budakian"}],"alternative_title":["Bulletin of the American Physical Society"],"oa_version":"Published Version","publisher":"American Physical Society","oa":1,"conference":{"name":"APS: American Physical Society","location":"Baltimore, MD, United States","end_date":"2016-03-18","start_date":"2016-03-14"},"_id":"10746","article_processing_charge":"No","issue":"2","publication_status":"published","publication":"APS March Meeting 2016","extern":"1","language":[{"iso":"eng"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Vortex states in superconducting (SC) structures, their dynamics and ways to manipulate them are topics of great interest. We report a new method of magnetic force microscopy (MFM) that allows the study of vortex states in mesoscopic SC samples. For the case of a SC ring, which is biased to a half-integer flux quantum, the flux modulation through the ring caused by the motion of the magnetic tip drives the ring between two consecutive fluxoid states. The corresponding current switching in the ring produces strong position-dependent forces on the cantilever. In the regime where the frequency of the thermally activated jumps between fluxoid states is close to the frequency of the cantilever, large changes in the cantilever frequency and dissipation are observed. This effect may be understood as a stochastic resonance (SR) process. These changes in the cantilever’s mechanical properties are used to “image” the barrier energies between fluxoid states. Additionally, SR imaging of the barrier energies are used to study the effect of the locally applied magnetic field from the MFM tip on the barrier heights. We report the results of measurements for Al rings. Further, the same imaging technique can be applied to more sophisticated SC structures such as arrays of Josephson junctions."}],"volume":61,"citation":{"ista":"Polshyn H, Naibert T, Chua V, Budakian R. 2016. Study of vortex states and dynamics in mesoscopic superconducting samples with MFM. APS March Meeting 2016. APS: American Physical Society, Bulletin of the American Physical Society, vol. 61, E25.00007.","apa":"Polshyn, H., Naibert, T., Chua, V., &#38; Budakian, R. (2016). Study of vortex states and dynamics in mesoscopic superconducting samples with MFM. In <i>APS March Meeting 2016</i> (Vol. 61). Baltimore, MD, United States: American Physical Society.","chicago":"Polshyn, Hryhoriy, Tyler Naibert, Victor Chua, and Raffi Budakian. “Study of Vortex States and Dynamics in Mesoscopic Superconducting Samples with MFM.” In <i>APS March Meeting 2016</i>, Vol. 61. American Physical Society, 2016.","mla":"Polshyn, Hryhoriy, et al. “Study of Vortex States and Dynamics in Mesoscopic Superconducting Samples with MFM.” <i>APS March Meeting 2016</i>, vol. 61, no. 2, E25.00007, American Physical Society, 2016.","short":"H. Polshyn, T. Naibert, V. Chua, R. Budakian, in:, APS March Meeting 2016, American Physical Society, 2016.","ama":"Polshyn H, Naibert T, Chua V, Budakian R. Study of vortex states and dynamics in mesoscopic superconducting samples with MFM. In: <i>APS March Meeting 2016</i>. Vol 61. American Physical Society; 2016.","ieee":"H. Polshyn, T. Naibert, V. Chua, and R. Budakian, “Study of vortex states and dynamics in mesoscopic superconducting samples with MFM,” in <i>APS March Meeting 2016</i>, Baltimore, MD, United States, 2016, vol. 61, no. 2."},"status":"public","article_number":"E25.00007","day":"01","date_published":"2016-03-01T00:00:00Z","type":"conference","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR16/Session/E25.7"}],"intvolume":"        61"},{"intvolume":"        61","type":"conference","main_file_link":[{"open_access":"1","url":"https://meetings.aps.org/Meeting/MAR16/Session/H25.6"}],"status":"public","article_number":"H25.00006","day":"01","date_published":"2016-03-01T00:00:00Z","citation":{"short":"T. Naibert, H. Polshyn, B. Wolin, M. Durkin, R. Garrido Menacho, I.M. Shem, V. Chua, T. Hughes, N. Mason, R. Budakian, in:, APS March Meeting 2016, American Physical Society, 2016.","mla":"Naibert, Tyler, et al. “Stochastic Resonance Magnetic Force Microscopy Imaging of Josephson Arrays.” <i>APS March Meeting 2016</i>, vol. 61, no. 2, H25.00006, American Physical Society, 2016.","chicago":"Naibert, Tyler, Hryhoriy Polshyn, Brian Wolin, Malcolm Durkin, Rita Garrido Menacho, Ian Mondragon Shem, Victor Chua, Taylor Hughes, Nadya Mason, and Raffi Budakian. “Stochastic Resonance Magnetic Force Microscopy Imaging of Josephson Arrays.” In <i>APS March Meeting 2016</i>, Vol. 61. American Physical Society, 2016.","ieee":"T. Naibert <i>et al.</i>, “Stochastic resonance magnetic force microscopy imaging of Josephson arrays,” in <i>APS March Meeting 2016</i>, Baltimore, MD, United States, 2016, vol. 61, no. 2.","ama":"Naibert T, Polshyn H, Wolin B, et al. Stochastic resonance magnetic force microscopy imaging of Josephson arrays. In: <i>APS March Meeting 2016</i>. Vol 61. American Physical Society; 2016.","ista":"Naibert T, Polshyn H, Wolin B, Durkin M, Garrido Menacho R, Shem IM, Chua V, Hughes T, Mason N, Budakian R. 2016. Stochastic resonance magnetic force microscopy imaging of Josephson arrays. APS March Meeting 2016. APS: American Physical Society, Bulletin of the American Physical Society, vol. 61, H25.00006.","apa":"Naibert, T., Polshyn, H., Wolin, B., Durkin, M., Garrido Menacho, R., Shem, I. M., … Budakian, R. (2016). Stochastic resonance magnetic force microscopy imaging of Josephson arrays. In <i>APS March Meeting 2016</i> (Vol. 61). Baltimore, MD, United States: American Physical Society."},"abstract":[{"text":"Vortex interactions are key to explaining the behavior of many two dimensional superconducting systems. We report on the development of a technique to locally probe vortex interactions in a 2D array of Josephson junctions. Scanning a magnetic tip attached to an ultra-soft cantilever over the array produces changes in the frequency of the cantilever along certain lines, forming geometric patterns in the scans. Different tip-surface separations and external magnetic fields produce a number of different patterns. These patterns correspond to tip locations in which two configurations of vortices in the lattice have degenerate energies. By imaging the locations of these degeneracies, information on the local vortex interactions may be obtained.","lang":"eng"}],"volume":61,"extern":"1","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","issue":"2","publication":"APS March Meeting 2016","publication_status":"published","conference":{"location":"Baltimore, MD, United States","name":"APS: American Physical Society","start_date":"2016-03-14","end_date":"2016-03-18"},"_id":"10747","publisher":"American Physical Society","oa":1,"title":"Stochastic resonance magnetic force microscopy imaging of Josephson arrays","author":[{"last_name":"Naibert","full_name":"Naibert, Tyler","first_name":"Tyler"},{"first_name":"Hryhoriy","full_name":"Polshyn, Hryhoriy","last_name":"Polshyn","id":"edfc7cb1-526e-11ec-b05a-e6ecc27e4e48","orcid":"0000-0001-8223-8896"},{"first_name":"Brian","full_name":"Wolin, Brian","last_name":"Wolin"},{"last_name":"Durkin","full_name":"Durkin, Malcolm","first_name":"Malcolm"},{"last_name":"Garrido Menacho","first_name":"Rita","full_name":"Garrido Menacho, Rita"},{"last_name":"Shem","first_name":"Ian Mondragon","full_name":"Shem, Ian Mondragon"},{"last_name":"Chua","first_name":"Victor","full_name":"Chua, Victor"},{"last_name":"Hughes","first_name":"Taylor","full_name":"Hughes, Taylor"},{"last_name":"Mason","full_name":"Mason, Nadya","first_name":"Nadya"},{"last_name":"Budakian","first_name":"Raffi","full_name":"Budakian, Raffi"}],"alternative_title":["Bulletin of the American Physical Society"],"oa_version":"Published Version","date_created":"2022-02-08T10:10:39Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-02-08T10:43:33Z","month":"03","publication_identifier":{"issn":["0003-0503"]},"year":"2016"},{"citation":{"apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., &#38; Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>","ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","ieee":"Ł. Łangowski <i>et al.</i>, “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” <i>Cell Discovery</i>, vol. 2. Nature Publishing Group, 2016.","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. 2016;2. doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>","mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>, vol. 2, 16018, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>."},"acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","status":"public","date_published":"2016-07-19T00:00:00Z","publist_id":"6299","article_number":"16018","day":"19","type":"journal_article","ec_funded":1,"intvolume":"         2","isi":1,"project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"_id":"1081","article_processing_charge":"No","publication":"Cell Discovery","publication_status":"published","scopus_import":"1","external_id":{"isi":["000414797400001"]},"quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"ddc":["580"],"file_date_updated":"2018-12-12T10:13:33Z","volume":2,"abstract":[{"text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.","lang":"eng"}],"author":[{"last_name":"Łangowski","first_name":"Łukasz","full_name":"Łangowski, Łukasz"},{"orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T"},{"full_name":"Li, Hongjiang","first_name":"Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"full_name":"Naramoto, Satoshi","first_name":"Satoshi","last_name":"Naramoto"},{"last_name":"Tanaka","first_name":"Hirokazu","full_name":"Tanaka, Hirokazu"},{"first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","oa_version":"Published Version","doi":"10.1038/celldisc.2016.18","oa":1,"publisher":"Nature Publishing Group","pubrep_id":"757","file":[{"date_created":"2018-12-12T10:13:33Z","date_updated":"2018-12-12T10:13:33Z","file_id":"5017","relation":"main_file","file_name":"IST-2017-757-v1+1_celldisc201618.pdf","creator":"system","file_size":5261671,"content_type":"application/pdf","access_level":"open_access"}],"has_accepted_license":"1","year":"2016","month":"07","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:02Z","date_updated":"2025-09-22T14:19:46Z"},{"intvolume":"        43","type":"conference","main_file_link":[{"url":"https://doi.org/10.22489/cinc.2016.090-500","open_access":"1"}],"status":"public","date_published":"2016-03-01T00:00:00Z","day":"01","acknowledgement":"The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen Wagner for their in depth review and constructive comments.","citation":{"ista":"Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing in Cardiology vol. 43, 309–312.","apa":"Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P., &#38; Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In <i>2016 Computing in Cardiology Conference</i> (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>","chicago":"Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini, Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” In <i>2016 Computing in Cardiology Conference</i>, 43:309–12. Computing in Cardiology, 2016. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>.","short":"P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri, in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp. 309–312.","mla":"Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” <i>2016 Computing in Cardiology Conference</i>, vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>.","ama":"Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In: <i>2016 Computing in Cardiology Conference</i>. Vol 43. Computing in Cardiology; 2016:309-312. doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>","ieee":"P. Rubel <i>et al.</i>, “SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography,” in <i>2016 Computing in Cardiology Conference</i>, Vancouver, Canada, 2016, vol. 43, pp. 309–312."},"department":[{"_id":"CampIT"}],"volume":43,"abstract":[{"lang":"eng","text":"The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. "}],"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","publication":"2016 Computing in Cardiology Conference","publication_status":"published","conference":{"start_date":"2016-09-11","end_date":"2016-09-14","location":"Vancouver, Canada","name":"CinC: Computing in Cardiology"},"_id":"10810","publisher":"Computing in Cardiology","oa":1,"doi":"10.22489/cinc.2016.090-500","page":"309-312","author":[{"full_name":"Rubel, Paul","first_name":"Paul","last_name":"Rubel"},{"first_name":"Danilo","full_name":"Pani, Danilo","last_name":"Pani"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","last_name":"Schlögl","full_name":"Schlögl, Alois","first_name":"Alois"},{"first_name":"Jocelyne","full_name":"Fayn, Jocelyne","last_name":"Fayn"},{"last_name":"Badilini","first_name":"Fabio","full_name":"Badilini, Fabio"},{"last_name":"Macfarlane","first_name":"Peter","full_name":"Macfarlane, Peter"},{"last_name":"Varri","first_name":"Alpo","full_name":"Varri, Alpo"}],"title":"SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-03-03T10:43:10Z","date_updated":"2022-03-04T07:34:45Z","month":"03","publication_identifier":{"issn":["2325-887X"]},"year":"2016"},{"citation":{"chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems Foundation, 2016.","mla":"Chalk, Matthew J., et al. <i>Relevant Sparse Codes with Variational Information Bottleneck</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 1965–73.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 1965–1973.","ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation."},"date_published":"2016-12-01T00:00:00Z","publist_id":"6298","day":"01","arxiv":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07332"}],"type":"conference","intvolume":"        29","related_material":{"link":[{"relation":"other","url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck"}]},"_id":"1082","conference":{"name":"NIPS: Neural Information Processing Systems","location":"Barcelona, Spain","start_date":"2016-12-05","end_date":"2016-12-10"},"publication_status":"published","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","external_id":{"arxiv":["1605.07332"]},"volume":29,"abstract":[{"lang":"eng","text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y."}],"department":[{"_id":"GaTk"}],"oa_version":"Preprint","alternative_title":["Advances in Neural Information Processing Systems"],"author":[{"first_name":"Matthew J","full_name":"Chalk, Matthew J","last_name":"Chalk","orcid":"0000-0001-7782-4436","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"title":"Relevant sparse codes with variational information bottleneck","page":"1965-1973","publisher":"Neural Information Processing Systems Foundation","oa":1,"year":"2016","month":"12","date_updated":"2025-06-03T11:33:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:03Z"},{"_id":"1083","isi":1,"publication":"Cerebral Cortex","publication_status":"published","issue":"3","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","external_id":{"isi":["000397636600048"]},"volume":27,"abstract":[{"text":" Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABABreceptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins. ","lang":"eng"}],"department":[{"_id":"RySh"}],"citation":{"mla":"Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” <i>Cerebral Cortex</i>, vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:<a href=\"https://doi.org/10.1093/cercor/bhw090\">10.1093/cercor/bhw090</a>.","short":"S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler, A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik, Cerebral Cortex 27 (2016) 2318–2334.","chicago":"Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller, Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” <i>Cerebral Cortex</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/cercor/bhw090\">https://doi.org/10.1093/cercor/bhw090</a>.","ieee":"S. Booker <i>et al.</i>, “KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons,” <i>Cerebral Cortex</i>, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016.","ama":"Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. <i>Cerebral Cortex</i>. 2016;27(3):2318-2334. doi:<a href=\"https://doi.org/10.1093/cercor/bhw090\">10.1093/cercor/bhw090</a>","ista":"Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334.","apa":"Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik, Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. <i>Cerebral Cortex</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/cercor/bhw090\">https://doi.org/10.1093/cercor/bhw090</a>"},"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation (3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland (I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider, Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided by Dr G.V. Ohning, CURE Center, UCLA, CA. ","publist_id":"6297","date_published":"2016-04-12T00:00:00Z","day":"12","status":"public","type":"journal_article","intvolume":"        27","year":"2016","month":"04","date_updated":"2025-09-22T14:19:11Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:03Z","oa_version":"None","author":[{"full_name":"Booker, Sam","first_name":"Sam","last_name":"Booker"},{"first_name":"Daniel","full_name":"Althof, Daniel","last_name":"Althof"},{"last_name":"Gross","full_name":"Gross, Anna","first_name":"Anna"},{"last_name":"Loreth","first_name":"Desiree","full_name":"Loreth, Desiree"},{"full_name":"Müller, Johanna","first_name":"Johanna","last_name":"Müller"},{"last_name":"Unger","first_name":"Andreas","full_name":"Unger, Andreas"},{"first_name":"Bernd","full_name":"Fakler, Bernd","last_name":"Fakler"},{"last_name":"Varro","first_name":"Andrea","full_name":"Varro, Andrea"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"last_name":"Gassmann","first_name":"Martin","full_name":"Gassmann, Martin"},{"last_name":"Bettler","first_name":"Bernhard","full_name":"Bettler, Bernhard"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"last_name":"Vida","full_name":"Vida, Imre","first_name":"Imre"},{"last_name":"Kulik","full_name":"Kulik, Ákos","first_name":"Ákos"}],"title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","page":"2318 - 2334","doi":"10.1093/cercor/bhw090","publisher":"Oxford University Press"},{"intvolume":"         6","publisher":"Taylor & Francis","type":"journal_article","day":"27","publist_id":"6289","page":"76 - 84","date_published":"2016-07-27T00:00:00Z","status":"public","doi":"10.1080/19490992.2016.1201620","citation":{"ista":"Uhler C, Shivashankar GV. 2016. Geometric control and modeling of genome reprogramming. BioArchitecture. 6(4), 76–84.","apa":"Uhler, C., &#38; Shivashankar, G. V. (2016). Geometric control and modeling of genome reprogramming. <i>BioArchitecture</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/19490992.2016.1201620\">https://doi.org/10.1080/19490992.2016.1201620</a>","mla":"Uhler, Caroline, and G. V. Shivashankar. “Geometric Control and Modeling of Genome Reprogramming.” <i>BioArchitecture</i>, vol. 6, no. 4, Taylor &#38; Francis, 2016, pp. 76–84, doi:<a href=\"https://doi.org/10.1080/19490992.2016.1201620\">10.1080/19490992.2016.1201620</a>.","short":"C. Uhler, G.V. Shivashankar, BioArchitecture 6 (2016) 76–84.","chicago":"Uhler, Caroline, and G V Shivashankar. “Geometric Control and Modeling of Genome Reprogramming.” <i>BioArchitecture</i>. Taylor &#38; Francis, 2016. <a href=\"https://doi.org/10.1080/19490992.2016.1201620\">https://doi.org/10.1080/19490992.2016.1201620</a>.","ieee":"C. Uhler and G. V. Shivashankar, “Geometric control and modeling of genome reprogramming,” <i>BioArchitecture</i>, vol. 6, no. 4. Taylor &#38; Francis, pp. 76–84, 2016.","ama":"Uhler C, Shivashankar GV. Geometric control and modeling of genome reprogramming. <i>BioArchitecture</i>. 2016;6(4):76-84. doi:<a href=\"https://doi.org/10.1080/19490992.2016.1201620\">10.1080/19490992.2016.1201620</a>"},"oa_version":"None","title":"Geometric control and modeling of genome reprogramming","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","last_name":"Uhler","full_name":"Uhler, Caroline","first_name":"Caroline"},{"last_name":"Shivashankar","full_name":"Shivashankar, G V","first_name":"G V"}],"abstract":[{"text":"Cell geometry is tightly coupled to gene expression patterns within the tissue microenvironment. This perspective synthesizes evidence that the 3D organization of chromosomes is a critical intermediate for geometric control of genomic programs. Using a combination of experiments and modeling we outline approaches to decipher the mechano-genomic code that governs cellular homeostasis and reprogramming.","lang":"eng"}],"date_updated":"2021-01-12T06:48:11Z","volume":6,"date_created":"2018-12-11T11:50:05Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","extern":"1","publication":"BioArchitecture","publication_status":"published","month":"07","issue":"4","_id":"1088","year":"2016"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2018-12-11T11:50:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:50:02Z","has_accepted_license":"1","file":[{"access_level":"open_access","file_size":564560,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf","date_updated":"2018-12-12T10:17:31Z","file_id":"5286","relation":"main_file","date_created":"2018-12-12T10:17:31Z"}],"year":"2016","month":"08","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"pubrep_id":"795","title":"Nested weighted limit-average automata of bounded width","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop"}],"alternative_title":["LIPIcs"],"oa_version":"Published Version","doi":"10.4230/LIPIcs.MFCS.2016.24","scopus_import":"1","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ddc":["004"],"abstract":[{"text":" While weighted automata provide a natural framework to express quantitative properties, many basic properties like average response time cannot be expressed with weighted automata. Nested weighted automata extend weighted automata and consist of a master automaton and a set of slave automata that are invoked by the master automaton. Nested weighted automata are strictly more expressive than weighted automata (e.g., average response time can be expressed with nested weighted automata), but the basic decision questions have higher complexity (e.g., for deterministic automata, the emptiness question for nested weighted automata is PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME). We consider a natural subclass of nested weighted automata where at any point at most a bounded number k of slave automata can be active. We focus on automata whose master value function is the limit average. We show that these nested weighted automata with bounded width are strictly more expressive than weighted automata (e.g., average response time with no overlapping requests can be expressed with bound k=1, but not with non-nested weighted automata). We show that the complexity of the basic decision problems (i.e., emptiness and universality) for the subclass with k constant matches the complexity for weighted automata. Moreover, when k is part of the input given in unary we establish PSPACE-completeness.","lang":"eng"}],"volume":58,"file_date_updated":"2018-12-12T10:17:31Z","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"conference":{"location":"Krakow; Poland","name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2016-08-26","start_date":"2016-08-22"},"_id":"1090","article_processing_charge":"No","publication_status":"published","type":"conference","ec_funded":1,"intvolume":"        58","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">https://doi.org/10.4230/LIPIcs.MFCS.2016.24</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Nested Weighted Limit-Average Automata of Bounded Width</i>. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">10.4230/LIPIcs.MFCS.2016.24</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted limit-average automata of bounded width. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">10.4230/LIPIcs.MFCS.2016.24</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted limit-average automata of bounded width,” presented at the MFCS: Mathematical Foundations of Computer Science, Krakow; Poland, 2016, vol. 58.","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata of bounded width. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 24.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Nested weighted limit-average automata of bounded width (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science, Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">https://doi.org/10.4230/LIPIcs.MFCS.2016.24</a>"},"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under grant 2014/15/D/ST6/04543.","status":"public","article_number":"24","day":"01","publist_id":"6286","date_published":"2016-08-01T00:00:00Z"},{"date_updated":"2025-04-15T07:12:21Z","date_created":"2018-12-11T11:50:06Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"08","year":"2016","acknowledged_ssus":[{"_id":"EM-Fac"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"]},"publisher":"Springer","page":"203 - 216","doi":"10.1007/978-1-4939-6352-2_12","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","title":"Immunogold protein localization on grid-glued freeze-fracture replicas","author":[{"full_name":"Harada, Harumi","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896","last_name":"Harada"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"}],"abstract":[{"lang":"eng","text":"Immunogold labeling of freeze-fracture replicas has recently been used for high-resolution visualization of protein localization in electron microscopy. This method has higher labeling efficiency than conventional immunogold methods for membrane molecules allowing precise quantitative measurements. However, one of the limitations of freeze-fracture replica immunolabeling is difficulty in keeping structural orientation and identifying labeled profiles in complex tissues like brain. The difficulty is partly due to fragmentation of freeze-fracture replica preparations during labeling procedures and limited morphological clues on the replica surface. To overcome these issues, we introduce here a grid-glued replica method combined with SEM observation. This method allows histological staining before dissolving the tissue and easy handling of replicas during immunogold labeling, and keeps the whole replica surface intact without fragmentation. The procedure described here is also useful for matched double-replica analysis allowing further identification of labeled profiles in corresponding P-face and E-face."}],"volume":1474,"department":[{"_id":"RySh"}],"language":[{"iso":"eng"}],"quality_controlled":"1","publication_status":"published","publication":"High-Resolution Imaging of Cellular Proteins","article_processing_charge":"No","_id":"1094","project":[{"name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","grant_number":"604102","call_identifier":"FP7"}],"intvolume":"      1474","ec_funded":1,"type":"book_chapter","day":"12","publist_id":"6281","date_published":"2016-08-12T00:00:00Z","status":"public","citation":{"ieee":"H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued freeze-fracture replicas,” in <i>High-Resolution Imaging of Cellular Proteins</i>, vol. 1474, Springer, 2016, pp. 203–216.","ama":"Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture replicas. In: <i>High-Resolution Imaging of Cellular Proteins</i>. Vol 1474. Springer; 2016:203-216. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">10.1007/978-1-4939-6352-2_12</a>","mla":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” <i>High-Resolution Imaging of Cellular Proteins</i>, vol. 1474, Springer, 2016, pp. 203–16, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">10.1007/978-1-4939-6352-2_12</a>.","short":"H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins, Springer, 2016, pp. 203–216.","chicago":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” In <i>High-Resolution Imaging of Cellular Proteins</i>, 1474:203–16. Springer, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">https://doi.org/10.1007/978-1-4939-6352-2_12</a>.","apa":"Harada, H., &#38; Shigemoto, R. (2016). Immunogold protein localization on grid-glued freeze-fracture replicas. In <i>High-Resolution Imaging of Cellular Proteins</i> (Vol. 1474, pp. 203–216). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">https://doi.org/10.1007/978-1-4939-6352-2_12</a>","ista":"Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods in Molecular Biology, vol. 1474, 203–216."},"acknowledgement":"We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron microscope imaging. This work was supported by the European Union (HBP—Project Ref. 604102). "},{"month":"08","year":"2016","has_accepted_license":"1","file":[{"file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","date_created":"2018-12-12T10:10:10Z","file_id":"4795","relation":"main_file","date_updated":"2018-12-12T10:10:10Z","content_type":"application/pdf","file_size":589747,"access_level":"open_access","creator":"system"}],"date_updated":"2025-04-15T06:25:58Z","date_created":"2018-12-11T11:50:07Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.4230/LIPIcs.CONCUR.2016.6","alternative_title":["LIPIcs"],"oa_version":"Published Version","title":"Local linearizability for concurrent container-type data structures","author":[{"first_name":"Andreas","full_name":"Haas, Andreas","last_name":"Haas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"full_name":"Holzer, Andreas","first_name":"Andreas","last_name":"Holzer"},{"last_name":"Kirsch","first_name":"Christoph","full_name":"Kirsch, Christoph"},{"first_name":"Michael","full_name":"Lippautz, Michael","last_name":"Lippautz"},{"last_name":"Payer","first_name":"Hannes","full_name":"Payer, Hannes"},{"last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","full_name":"Sezgin, Ali"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"},{"last_name":"Veith","full_name":"Veith, Helmut","first_name":"Helmut"}],"pubrep_id":"793","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","publication":"Leibniz International Proceedings in Informatics","_id":"1095","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"conference":{"name":"CONCUR: Concurrency Theory","location":"Quebec City; Canada","end_date":"2016-08-26","start_date":"2016-08-23"},"abstract":[{"lang":"eng","text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. "}],"volume":59,"file_date_updated":"2018-12-12T10:10:10Z","department":[{"_id":"ToHe"}],"ddc":["004"],"language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":1,"article_number":"6","day":"01","publist_id":"6280","date_published":"2016-08-01T00:00:00Z","status":"public","acknowledgement":"This work has been supported by the National Research Network RiSE on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23, S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1, the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","citation":{"ama":"Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent container-type data structures. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">10.4230/LIPIcs.CONCUR.2016.6</a>","ieee":"A. Haas <i>et al.</i>, “Local linearizability for concurrent container-type data structures,” in <i>Leibniz International Proceedings in Informatics</i>, Quebec City; Canada, 2016, vol. 59.","chicago":"Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability for Concurrent Container-Type Data Structures.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.6</a>.","short":"A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A. Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type Data Structures.” <i>Leibniz International Proceedings in Informatics</i>, vol. 59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">10.4230/LIPIcs.CONCUR.2016.6</a>.","apa":"Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H., … Veith, H. (2016). Local linearizability for concurrent container-type data structures. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 59). Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.6</a>","ista":"Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A, Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 6."},"intvolume":"        59","ec_funded":1,"type":"conference"},{"date_published":"2016-11-01T00:00:00Z","publist_id":"6278","day":"01","article_number":"227","status":"public","citation":{"ista":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.","apa":"Du, T., Schulz, A., Zhu, B., Bickel, B., &#38; Matusik, W. (2016). Computational multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. <a href=\"https://doi.org/10.1145/2980179.2982427\">https://doi.org/10.1145/2980179.2982427</a>","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.","mla":"Du, Tao, et al. <i>Computational Multicopter Design</i>. Vol. 35, no. 6, 227, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2980179.2982427\">10.1145/2980179.2982427</a>.","chicago":"Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational Multicopter Design,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2980179.2982427\">https://doi.org/10.1145/2980179.2982427</a>.","ieee":"T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2980179.2982427\">10.1145/2980179.2982427</a>"},"acknowledgement":"We thank Nobuyuki Umetani for his insightful suggestions in our discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing mechanical parts and providing 3D printing technical support; Charles Blouin from RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis work was partially supported by Air Force Research Laboratory’s sponsorship of Julia: A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2- 0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967, MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 645599. ","intvolume":"        35","ec_funded":1,"type":"conference","publication_status":"published","issue":"6","article_processing_charge":"No","_id":"1097","conference":{"name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","location":"Macao, China","start_date":"2016-12-05","end_date":"2016-12-08"},"isi":1,"project":[{"grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation","call_identifier":"H2020"}],"file_date_updated":"2018-12-12T10:17:42Z","volume":35,"abstract":[{"lang":"eng","text":"We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics."}],"ddc":["006"],"department":[{"_id":"BeBi"}],"quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000388446200069"]},"scopus_import":"1","doi":"10.1145/2980179.2982427","oa_version":"Submitted Version","alternative_title":["ACM Transactions on Graphics"],"author":[{"last_name":"Du","full_name":"Du, Tao","first_name":"Tao"},{"first_name":"Adriana","full_name":"Schulz, Adriana","last_name":"Schulz"},{"last_name":"Zhu","first_name":"Bo","full_name":"Zhu, Bo"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","full_name":"Bickel, Bernd","first_name":"Bernd"},{"full_name":"Matusik, Wojciech","first_name":"Wojciech","last_name":"Matusik"}],"title":"Computational multicopter design","pubrep_id":"759","oa":1,"publisher":"ACM","month":"11","year":"2016","file":[{"file_name":"IST-2017-759-v1+1_copter.pdf","relation":"main_file","file_id":"5298","date_updated":"2018-12-12T10:17:42Z","date_created":"2018-12-12T10:17:42Z","access_level":"open_access","content_type":"application/pdf","file_size":33114420,"creator":"system"}],"has_accepted_license":"1","date_updated":"2025-09-22T14:17:29Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:07Z"},{"page":"3619-3627","title":"Lifelong learning with weighted majority votes","author":[{"full_name":"Pentina, Anastasia","first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","last_name":"Pentina"},{"last_name":"Urner","full_name":"Urner, Ruth","first_name":"Ruth"}],"alternative_title":["Advances in Neural Information Processing Systems"],"oa_version":"Published Version","pubrep_id":"775","oa":1,"publisher":"Neural Information Processing Systems Foundation","month":"12","has_accepted_license":"1","file":[{"file_size":237111,"content_type":"application/pdf","access_level":"open_access","creator":"system","file_name":"IST-2017-775-v1+1_main.pdf","date_created":"2018-12-12T10:12:42Z","date_updated":"2018-12-12T10:12:42Z","relation":"main_file","file_id":"4961"},{"file_name":"IST-2017-775-v1+2_supplementary.pdf","date_created":"2018-12-12T10:12:43Z","relation":"main_file","file_id":"4962","date_updated":"2018-12-12T10:12:43Z","content_type":"application/pdf","file_size":185818,"access_level":"open_access","creator":"system"}],"year":"2016","date_created":"2018-12-11T11:50:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-03T11:35:58Z","status":"public","day":"01","publist_id":"6277","date_published":"2016-12-01T00:00:00Z","acknowledgement":"This work was in parts funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.\r\n\r\n","citation":{"chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems Foundation, 2016.","short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems Foundation, 2016, pp. 3619–3627.","mla":"Pentina, Anastasia, and Ruth Urner. <i>Lifelong Learning with Weighted Majority Votes</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3619–27.","ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3619-3627.","ieee":"A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 3619–3627.","ista":"Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3619–3627.","apa":"Pentina, A., &#38; Urner, R. (2016). Lifelong learning with weighted majority votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation."},"intvolume":"        29","type":"conference","ec_funded":1,"article_processing_charge":"No","publication_status":"published","project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"conference":{"end_date":"2016-12-10","start_date":"2016-12-05","location":"Barcelona, Spain","name":"NIPS: Neural Information Processing Systems"},"_id":"1098","department":[{"_id":"ChLa"}],"ddc":["006"],"abstract":[{"text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.","lang":"eng"}],"file_date_updated":"2018-12-12T10:12:43Z","volume":29,"scopus_import":"1","language":[{"iso":"eng"}],"quality_controlled":"1"},{"has_accepted_license":"1","file":[{"creator":"system","file_size":11122029,"content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:12:01Z","date_updated":"2018-12-12T10:12:01Z","relation":"main_file","file_id":"4918","file_name":"IST-2017-760-v1+1_flexmolds.pdf"}],"year":"2016","month":"11","date_created":"2018-12-11T11:50:08Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:16:02Z","title":"FlexMolds: Automatic design of flexible shells for molding","author":[{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"first_name":"Nico","full_name":"Pietroni, Nico","last_name":"Pietroni"},{"full_name":"Bickel, Bernd","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"full_name":"Cignoni, Paolo","first_name":"Paolo","last_name":"Cignoni"}],"alternative_title":["ACM Transactions on Graphics"],"oa_version":"Submitted Version","doi":"10.1145/2980179.2982397","oa":1,"publisher":"ACM","pubrep_id":"760","project":[{"_id":"25082902-B435-11E9-9278-68D0E5697425","grant_number":"645599","name":"Soft-bodied intelligence for Manipulation","call_identifier":"H2020"}],"conference":{"location":"Macao, China","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","start_date":"2016-12-05","end_date":"2016-12-08"},"isi":1,"_id":"1099","article_processing_charge":"No","issue":"6","publication_status":"published","external_id":{"isi":["000388446200065"]},"scopus_import":"1","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"BeBi"}],"ddc":["000","005"],"abstract":[{"text":"We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies.","lang":"eng"}],"volume":35,"file_date_updated":"2018-12-12T10:12:01Z","acknowledgement":"The armadillo, bunny and dragon models are courtesy of the Stanford  3D  Scanning  Repository.   The  bimba,  fertility  and  elephant models are courtesy of the AIM@SHAPE Shape Repository.  \r\nThis project has received funding from the European Union’s Horizon 2020  research  and  innovation  programme  under  grant  agreement\r\nNo. 645599.","citation":{"ieee":"L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","ama":"Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of flexible shells for molding. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","mla":"Malomo, Luigi, et al. <i>FlexMolds: Automatic Design of Flexible Shells for Molding</i>. Vol. 35, no. 6, 223, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>.","chicago":"Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds: Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>.","apa":"Malomo, L., Pietroni, N., Bickel, B., &#38; Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223."},"status":"public","article_number":"223","day":"01","publist_id":"6276","date_published":"2016-11-01T00:00:00Z","type":"conference","ec_funded":1,"intvolume":"        35"},{"acknowledgement":"J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships. C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator Award and a Discovery Project and Future\r\nFellowship from the Australian Research Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153) and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure.","citation":{"apa":"Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L., O’Mara, M., &#38; Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>","ista":"Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 1(11), 1286–1290.","ieee":"J. Mitchell <i>et al.</i>, “Rangefinder: A semisynthetic FRET sensor design algorithm,” <i>ACS SENSORS</i>, vol. 1, no. 11. American Chemical Society, pp. 1286–1290, 2016.","ama":"Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. 2016;1(11):1286-1290. doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>","mla":"Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>, vol. 1, no. 11, American Chemical Society, 2016, pp. 1286–90, doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290.","chicago":"Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>."},"status":"public","day":"10","publist_id":"6274","date_published":"2016-11-10T00:00:00Z","type":"journal_article","intvolume":"         1","isi":1,"_id":"1101","article_processing_charge":"No","issue":"11","publication":"ACS SENSORS","publication_status":"published","scopus_import":"1","external_id":{"isi":["000388914800003"]},"language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"HaJa"}],"abstract":[{"lang":"eng","text":"Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of &gt;300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest."}],"volume":1,"title":"Rangefinder: A semisynthetic FRET sensor design algorithm","author":[{"last_name":"Mitchell","first_name":"Joshua","full_name":"Mitchell, Joshua"},{"last_name":"Whitfield","full_name":"Whitfield, Jason","first_name":"Jason"},{"full_name":"Zhang, William","first_name":"William","last_name":"Zhang"},{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"},{"last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","full_name":"Janovjak, Harald L"},{"full_name":"O'Mara, Megan","first_name":"Megan","last_name":"O'Mara"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"oa_version":"None","doi":"10.1021/acssensors.6b00576","page":"1286 - 1290","publisher":"American Chemical Society","year":"2016","month":"11","date_created":"2018-12-11T11:50:09Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-22T14:14:58Z"}]