[{"oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"citation":{"short":"L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021.","apa":"Portinale, L. (2021). <i>Discrete-to-continuum limits of transport problems and gradient flows in the space of measures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10030\">https://doi.org/10.15479/at:ista:10030</a>","chicago":"Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10030\">https://doi.org/10.15479/at:ista:10030</a>.","ieee":"L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021.","mla":"Portinale, Lorenzo. <i>Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10030\">10.15479/at:ista:10030</a>.","ama":"Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10030\">10.15479/at:ista:10030</a>","ista":"Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria."},"status":"public","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"date_created":"2021-09-21T09:14:15Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2026-04-08T07:00:04Z","_id":"10030","file":[{"file_name":"tex_and_pictures.zip","access_level":"closed","file_id":"10032","file_size":3876668,"content_type":"application/x-zip-compressed","checksum":"8cd60dcb8762e8f21867e21e8001e183","date_updated":"2022-03-10T12:14:42Z","relation":"source_file","date_created":"2021-09-21T09:17:34Z","creator":"cchlebak"},{"access_level":"open_access","file_id":"10047","file_name":"thesis_portinale_Final (1).pdf","relation":"main_file","date_updated":"2021-09-27T11:14:31Z","checksum":"9789e9d967c853c1503ec7f307170279","creator":"cchlebak","date_created":"2021-09-27T11:14:31Z","file_size":2532673,"content_type":"application/pdf"}],"date_published":"2021-09-22T00:00:00Z","author":[{"last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","full_name":"Portinale, Lorenzo"}],"publication_status":"published","title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","file_date_updated":"2022-03-10T12:14:42Z","doi":"10.15479/at:ista:10030","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9792"},{"id":"10022","relation":"part_of_dissertation","status":"public"},{"id":"7573","relation":"part_of_dissertation","status":"public"}]},"month":"09","oa":1,"article_processing_charge":"No","OA_place":"publisher","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245.","has_accepted_license":"1","ddc":["515"],"publisher":"Institute of Science and Technology Austria","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces.","lang":"eng"}],"day":"22","project":[{"grant_number":"W1245","call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and dispersion in nonlinear partial differential equations"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"fulldoi":"https://doi.org/10.15479/at:ista:10030","supervisor":[{"full_name":"Maas, Jan","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","last_name":"Maas"}],"year":"2021","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"type":"dissertation"},{"month":"09","publication":"Advances in Mathematics","external_id":{"arxiv":["1610.00212"],"isi":["000707040300031"]},"oa":1,"arxiv":1,"article_processing_charge":"Yes (via OA deal)","publisher":"Elsevier","corr_author":"1","acknowledgement":"The author would like to express his gratitude to D. Gaitsgory, without whose tireless guidance and encouragement in pursuing this problem, this work would not have been possible. The author is grateful to his advisor B.C. Ngô for many years of patient guidance and support. This paper is revised while the author is a postdoc in Hausel group at IST Austria. We thank him and the group for providing a wonderful research environment. The author also gratefully acknowledges the support of the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization Homology,” Austrian Science Fund (FWF): M 2751.","ddc":["514"],"has_accepted_license":"1","day":"21","volume":392,"publication_identifier":{"eissn":["1090-2082"],"issn":["0001-8708"]},"abstract":[{"text":"The ⊗*-monoidal structure on the category of sheaves on the Ran space is not pro-nilpotent in the sense of [3]. However, under some connectivity assumptions, we prove that Koszul duality induces an equivalence of categories and that this equivalence behaves nicely with respect to Verdier duality on the Ran space and integrating along the Ran space, i.e. taking factorization homology. Based on ideas sketched in [4], we show that these results also offer a simpler alternative to one of the two main steps in the proof of the Atiyah-Bott formula given in [7] and [5].","lang":"eng"}],"scopus_import":"1","fulldoi":"https://doi.org/10.1016/j.aim.2021.107992","project":[{"grant_number":"M02751","call_identifier":"FWF","_id":"26B96266-B435-11E9-9278-68D0E5697425","name":"Algebro-Geometric Applications of Factorization Homology"}],"year":"2021","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","status":"public","department":[{"_id":"TaHa"}],"citation":{"short":"Q.P. Ho, Advances in Mathematics 392 (2021).","apa":"Ho, Q. P. (2021). The Atiyah-Bott formula and connectivity in chiral Koszul duality. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2021.107992\">https://doi.org/10.1016/j.aim.2021.107992</a>","chicago":"Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.” <i>Advances in Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.aim.2021.107992\">https://doi.org/10.1016/j.aim.2021.107992</a>.","ieee":"Q. P. Ho, “The Atiyah-Bott formula and connectivity in chiral Koszul duality,” <i>Advances in Mathematics</i>, vol. 392. Elsevier, 2021.","mla":"Ho, Quoc P. “The Atiyah-Bott Formula and Connectivity in Chiral Koszul Duality.” <i>Advances in Mathematics</i>, vol. 392, 107992, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107992\">10.1016/j.aim.2021.107992</a>.","ama":"Ho QP. The Atiyah-Bott formula and connectivity in chiral Koszul duality. <i>Advances in Mathematics</i>. 2021;392. doi:<a href=\"https://doi.org/10.1016/j.aim.2021.107992\">10.1016/j.aim.2021.107992</a>","ista":"Ho QP. 2021. The Atiyah-Bott formula and connectivity in chiral Koszul duality. Advances in Mathematics. 392, 107992."},"quality_controlled":"1","article_number":"107992","date_updated":"2025-04-14T09:09:35Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"10033","intvolume":"       392","date_created":"2021-09-21T15:58:59Z","keyword":["Chiral algebras","Chiral homology","Factorization algebras","Koszul duality","Ran space"],"date_published":"2021-09-21T00:00:00Z","publication_status":"published","author":[{"full_name":"Ho, Quoc P","first_name":"Quoc P","orcid":"0000-0001-6889-1418","last_name":"Ho","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_size":840635,"content_type":"application/pdf","date_created":"2021-09-21T15:58:52Z","creator":"qho","date_updated":"2021-09-21T15:58:52Z","checksum":"f3c0086d41af11db31c00014efb38072","relation":"main_file","file_name":"1-s2.0-S000187082100431X-main.pdf","file_id":"10034","access_level":"open_access"}],"isi":1,"file_date_updated":"2021-09-21T15:58:52Z","title":"The Atiyah-Bott formula and connectivity in chiral Koszul duality","doi":"10.1016/j.aim.2021.107992"},{"file_date_updated":"2022-05-31T09:10:15Z","isi":1,"title":"RIM-binding protein 2 organizes Ca<sup>21</sup> channel topography and regulates release probability and vesicle replenishment at a fast central synapse","doi":"10.1523/JNEUROSCI.0586-21.2021","publication_status":"published","pmid":1,"author":[{"full_name":"Butola, Tanvi","first_name":"Tanvi","last_name":"Butola"},{"full_name":"Alvanos, Theocharis","last_name":"Alvanos","first_name":"Theocharis"},{"full_name":"Hintze, Anika","first_name":"Anika","last_name":"Hintze"},{"full_name":"Koppensteiner, Peter","first_name":"Peter","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948","last_name":"Koppensteiner"},{"last_name":"Kleindienst","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Kleindienst, David"},{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi"},{"full_name":"Wichmann, Carolin","last_name":"Wichmann","first_name":"Carolin"},{"last_name":"Moser","first_name":"Tobias","full_name":"Moser, Tobias"}],"file":[{"access_level":"open_access","file_id":"11423","file_name":"2021_JourNeuroscience_Butola.pdf","relation":"main_file","checksum":"769ab627c7355a50ccfd445e43a5f351","date_updated":"2022-05-31T09:10:15Z","creator":"dernst","date_created":"2022-05-31T09:10:15Z","success":1,"file_size":11571961,"content_type":"application/pdf"}],"date_published":"2021-09-15T00:00:00Z","page":"7742-7767","intvolume":"        41","date_created":"2021-09-27T14:33:13Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2023-08-14T06:56:30Z","_id":"10051","department":[{"_id":"RySh"}],"citation":{"ista":"Butola T, Alvanos T, Hintze A, Koppensteiner P, Kleindienst D, Shigemoto R, Wichmann C, Moser T. 2021. RIM-binding protein 2 organizes Ca<sup>21</sup> channel topography and regulates release probability and vesicle replenishment at a fast central synapse. Journal of Neuroscience. 41(37), 7742–7767.","ama":"Butola T, Alvanos T, Hintze A, et al. RIM-binding protein 2 organizes Ca<sup>21</sup> channel topography and regulates release probability and vesicle replenishment at a fast central synapse. <i>Journal of Neuroscience</i>. 2021;41(37):7742-7767. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0586-21.2021\">10.1523/JNEUROSCI.0586-21.2021</a>","mla":"Butola, Tanvi, et al. “RIM-Binding Protein 2 Organizes Ca<sup>21</sup> Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse.” <i>Journal of Neuroscience</i>, vol. 41, no. 37, Society for Neuroscience, 2021, pp. 7742–67, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0586-21.2021\">10.1523/JNEUROSCI.0586-21.2021</a>.","ieee":"T. Butola <i>et al.</i>, “RIM-binding protein 2 organizes Ca<sup>21</sup> channel topography and regulates release probability and vesicle replenishment at a fast central synapse,” <i>Journal of Neuroscience</i>, vol. 41, no. 37. Society for Neuroscience, pp. 7742–7767, 2021.","apa":"Butola, T., Alvanos, T., Hintze, A., Koppensteiner, P., Kleindienst, D., Shigemoto, R., … Moser, T. (2021). RIM-binding protein 2 organizes Ca<sup>21</sup> channel topography and regulates release probability and vesicle replenishment at a fast central synapse. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0586-21.2021\">https://doi.org/10.1523/JNEUROSCI.0586-21.2021</a>","chicago":"Butola, Tanvi, Theocharis Alvanos, Anika Hintze, Peter Koppensteiner, David Kleindienst, Ryuichi Shigemoto, Carolin Wichmann, and Tobias Moser. “RIM-Binding Protein 2 Organizes Ca<sup>21</sup> Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2021. <a href=\"https://doi.org/10.1523/JNEUROSCI.0586-21.2021\">https://doi.org/10.1523/JNEUROSCI.0586-21.2021</a>.","short":"T. Butola, T. Alvanos, A. Hintze, P. Koppensteiner, D. Kleindienst, R. Shigemoto, C. Wichmann, T. Moser, Journal of Neuroscience 41 (2021) 7742–7767."},"status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","issue":"37","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","fulldoi":"https://doi.org/10.1523/JNEUROSCI.0586-21.2021","year":"2021","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"abstract":[{"lang":"eng","text":"Rab-interacting molecule (RIM)-binding protein 2 (BP2) is a multidomain protein of the presynaptic active zone (AZ). By binding to RIM, bassoon (Bsn), and voltage-gated Ca2+ channels (CaV), it is considered to be a central organizer of the topography of CaV and release sites of synaptic vesicles (SVs) at the AZ. Here, we used RIM-BP2 knock-out (KO) mice and their wild-type (WT) littermates of either sex to investigate the role of RIM-BP2 at the endbulb of Held synapse of auditory nerve fibers (ANFs) with bushy cells (BCs) of the cochlear nucleus, a fast relay of the auditory pathway with high release probability. Disruption of RIM-BP2 lowered release probability altering short-term plasticity and reduced evoked EPSCs. Analysis of SV pool dynamics during high-frequency train stimulation indicated a reduction of SVs with high release probability but an overall normal size of the readily releasable SV pool (RRP). The Ca2+-dependent fast component of SV replenishment after RRP depletion was slowed. Ultrastructural analysis by superresolution light and electron microscopy revealed an impaired topography of presynaptic CaV and a reduction of docked and membrane-proximal SVs at the AZ. We conclude that RIM-BP2 organizes the topography of CaV, and promotes SV tethering and docking. This way RIM-BP2 is critical for establishing a high initial release probability as required to reliably signal sound onset information that we found to be degraded in BCs of RIM-BP2-deficient mice in vivo. SIGNIFICANCE STATEMENT: Rab-interacting molecule (RIM)-binding proteins (BPs) are key organizers of the active zone (AZ). Using a multidisciplinary approach to the calyceal endbulb of Held synapse that transmits auditory information at rates of up to hundreds of Hertz with submillisecond precision we demonstrate a requirement for RIM-BP2 for normal auditory signaling. Endbulb synapses lacking RIM-BP2 show a reduced release probability despite normal whole-terminal Ca2+ influx and abundance of the key priming protein Munc13-1, a reduced rate of SV replenishment, as well as an altered topography of voltage-gated (CaV)2.1 Ca2+ channels, and fewer docked and membrane proximal synaptic vesicles (SVs). This hampers transmission of sound onset information likely affecting downstream neural computations such as of sound localization."}],"scopus_import":"1","day":"15","volume":41,"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Collaborative Sensory Research Center 1286 [to C.W. (A4) and T.M. (B5)] and under Germany’s Excellence Strategy Grant EXC 2067/1-390729940. We thank S. Gerke, A.J. Goldak, and C. Senger-Freitag for expert technical assistance; G. Hoch for developing image analysis routines; and S. Chepurwar and N. Strenzke for technical support and discussion regarding in vivo experiments. We also thank Dr. Christian Rosenmund, Dr. Katharina Grauel, and Dr. Stephan Sigrist for providing RIM-BP2 KO mice and Dr. Masahiko Watanabe for providing the anti-neurexin-antibody, and Dr. Toshihisa Ohtsuka for the anti-ELKS-antibody. J. Neef for help with the STED imaging and image analysis; E. Neher and S. Rizzoli for discussion and comments on the manuscript; K. Eguchi for help with the statistical analysis; and C. H. Huang and J. Neef for constant support and scientific discussion.","has_accepted_license":"1","ddc":["570"],"publisher":"Society for Neuroscience","oa":1,"article_processing_charge":"No","publication":"Journal of Neuroscience","external_id":{"isi":["000752287700005"],"pmid":["34353898"]},"month":"09"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","fulldoi":"https://doi.org/10.4230/LIPIcs.CONCUR.2021.18","conference":{"start_date":"2021-08-23","end_date":"2021-08-27","name":"CONCUR: Conference on Concurrency Theory","location":"Paris, France"},"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"type":"conference","external_id":{"arxiv":["2107.04683"]},"publication":"32nd International Conference on Concurrency Theory","arxiv":1,"article_processing_charge":"No","oa":1,"month":"08","volume":203,"day":"13","scopus_import":"1","abstract":[{"lang":"eng","text":"A deterministic finite automaton (DFA) 𝒜 is composite if its language L(𝒜) can be decomposed into an intersection ⋂_{i = 1}^k L(𝒜_i) of languages of smaller DFAs. Otherwise, 𝒜 is prime. This notion of primality was introduced by Kupferman and Mosheiff in 2013, and while they proved that we can decide whether a DFA is composite, the precise complexity of this problem is still open, with a doubly-exponential gap between the upper and lower bounds. In this work, we focus on permutation DFAs, i.e., those for which the transition monoid is a group. We provide an NP algorithm to decide whether a permutation DFA is composite, and show that the difficulty of this problem comes from the number of non-accepting states of the instance: we give a fixed-parameter tractable algorithm with the number of rejecting states as the parameter. Moreover, we investigate the class of commutative permutation DFAs. Their structural properties allow us to decide compositionality in NL, and even in LOGSPACE if the alphabet size is fixed. Despite this low complexity, we show that complex behaviors still arise in this class: we provide a family of composite DFAs each requiring polynomially many factors with respect to its size. We also consider the variant of the problem that asks whether a DFA is k-factor composite, that is, decomposable into k smaller DFAs, for some given integer k ∈ ℕ. We show that, for commutative permutation DFAs, restricting the number of factors makes the decision computationally harder, and yields a problem with tight bounds: it is NP-complete. Finally, we show that in general, this problem is in PSPACE, and it is in LOGSPACE for DFAs with a singleton alphabet."}],"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-9597-7203-7"]},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["000"],"has_accepted_license":"1","acknowledgement":"Ismaël Jecker: Marie Skłodowska-Curie Grant Agreement No. 754411. Nicolas Mazzocchi: BOSCO project PGC2018-102210-B-I00 (MCIU/AEI/FEDER, UE), BLOQUESCM project S2018/TCS-4339, and MINECO grant RYC-2016-20281.\r\nPetra Wolf : DFG project FE 560/9-1.\r\n","doi":"10.4230/LIPIcs.CONCUR.2021.18","file_date_updated":"2021-10-01T11:10:53Z","title":"Decomposing permutation automata","publication_status":"published","author":[{"first_name":"Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","last_name":"Jecker","full_name":"Jecker, Ismael R"},{"first_name":"Nicolas","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas"},{"last_name":"Wolf","first_name":"Petra","full_name":"Wolf, Petra"}],"date_published":"2021-08-13T00:00:00Z","file":[{"file_size":1003552,"content_type":"application/pdf","creator":"cchlebak","date_created":"2021-10-01T11:10:53Z","success":1,"relation":"main_file","date_updated":"2021-10-01T11:10:53Z","checksum":"4722c81be82265cf45e78adf9db91250","file_name":"2021_CONCUR_Jecker.pdf","file_id":"10064","access_level":"open_access"}],"status":"public","citation":{"short":"I.R. Jecker, N. Mazzocchi, P. Wolf, in:, 32nd International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","chicago":"Jecker, Ismael R, Nicolas Mazzocchi, and Petra Wolf. “Decomposing Permutation Automata.” In <i>32nd International Conference on Concurrency Theory</i>, Vol. 203. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2021.18\">https://doi.org/10.4230/LIPIcs.CONCUR.2021.18</a>.","apa":"Jecker, I. R., Mazzocchi, N., &#38; Wolf, P. (2021). Decomposing permutation automata. In <i>32nd International Conference on Concurrency Theory</i> (Vol. 203). Paris, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2021.18\">https://doi.org/10.4230/LIPIcs.CONCUR.2021.18</a>","ieee":"I. R. Jecker, N. Mazzocchi, and P. Wolf, “Decomposing permutation automata,” in <i>32nd International Conference on Concurrency Theory</i>, Paris, France, 2021, vol. 203.","mla":"Jecker, Ismael R., et al. “Decomposing Permutation Automata.” <i>32nd International Conference on Concurrency Theory</i>, vol. 203, 18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2021.18\">10.4230/LIPIcs.CONCUR.2021.18</a>.","ista":"Jecker IR, Mazzocchi N, Wolf P. 2021. Decomposing permutation automata. 32nd International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 203, 18.","ama":"Jecker IR, Mazzocchi N, Wolf P. Decomposing permutation automata. In: <i>32nd International Conference on Concurrency Theory</i>. Vol 203. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2021.18\">10.4230/LIPIcs.CONCUR.2021.18</a>"},"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","ec_funded":1,"_id":"10052","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-05-14T10:55:28Z","quality_controlled":"1","article_number":"18","date_created":"2021-09-27T14:33:14Z","intvolume":"       203","alternative_title":["LIPIcs"]},{"month":"07","publication":"48th International Colloquium on Automata, Languages, and Programming","oa":1,"article_processing_charge":"No","corr_author":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Krishnendu Chatterjee: Supported by the ERC CoG 863818 (ForM-SMArt). Monika Henzinger: Supported by the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N. Sagar Sudhir Kale: Partially supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. Alexander Svozil: Fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003.","ddc":["000"],"has_accepted_license":"1","day":"02","volume":198,"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-195-5"]},"abstract":[{"lang":"eng","text":"Graphs and games on graphs are fundamental models for the analysis of reactive systems, in particular, for model-checking and the synthesis of reactive systems. The class of ω-regular languages provides a robust specification formalism for the desired properties of reactive systems. In the classical infinitary formulation of the liveness part of an ω-regular specification, a \"good\" event must happen eventually without any bound between the good events. A stronger notion of liveness is bounded liveness, which requires that good events happen within d transitions. Given a graph or a game graph with n vertices, m edges, and a bounded liveness objective, the previous best-known algorithmic bounds are as follows: (i) O(dm) for graphs, which in the worst-case is O(n³); and (ii) O(n² d²) for games on graphs. Our main contributions improve these long-standing algorithmic bounds. For graphs we present: (i) a randomized algorithm with one-sided error with running time O(n^{2.5} log n) for the bounded liveness objectives; and (ii) a deterministic linear-time algorithm for the complement of bounded liveness objectives. For games on graphs, we present an O(n² d) time algorithm for the bounded liveness objectives."}],"scopus_import":"1","fulldoi":"https://doi.org/10.4230/LIPIcs.ICALP.2021.124","conference":{"start_date":"2021-07-12","end_date":"2021-07-16","location":"Glasgow, Scotland","name":"ICALP: Automata, Languages and Programming"},"project":[{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","status":"public","department":[{"_id":"KrCh"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Bounded Liveness in Graphs and Game Graphs.” <i>48th International Colloquium on Automata, Languages, and Programming</i>, vol. 198, 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2021.124\">10.4230/LIPIcs.ICALP.2021.124</a>.","ama":"Chatterjee K, Henzinger M, Kale SS, Svozil A. Faster algorithms for bounded liveness in graphs and game graphs. In: <i>48th International Colloquium on Automata, Languages, and Programming</i>. Vol 198. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2021.124\">10.4230/LIPIcs.ICALP.2021.124</a>","ista":"Chatterjee K, Henzinger M, Kale SS, Svozil A. 2021. Faster algorithms for bounded liveness in graphs and game graphs. 48th International Colloquium on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 198, 124.","ieee":"K. Chatterjee, M. Henzinger, S. S. Kale, and A. Svozil, “Faster algorithms for bounded liveness in graphs and game graphs,” in <i>48th International Colloquium on Automata, Languages, and Programming</i>, Glasgow, Scotland, 2021, vol. 198.","apa":"Chatterjee, K., Henzinger, M., Kale, S. S., &#38; Svozil, A. (2021). Faster algorithms for bounded liveness in graphs and game graphs. In <i>48th International Colloquium on Automata, Languages, and Programming</i> (Vol. 198). Glasgow, Scotland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2021.124\">https://doi.org/10.4230/LIPIcs.ICALP.2021.124</a>","chicago":"Chatterjee, Krishnendu, Monika Henzinger, Sagar Sudhir Kale, and Alexander Svozil. “Faster Algorithms for Bounded Liveness in Graphs and Game Graphs.” In <i>48th International Colloquium on Automata, Languages, and Programming</i>, Vol. 198. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2021.124\">https://doi.org/10.4230/LIPIcs.ICALP.2021.124</a>.","short":"K. Chatterjee, M. Henzinger, S.S. Kale, A. Svozil, in:, 48th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021."},"alternative_title":["LIPIcs"],"quality_controlled":"1","article_number":"124","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"10054","date_updated":"2025-05-14T10:55:19Z","intvolume":"       198","date_created":"2021-09-27T14:33:15Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Kale, Sagar Sudhir","first_name":"Sagar Sudhir","last_name":"Kale"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}],"publication_status":"published","file":[{"file_name":"2021_LIPIcs_Chatterjee.pdf","file_id":"10062","access_level":"open_access","content_type":"application/pdf","file_size":854576,"success":1,"date_created":"2021-10-01T08:49:26Z","creator":"cchlebak","date_updated":"2021-10-01T08:49:26Z","checksum":"5a3fed8dbba8c088cbeac1e24cc10bc5","relation":"main_file"}],"date_published":"2021-07-02T00:00:00Z","file_date_updated":"2021-10-01T08:49:26Z","title":"Faster algorithms for bounded liveness in graphs and game graphs","doi":"10.4230/LIPIcs.ICALP.2021.124"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","fulldoi":"https://doi.org/10.4230/LIPIcs.STACS.2021.44","conference":{"location":"Saarbrücken, Germany","name":"STACS: Symposium on Theoretical Aspects of Computer Science","end_date":"2021-03-19","start_date":"2021-03-16"},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"type":"conference","article_processing_charge":"No","oa":1,"external_id":{"isi":["000635691700044"]},"publication":"38th International Symposium on Theoretical Aspects of Computer Science","month":"03","scopus_import":"1","abstract":[{"text":"Repeated idempotent elements are commonly used to characterise iterable behaviours in abstract models of computation. Therefore, given a monoid M, it is natural to ask how long a sequence of elements of M needs to be to ensure the presence of consecutive idempotent factors. This question is formalised through the notion of the Ramsey function R_M associated to M, obtained by mapping every k ∈ ℕ to the minimal integer R_M(k) such that every word u ∈ M^* of length R_M(k) contains k consecutive non-empty factors that correspond to the same idempotent element of M. In this work, we study the behaviour of the Ramsey function R_M by investigating the regular 𝒟-length of M, defined as the largest size L(M) of a submonoid of M isomorphic to the set of natural numbers {1,2, …, L(M)} equipped with the max operation. We show that the regular 𝒟-length of M determines the degree of R_M, by proving that k^L(M) ≤ R_M(k) ≤ (k|M|⁴)^L(M). To allow applications of this result, we provide the value of the regular 𝒟-length of diverse monoids. In particular, we prove that the full monoid of n × n Boolean matrices, which is used to express transition monoids of non-deterministic automata, has a regular 𝒟-length of (n²+n+2)/2.","lang":"eng"}],"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-9597-7180-1"]},"volume":187,"day":"10","has_accepted_license":"1","ddc":["000"],"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. I wish to thank Michaël Cadilhac, Emmanuel Filiot and Charles Paperman for their valuable insights concerning Green’s relations.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.4230/LIPIcs.STACS.2021.44","isi":1,"title":"A Ramsey theorem for finite monoids","file_date_updated":"2021-10-01T09:55:00Z","date_published":"2021-03-10T00:00:00Z","file":[{"access_level":"open_access","file_id":"10063","file_name":"2021_LIPIcs_Jecker.pdf","date_updated":"2021-10-01T09:55:00Z","checksum":"17432a05733f408de300e17e390a90e4","relation":"main_file","date_created":"2021-10-01T09:55:00Z","success":1,"creator":"cchlebak","content_type":"application/pdf","file_size":720250}],"publication_status":"published","author":[{"id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","last_name":"Jecker","first_name":"Ismael R","full_name":"Jecker, Ismael R"}],"citation":{"ieee":"I. R. Jecker, “A Ramsey theorem for finite monoids,” in <i>38th International Symposium on Theoretical Aspects of Computer Science</i>, Saarbrücken, Germany, 2021, vol. 187.","ista":"Jecker IR. 2021. A Ramsey theorem for finite monoids. 38th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 187, 44.","ama":"Jecker IR. A Ramsey theorem for finite monoids. In: <i>38th International Symposium on Theoretical Aspects of Computer Science</i>. Vol 187. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2021.44\">10.4230/LIPIcs.STACS.2021.44</a>","mla":"Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” <i>38th International Symposium on Theoretical Aspects of Computer Science</i>, vol. 187, 44, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.STACS.2021.44\">10.4230/LIPIcs.STACS.2021.44</a>.","short":"I.R. Jecker, in:, 38th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","chicago":"Jecker, Ismael R. “A Ramsey Theorem for Finite Monoids.” In <i>38th International Symposium on Theoretical Aspects of Computer Science</i>, Vol. 187. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2021.44\">https://doi.org/10.4230/LIPIcs.STACS.2021.44</a>.","apa":"Jecker, I. R. (2021). A Ramsey theorem for finite monoids. In <i>38th International Symposium on Theoretical Aspects of Computer Science</i> (Vol. 187). Saarbrücken, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.STACS.2021.44\">https://doi.org/10.4230/LIPIcs.STACS.2021.44</a>"},"department":[{"_id":"KrCh"}],"status":"public","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"date_created":"2021-09-27T14:33:15Z","intvolume":"       187","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-05-14T10:55:11Z","_id":"10055","article_number":"44","quality_controlled":"1","alternative_title":["LIPIcs"]},{"fulldoi":"https://doi.org/10.1038/s41598-021-98411-z","year":"2021","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","type":"journal_article","month":"09","oa":1,"article_processing_charge":"Yes","external_id":{"pmid":["34584125"],"isi":["000701575500083"]},"publication":"Scientific Reports","acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the study and all the midwives and doctors for the computerized obstetrical data.","ddc":["618"],"has_accepted_license":"1","corr_author":"1","publisher":"Springer Nature","publication_identifier":{"eissn":["2045-2322"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"The extent to which women differ in the course of blood cell counts throughout pregnancy, and the importance of these changes to pregnancy outcomes has not been well defined. Here, we develop a series of statistical analyses of repeated measures data to reveal the degree to which women differ in the course of pregnancy, predict the changes that occur, and determine the importance of these changes for post-partum hemorrhage (PPH) which is one of the leading causes of maternal mortality. We present a prospective cohort of 4082 births recorded at the University Hospital, Lausanne, Switzerland between 2009 and 2014 where full labour records could be obtained, along with complete blood count data taken at hospital admission. We find significant differences, at a [Formula: see text] level, among women in how blood count values change through pregnancy for mean corpuscular hemoglobin, mean corpuscular volume, mean platelet volume, platelet count and red cell distribution width. We find evidence that almost all complete blood count values show trimester-specific associations with PPH. For example, high platelet count (OR 1.20, 95% CI 1.01-1.53), high mean platelet volume (OR 1.58, 95% CI 1.04-2.08), and high erythrocyte levels (OR 1.36, 95% CI 1.01-1.57) in trimester 1 increased PPH, but high values in trimester 3 decreased PPH risk (OR 0.85, 0.79, 0.67 respectively). We show that differences among women in the course of blood cell counts throughout pregnancy have an important role in shaping pregnancy outcome and tracking blood count value changes through pregnancy improves identification of women at increased risk of postpartum hemorrhage. This study provides greater understanding of the complex changes in blood count values that occur through pregnancy and provides indicators to guide the stratification of patients into risk groups."}],"day":"28","volume":11,"date_published":"2021-09-28T00:00:00Z","file":[{"file_id":"10091","access_level":"open_access","file_name":"2021_ScientificReports_Robinson.pdf","creator":"cchlebak","success":1,"date_created":"2021-10-05T14:56:48Z","relation":"main_file","date_updated":"2021-10-05T14:56:48Z","checksum":"f002ec22f609f58e1263b79e7f79601e","file_size":6970368,"content_type":"application/pdf"}],"pmid":1,"author":[{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"full_name":"Patxot, Marion","first_name":"Marion","last_name":"Patxot"},{"full_name":"Stojanov, Miloš","last_name":"Stojanov","first_name":"Miloš"},{"last_name":"Blum","first_name":"Sabine","full_name":"Blum, Sabine"},{"full_name":"Baud, David","first_name":"David","last_name":"Baud"}],"publication_status":"published","title":"Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy","isi":1,"file_date_updated":"2021-10-05T14:56:48Z","doi":"10.1038/s41598-021-98411-z","oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"MaRo"}],"citation":{"ieee":"M. R. Robinson, M. Patxot, M. Stojanov, S. Blum, and D. Baud, “Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy,” <i>Scientific Reports</i>, vol. 11. Springer Nature, 2021.","mla":"Robinson, Matthew Richard, et al. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” <i>Scientific Reports</i>, vol. 11, 19238, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-98411-z\">10.1038/s41598-021-98411-z</a>.","ama":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. <i>Scientific Reports</i>. 2021;11. doi:<a href=\"https://doi.org/10.1038/s41598-021-98411-z\">10.1038/s41598-021-98411-z</a>","ista":"Robinson MR, Patxot M, Stojanov M, Blum S, Baud D. 2021. Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. Scientific Reports. 11, 19238.","short":"M.R. Robinson, M. Patxot, M. Stojanov, S. Blum, D. Baud, Scientific Reports 11 (2021).","chicago":"Robinson, Matthew Richard, Marion Patxot, Miloš Stojanov, Sabine Blum, and David Baud. “Postpartum Hemorrhage Risk Is Driven by Changes in Blood Composition through Pregnancy.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-98411-z\">https://doi.org/10.1038/s41598-021-98411-z</a>.","apa":"Robinson, M. R., Patxot, M., Stojanov, M., Blum, S., &#38; Baud, D. (2021). Postpartum hemorrhage risk is driven by changes in blood composition through pregnancy. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-98411-z\">https://doi.org/10.1038/s41598-021-98411-z</a>"},"status":"public","intvolume":"        11","date_created":"2021-10-03T22:01:21Z","article_number":"19238","quality_controlled":"1","_id":"10069","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2024-10-09T21:00:57Z"},{"author":[{"full_name":"Dello Schiavo, Lorenzo","first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","orcid":"0000-0002-9881-6870"},{"first_name":"Kohei","last_name":"Suzuki","full_name":"Suzuki, Kohei"}],"publication_status":"published","date_published":"2021-09-15T00:00:00Z","isi":1,"title":"Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces","doi":"10.1016/j.jfa.2021.109234","intvolume":"       281","date_created":"2021-10-03T22:01:21Z","quality_controlled":"1","article_number":"109234","_id":"10070","date_updated":"2025-04-14T07:27:45Z","ec_funded":1,"oa_version":"Preprint","language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2008.01492"}],"citation":{"short":"L. Dello Schiavo, K. Suzuki, Journal of Functional Analysis 281 (2021).","chicago":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” <i>Journal of Functional Analysis</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">https://doi.org/10.1016/j.jfa.2021.109234</a>.","apa":"Dello Schiavo, L., &#38; Suzuki, K. (2021). Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">https://doi.org/10.1016/j.jfa.2021.109234</a>","ieee":"L. Dello Schiavo and K. Suzuki, “Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces,” <i>Journal of Functional Analysis</i>, vol. 281, no. 11. Elsevier, 2021.","mla":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Rademacher-Type Theorems and Sobolev-to-Lipschitz Properties for Strongly Local Dirichlet Spaces.” <i>Journal of Functional Analysis</i>, vol. 281, no. 11, 109234, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">10.1016/j.jfa.2021.109234</a>.","ama":"Dello Schiavo L, Suzuki K. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. <i>Journal of Functional Analysis</i>. 2021;281(11). doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109234\">10.1016/j.jfa.2021.109234</a>","ista":"Dello Schiavo L, Suzuki K. 2021. Rademacher-type theorems and Sobolev-to-Lipschitz properties for strongly local Dirichlet spaces. Journal of Functional Analysis. 281(11), 109234."},"status":"public","article_type":"original","type":"journal_article","fulldoi":"https://doi.org/10.1016/j.jfa.2021.109234","project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"}],"year":"2021","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"11","acknowledgement":"The authors are grateful to Professor Kazuhiro Kuwae for kindly providing a copy of [49]. They are also grateful to Dr. Bang-Xian Han for helpful discussions on the Sobolev-to-Lipschitz property on metric measure spaces. They wish to express their deepest gratitude to an anonymous Reviewer, whose punctual remarks and comments greatly improved the accessibility and overall quality of the initial submission. This work was completed while L.D.S. was a member of the Institut für Angewandte Mathematik of the University of Bonn. He acknowledges funding of his position at that time by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through the Sonderforschungsbereich (Sfb, Collaborative Research Center) 1060 - project number 211504053. He also acknowledges funding of his current position by the Austrian Science Fund (FWF) grant F65, and by the European Research Council (ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas). K.S. gratefully acknowledges funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier International Research Center Initiative (WPI), MEXT, Japan; and JSPS Grant-in-Aid for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials Design”, Grant Number 17H06465.","publisher":"Elsevier","corr_author":"1","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"We extensively discuss the Rademacher and Sobolev-to-Lipschitz properties for generalized intrinsic distances on strongly local Dirichlet spaces possibly without square field operator. We present many non-smooth and infinite-dimensional examples. As an application, we prove the integral Varadhan short-time asymptotic with respect to a given distance function for a large class of strongly local Dirichlet forms."}],"day":"15","volume":281,"month":"09","oa":1,"article_processing_charge":"No","arxiv":1,"publication":"Journal of Functional Analysis","external_id":{"arxiv":["2008.01492"],"isi":["000703896600005"]}},{"year":"2021","fulldoi":"https://doi.org/10.1090/noti2349","issue":"9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"letter_note","type":"journal_article","month":"10","publication":"Notices of the American Mathematical Society","article_processing_charge":"No","oa":1,"publisher":"American Mathematical Society","ddc":["500"],"volume":68,"day":"01","scopus_import":"1","publication_identifier":{"eissn":["1088-9477"],"issn":["0002-9920"]},"page":"1511-1514","author":[{"full_name":"Adams, Henry","first_name":"Henry","last_name":"Adams"},{"full_name":"Kourimska, Hana","last_name":"Kourimska","orcid":"0000-0001-7841-0091","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","first_name":"Hana"},{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss","orcid":"0000-0002-1780-2689","first_name":"Teresa","full_name":"Heiss, Teresa"},{"full_name":"Percival, Sarah","first_name":"Sarah","last_name":"Percival"},{"full_name":"Ziegelmeier, Lori","last_name":"Ziegelmeier","first_name":"Lori"}],"publication_status":"published","date_published":"2021-10-01T00:00:00Z","doi":"10.1090/noti2349","title":"How to tutorial-a-thon","language":[{"iso":"eng"}],"oa_version":"Published Version","status":"public","citation":{"chicago":"Adams, Henry, Hana Kourimska, Teresa Heiss, Sarah Percival, and Lori Ziegelmeier. “How to Tutorial-a-Thon.” <i>Notices of the American Mathematical Society</i>. American Mathematical Society, 2021. <a href=\"https://doi.org/10.1090/noti2349\">https://doi.org/10.1090/noti2349</a>.","apa":"Adams, H., Kourimska, H., Heiss, T., Percival, S., &#38; Ziegelmeier, L. (2021). How to tutorial-a-thon. <i>Notices of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/noti2349\">https://doi.org/10.1090/noti2349</a>","short":"H. Adams, H. Kourimska, T. Heiss, S. Percival, L. Ziegelmeier, Notices of the American Mathematical Society 68 (2021) 1511–1514.","mla":"Adams, Henry, et al. “How to Tutorial-a-Thon.” <i>Notices of the American Mathematical Society</i>, vol. 68, no. 9, American Mathematical Society, 2021, pp. 1511–14, doi:<a href=\"https://doi.org/10.1090/noti2349\">10.1090/noti2349</a>.","ista":"Adams H, Kourimska H, Heiss T, Percival S, Ziegelmeier L. 2021. How to tutorial-a-thon. Notices of the American Mathematical Society. 68(9), 1511–1514.","ama":"Adams H, Kourimska H, Heiss T, Percival S, Ziegelmeier L. How to tutorial-a-thon. <i>Notices of the American Mathematical Society</i>. 2021;68(9):1511-1514. doi:<a href=\"https://doi.org/10.1090/noti2349\">10.1090/noti2349</a>","ieee":"H. Adams, H. Kourimska, T. Heiss, S. Percival, and L. Ziegelmeier, “How to tutorial-a-thon,” <i>Notices of the American Mathematical Society</i>, vol. 68, no. 9. American Mathematical Society, pp. 1511–1514, 2021."},"department":[{"_id":"HeEd"}],"main_file_link":[{"open_access":"1","url":"http://www.ams.org/notices/"}],"alternative_title":["Early Career"],"date_updated":"2026-06-18T08:36:13Z","_id":"10071","quality_controlled":"1","date_created":"2021-10-03T22:01:22Z","intvolume":"        68"},{"abstract":[{"lang":"eng","text":"The Lovász Local Lemma (LLL) is a powerful tool in probabilistic combinatorics which can be used to establish the existence of objects that satisfy certain properties. The breakthrough paper of Moser and Tardos and follow-up works revealed that the LLL has intimate connections with a class of stochastic local search algorithms for finding such desirable objects. In particular, it can be seen as a sufficient condition for this type of algorithms to converge fast. Besides conditions for existence of and fast convergence to desirable objects, one may naturally ask further questions regarding properties of these algorithms. For instance, \"are they parallelizable?\", \"how many solutions can they output?\", \"what is the expected \"weight\" of a solution?\", etc. These questions and more have been answered for a class of LLL-inspired algorithms called commutative. In this paper we introduce a new, very natural and more general notion of commutativity (essentially matrix commutativity) which allows us to show a number of new refined properties of LLL-inspired local search algorithms with significantly simpler proofs."}],"scopus_import":"1","publication_identifier":{"isbn":["978-3-9597-7207-5"],"issn":["1868-8969"]},"volume":207,"day":"15","ddc":["000"],"has_accepted_license":"1","acknowledgement":"Fotis Iliopoulos: This material is based upon work directly supported by the IAS Fund for Math and indirectly supported by the National Science Foundation Grant No. CCF-1900460. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. This work is also supported by the National Science Foundation Grant No. CCF-1815328.\r\nVladimir Kolmogorov: Supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"Yes","arxiv":1,"oa":1,"external_id":{"arxiv":["2008.05569"]},"publication":"Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques","month":"09","related_material":{"record":[{"id":"21143","relation":"later_version","status":"public"}]},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","fulldoi":"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31","project":[{"grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"conference":{"end_date":"2021-08-18","location":"Virtual","name":"APPROX/RANDOM: Approximation Algorithms for Combinatorial Optimization Problems/ Randomization and Computation","start_date":"2021-08-16"},"date_created":"2021-10-03T22:01:22Z","intvolume":"       207","date_updated":"2026-02-10T09:59:59Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"10072","article_number":"31","quality_controlled":"1","alternative_title":["LIPIcs"],"citation":{"apa":"Harris, D. G., Iliopoulos, F., &#38; Kolmogorov, V. (2021). A new notion of commutativity for the algorithmic Lovász Local Lemma. In <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i> (Vol. 207). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>","chicago":"Harris, David G., Fotis Iliopoulos, and Vladimir Kolmogorov. “A New Notion of Commutativity for the Algorithmic Lovász Local Lemma.” In <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>, Vol. 207. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>.","short":"D.G. Harris, F. Iliopoulos, V. Kolmogorov, in:, Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","ista":"Harris DG, Iliopoulos F, Kolmogorov V. 2021. A new notion of commutativity for the algorithmic Lovász Local Lemma. Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques. APPROX/RANDOM: Approximation Algorithms for Combinatorial Optimization Problems/ Randomization and Computation, LIPIcs, vol. 207, 31.","ama":"Harris DG, Iliopoulos F, Kolmogorov V. A new notion of commutativity for the algorithmic Lovász Local Lemma. In: <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>. Vol 207. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>","mla":"Harris, David G., et al. “A New Notion of Commutativity for the Algorithmic Lovász Local Lemma.” <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>, vol. 207, 31, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2021.31\">10.4230/LIPIcs.APPROX/RANDOM.2021.31</a>.","ieee":"D. G. Harris, F. Iliopoulos, and V. Kolmogorov, “A new notion of commutativity for the algorithmic Lovász Local Lemma,” in <i>Approximation, Randomization, and Combinatorial Optimization. Algorithms and Techniques</i>, Virtual, 2021, vol. 207."},"department":[{"_id":"VlKo"}],"status":"public","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.APPROX/RANDOM.2021.31","file_date_updated":"2021-10-06T13:51:54Z","title":"A new notion of commutativity for the algorithmic Lovász Local Lemma","file":[{"file_name":"2021_LIPIcs_Harris.pdf","file_id":"10098","access_level":"open_access","content_type":"application/pdf","file_size":804472,"success":1,"date_created":"2021-10-06T13:51:54Z","creator":"cchlebak","checksum":"9d2544d53aa5b01565c6891d97a4d765","date_updated":"2021-10-06T13:51:54Z","relation":"main_file"}],"date_published":"2021-09-15T00:00:00Z","author":[{"first_name":"David G.","last_name":"Harris","full_name":"Harris, David G."},{"last_name":"Iliopoulos","first_name":"Fotis","full_name":"Iliopoulos, Fotis"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"}],"publication_status":"published"},{"acknowledgement":"The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n","has_accepted_license":"1","ddc":["540"],"publisher":"MDPI","corr_author":"1","publication_identifier":{"eissn":["1996-1944"]},"scopus_import":"1","abstract":[{"text":"Thermoelectric materials enable the direct conversion between heat and electricity. SnTe is a promising candidate due to its high charge transport performance. Here, we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe nanoparticles (NP), followed by a unique surface treatment prior NP consolidation. This synthetic approach allowed optimizing the charge and phonon transport synergistically. The novelty of this strategy was the use of a soluble PbS molecular complex prepared using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite is formed. The presence of PbS complexes significantly compensates for the Sn vacancy and increases the average grain size of the nanocomposite, thus improving the carrier mobility. Moreover, lattice thermal conductivity is also reduced by the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct rational surface treatment on NP-based thermoelectrics.","lang":"eng"}],"day":"19","volume":14,"month":"09","oa":1,"article_processing_charge":"Yes","external_id":{"pmid":["34576640"],"isi":["000700689400001"]},"publication":"Materials","acknowledged_ssus":[{"_id":"EM-Fac"}],"article_type":"original","type":"journal_article","project":[{"grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","name":"Bottom-up Engineering for Thermoelectric Applications"}],"fulldoi":"https://doi.org/10.3390/ma14185416","year":"2021","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"18","intvolume":"        14","date_created":"2021-10-03T22:01:23Z","quality_controlled":"1","article_number":"5416","date_updated":"2025-04-14T09:29:32Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"10073","oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"citation":{"apa":"Chang, C., &#38; Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. <i>Materials</i>. MDPI. <a href=\"https://doi.org/10.3390/ma14185416\">https://doi.org/10.3390/ma14185416</a>","chicago":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” <i>Materials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ma14185416\">https://doi.org/10.3390/ma14185416</a>.","short":"C. Chang, M. Ibáñez, Materials 14 (2021).","mla":"Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” <i>Materials</i>, vol. 14, no. 18, 5416, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ma14185416\">10.3390/ma14185416</a>.","ista":"Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416.","ama":"Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. <i>Materials</i>. 2021;14(18). doi:<a href=\"https://doi.org/10.3390/ma14185416\">10.3390/ma14185416</a>","ieee":"C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” <i>Materials</i>, vol. 14, no. 18. MDPI, 2021."},"status":"public","publication_status":"published","pmid":1,"file":[{"file_size":4404141,"content_type":"application/pdf","relation":"main_file","checksum":"4929dfc673a3ae77c010b6174279cc1d","date_updated":"2021-10-14T11:56:39Z","creator":"cchlebak","success":1,"date_created":"2021-10-14T11:56:39Z","file_name":"2021_Materials_Chang.pdf","access_level":"open_access","file_id":"10140"}],"author":[{"first_name":"Cheng","orcid":"0000-0002-9515-4277","last_name":"Chang","id":"9E331C2E-9F27-11E9-AE48-5033E6697425","full_name":"Chang, Cheng"},{"full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"}],"date_published":"2021-09-19T00:00:00Z","file_date_updated":"2021-10-14T11:56:39Z","isi":1,"title":"Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites","doi":"10.3390/ma14185416"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["000"],"has_accepted_license":"1","acknowledgement":"Ismaël Jecker: Funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 754411. Karoliina Lehtinen: Funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 892704.","volume":202,"day":"18","abstract":[{"text":"We study the expressiveness and succinctness of good-for-games pushdown automata (GFG-PDA) over finite words, that is, pushdown automata whose nondeterminism can be resolved based on the run constructed so far, but independently of the remainder of the input word. We prove that GFG-PDA recognise more languages than deterministic PDA (DPDA) but not all context-free languages (CFL). This class is orthogonal to unambiguous CFL. We further show that GFG-PDA can be exponentially more succinct than DPDA, while PDA can be double-exponentially more succinct than GFG-PDA. We also study GFGness in visibly pushdown automata (VPA), which enjoy better closure properties than PDA, and for which we show GFGness to be ExpTime-complete. GFG-VPA can be exponentially more succinct than deterministic VPA, while VPA can be exponentially more succinct than GFG-VPA. Both of these lower bounds are tight. Finally, we study the complexity of resolving nondeterminism in GFG-PDA. Every GFG-PDA has a positional resolver, a function that resolves nondeterminism and that is only dependant on the current configuration. Pushdown transducers are sufficient to implement the resolvers of GFG-VPA, but not those of GFG-PDA. GFG-PDA with finite-state resolvers are determinisable.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"isbn":["978-3-9597-7201-3"],"issn":["1868-8969"]},"month":"08","external_id":{"arxiv":["2105.02611"]},"publication":"46th International Symposium on Mathematical Foundations of Computer Science","arxiv":1,"article_processing_charge":"No","oa":1,"type":"conference","year":"2021","fulldoi":"https://doi.org/10.4230/LIPIcs.MFCS.2021.53","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","location":"Tallinn, Estonia","end_date":"2021-08-27","start_date":"2021-08-23"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"date_updated":"2025-05-14T10:54:50Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"10075","article_number":"53","quality_controlled":"1","date_created":"2021-10-03T22:01:23Z","intvolume":"       202","language":[{"iso":"eng"}],"oa_version":"Published Version","ec_funded":1,"status":"public","citation":{"apa":"Guha, S., Jecker, I. R., Lehtinen, K., &#38; Zimmermann, M. (2021). A bit of nondeterminism makes pushdown automata expressive and succinct. In <i>46th International Symposium on Mathematical Foundations of Computer Science</i> (Vol. 202). Tallinn, Estonia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">https://doi.org/10.4230/LIPIcs.MFCS.2021.53</a>","chicago":"Guha, Shibashis, Ismael R Jecker, Karoliina Lehtinen, and Martin Zimmermann. “A Bit of Nondeterminism Makes Pushdown Automata Expressive and Succinct.” In <i>46th International Symposium on Mathematical Foundations of Computer Science</i>, Vol. 202. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">https://doi.org/10.4230/LIPIcs.MFCS.2021.53</a>.","short":"S. Guha, I.R. Jecker, K. Lehtinen, M. Zimmermann, in:, 46th International Symposium on Mathematical Foundations of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","ista":"Guha S, Jecker IR, Lehtinen K, Zimmermann M. 2021. A bit of nondeterminism makes pushdown automata expressive and succinct. 46th International Symposium on Mathematical Foundations of Computer Science. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 202, 53.","ama":"Guha S, Jecker IR, Lehtinen K, Zimmermann M. A bit of nondeterminism makes pushdown automata expressive and succinct. In: <i>46th International Symposium on Mathematical Foundations of Computer Science</i>. Vol 202. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">10.4230/LIPIcs.MFCS.2021.53</a>","mla":"Guha, Shibashis, et al. “A Bit of Nondeterminism Makes Pushdown Automata Expressive and Succinct.” <i>46th International Symposium on Mathematical Foundations of Computer Science</i>, vol. 202, 53, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2021.53\">10.4230/LIPIcs.MFCS.2021.53</a>.","ieee":"S. Guha, I. R. Jecker, K. Lehtinen, and M. Zimmermann, “A bit of nondeterminism makes pushdown automata expressive and succinct,” in <i>46th International Symposium on Mathematical Foundations of Computer Science</i>, Tallinn, Estonia, 2021, vol. 202."},"department":[{"_id":"KrCh"}],"author":[{"first_name":"Shibashis","last_name":"Guha","full_name":"Guha, Shibashis"},{"full_name":"Jecker, Ismael R","first_name":"Ismael R","last_name":"Jecker","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425"},{"full_name":"Lehtinen, Karoliina","last_name":"Lehtinen","first_name":"Karoliina"},{"first_name":"Martin","last_name":"Zimmermann","full_name":"Zimmermann, Martin"}],"file":[{"relation":"main_file","checksum":"f4d407d43a97330c3fb11e6a7a6fbfb2","date_updated":"2021-10-06T12:44:05Z","creator":"cchlebak","date_created":"2021-10-06T12:44:05Z","success":1,"file_size":825567,"content_type":"application/pdf","access_level":"open_access","file_id":"10097","file_name":"2021_LIPIcs_Guha.pdf"}],"date_published":"2021-08-18T00:00:00Z","publication_status":"published","doi":"10.4230/LIPIcs.MFCS.2021.53","file_date_updated":"2021-10-06T12:44:05Z","title":"A bit of nondeterminism makes pushdown automata expressive and succinct"},{"date_created":"2021-10-03T22:01:24Z","quality_controlled":"1","date_updated":"2025-07-10T11:49:40Z","_id":"10076","alternative_title":["LNCS"],"department":[{"_id":"ElKo"}],"main_file_link":[{"url":"https://research.fb.com/publications/reactive-key-loss-protection-in-blockchains/","open_access":"1"}],"citation":{"ama":"Blackshear S, Chalkias K, Chatzigiannis P, et al. Reactive key-loss protection in blockchains. In: <i>FC 2021 Workshops</i>. Vol 12676. Springer Nature; 2021:431-450. doi:<a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">10.1007/978-3-662-63958-0_34</a>","ista":"Blackshear S, Chalkias K, Chatzigiannis P, Faizullabhoy R, Khaburzaniya I, Kokoris Kogias E, Lind J, Wong D, Zakian T. 2021. Reactive key-loss protection in blockchains. FC 2021 Workshops. FC: Financial Cryptography and Data Security, LNCS, vol. 12676, 431–450.","mla":"Blackshear, Sam, et al. “Reactive Key-Loss Protection in Blockchains.” <i>FC 2021 Workshops</i>, vol. 12676, Springer Nature, 2021, pp. 431–50, doi:<a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">10.1007/978-3-662-63958-0_34</a>.","ieee":"S. Blackshear <i>et al.</i>, “Reactive key-loss protection in blockchains,” in <i>FC 2021 Workshops</i>, Virtual, 2021, vol. 12676, pp. 431–450.","apa":"Blackshear, S., Chalkias, K., Chatzigiannis, P., Faizullabhoy, R., Khaburzaniya, I., Kokoris Kogias, E., … Zakian, T. (2021). Reactive key-loss protection in blockchains. In <i>FC 2021 Workshops</i> (Vol. 12676, pp. 431–450). Virtual: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">https://doi.org/10.1007/978-3-662-63958-0_34</a>","chicago":"Blackshear, Sam, Konstantinos Chalkias, Panagiotis Chatzigiannis, Riyaz Faizullabhoy, Irakliy Khaburzaniya, Eleftherios Kokoris Kogias, Joshua Lind, David Wong, and Tim Zakian. “Reactive Key-Loss Protection in Blockchains.” In <i>FC 2021 Workshops</i>, 12676:431–50. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-662-63958-0_34\">https://doi.org/10.1007/978-3-662-63958-0_34</a>.","short":"S. Blackshear, K. Chalkias, P. Chatzigiannis, R. Faizullabhoy, I. Khaburzaniya, E. Kokoris Kogias, J. Lind, D. Wong, T. Zakian, in:, FC 2021 Workshops, Springer Nature, 2021, pp. 431–450."},"status":"public","oa_version":"Preprint","language":[{"iso":"eng"}],"isi":1,"title":"Reactive key-loss protection in blockchains","doi":"10.1007/978-3-662-63958-0_34","publication_status":"published","date_published":"2021-09-17T00:00:00Z","author":[{"last_name":"Blackshear","first_name":"Sam","full_name":"Blackshear, Sam"},{"first_name":"Konstantinos","last_name":"Chalkias","full_name":"Chalkias, Konstantinos"},{"full_name":"Chatzigiannis, Panagiotis","first_name":"Panagiotis","last_name":"Chatzigiannis"},{"full_name":"Faizullabhoy, Riyaz","first_name":"Riyaz","last_name":"Faizullabhoy"},{"full_name":"Khaburzaniya, Irakliy","first_name":"Irakliy","last_name":"Khaburzaniya"},{"full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Lind, Joshua","last_name":"Lind","first_name":"Joshua"},{"first_name":"David","last_name":"Wong","full_name":"Wong, David"},{"first_name":"Tim","last_name":"Zakian","full_name":"Zakian, Tim"}],"page":"431-450","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["978-3-662-63958-0"],"isbn":["978-3-6626-3957-3"]},"scopus_import":"1","abstract":[{"text":"We present a novel approach for blockchain asset owners to reclaim their funds in case of accidental private-key loss or transfer to a mistyped address. Our solution can be deployed upon failure or absence of proactively implemented backup mechanisms, such as secret sharing and cold storage. The main advantages against previous proposals is it does not require any prior action from users and works with both single-key and multi-sig accounts. We achieve this by a 3-phase   Commit()→Reveal()→Claim()−or−Challenge()  smart contract that enables accessing funds of addresses for which the spending key is not available. We provide an analysis of the threat and incentive models and formalize the concept of reactive KEy-Loss Protection (KELP).","lang":"eng"}],"day":"17","volume":"12676 ","acknowledgement":"The authors would like to thank all anonymous reviewers of FC21 WTSC workshop for comments and suggestions that greatly improved the quality of this paper.","publisher":"Springer Nature","oa":1,"article_processing_charge":"No","publication":"FC 2021 Workshops","external_id":{"isi":["000713005000034"]},"month":"09","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1007/978-3-662-63958-0_34","conference":{"end_date":"2021-03-05","location":"Virtual","name":"FC: Financial Cryptography and Data Security","start_date":"2021-03-01"},"year":"2021"},{"keyword":["virology","infectious diseases"],"publication_status":"published","file":[{"file_name":"2021_Viruses_Obr.pdf","file_id":"10115","access_level":"open_access","file_size":4146796,"content_type":"application/pdf","creator":"cchlebak","success":1,"date_created":"2021-10-08T10:38:15Z","relation":"main_file","checksum":"bcfd72a12977d48e22df3d0cc55aacf1","date_updated":"2021-10-08T10:38:15Z"}],"date_published":"2021-09-17T00:00:00Z","pmid":1,"author":[{"full_name":"Obr, Martin","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Obr","orcid":"0000-0003-1756-6564"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"}],"doi":"10.3390/v13091853","title":"A structural perspective of the role of IP6 in immature and mature retroviral assembly","file_date_updated":"2021-10-08T10:38:15Z","isi":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","status":"public","citation":{"chicago":"Obr, Martin, Florian KM Schur, and Robert A. Dick. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>.","apa":"Obr, M., Schur, F. K., &#38; Dick, R. A. (2021). A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. MDPI. <a href=\"https://doi.org/10.3390/v13091853\">https://doi.org/10.3390/v13091853</a>","short":"M. Obr, F.K. Schur, R.A. Dick, Viruses 13 (2021).","ama":"Obr M, Schur FK, Dick RA. A structural perspective of the role of IP6 in immature and mature retroviral assembly. <i>Viruses</i>. 2021;13(9). doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>","ista":"Obr M, Schur FK, Dick RA. 2021. A structural perspective of the role of IP6 in immature and mature retroviral assembly. Viruses. 13(9), 1853.","mla":"Obr, Martin, et al. “A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly.” <i>Viruses</i>, vol. 13, no. 9, 1853, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/v13091853\">10.3390/v13091853</a>.","ieee":"M. Obr, F. K. Schur, and R. A. Dick, “A structural perspective of the role of IP6 in immature and mature retroviral assembly,” <i>Viruses</i>, vol. 13, no. 9. MDPI, 2021."},"department":[{"_id":"FlSc"}],"_id":"10103","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-04-15T08:24:49Z","quality_controlled":"1","article_number":"1853","date_created":"2021-10-07T09:13:29Z","intvolume":"        13","year":"2021","project":[{"grant_number":"P31445","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","name":"Structural conservation and diversity in retroviral capsid"}],"fulldoi":"https://doi.org/10.3390/v13091853","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","article_type":"original","type":"journal_article","month":"09","external_id":{"pmid":["34578434"],"isi":["000699841100001"]},"publication":"Viruses","article_processing_charge":"Yes","oa":1,"corr_author":"1","publisher":"MDPI","has_accepted_license":"1","ddc":["616"],"acknowledgement":"We thank Volker M. Vogt for his critical comments in preparation of the review.","volume":13,"day":"17","scopus_import":"1","abstract":[{"text":"The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses.","lang":"eng"}],"publication_identifier":{"issn":["1999-4915"]}},{"page":"231-243","date_published":"2021-10-06T00:00:00Z","file":[{"file_name":"differentialmonitoring-cameraready-openaccess.pdf","file_id":"10109","access_level":"open_access","file_size":350632,"content_type":"application/pdf","success":1,"date_created":"2021-10-07T23:32:18Z","creator":"fmuehlbo","checksum":"554c7fdb259eda703a8b6328a6dad55a","date_updated":"2021-10-07T23:32:18Z","relation":"main_file"}],"publication_status":"published","author":[{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","orcid":"0000-0003-1548-0177","first_name":"Fabian","full_name":"Mühlböck, Fabian"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"keyword":["run-time verification","software engineering","implicit specification"],"doi":"10.1007/978-3-030-88494-9_12","title":"Differential monitoring","file_date_updated":"2021-10-07T23:32:18Z","isi":1,"oa_version":"Preprint","language":[{"iso":"eng"}],"citation":{"ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in <i>International Conference on Runtime Verification</i>, Virtual, 2021, vol. 12974, pp. 231–243.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” <i>International Conference on Runtime Verification</i>, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>.","ama":"Mühlböck F, Henzinger TA. Differential monitoring. In: <i>International Conference on Runtime Verification</i>. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In <i>International Conference on Runtime Verification</i>, 12974:231–43. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>.","apa":"Mühlböck, F., &#38; Henzinger, T. A. (2021). Differential monitoring. In <i>International Conference on Runtime Verification</i> (Vol. 12974, pp. 231–243). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>"},"department":[{"_id":"ToHe"}],"status":"public","alternative_title":["LNCS"],"date_created":"2021-10-07T23:30:10Z","intvolume":"     12974","date_updated":"2025-04-15T06:26:12Z","_id":"10108","quality_controlled":"1","year":"2021","fulldoi":"https://doi.org/10.1007/978-3-030-88494-9_12","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"}],"conference":{"name":"RV: Runtime Verification","location":"Virtual","end_date":"2021-10-14","start_date":"2021-10-11"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","place":"Cham","type":"conference","month":"10","related_material":{"record":[{"id":"9946","relation":"extended_version","status":"public"}]},"article_processing_charge":"No","oa":1,"external_id":{"isi":["000719383800012"]},"publication":"International Conference on Runtime Verification","ddc":["005"],"has_accepted_license":"1","acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","publisher":"Springer Nature","corr_author":"1","scopus_import":"1","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"publication_identifier":{"eisbn":["978-3-030-88494-9"],"isbn":["978-3-030-88493-2"],"issn":["0302-9743"],"eissn":["1611-3349"]},"volume":12974,"day":"06"},{"intvolume":"        10","date_created":"2021-10-10T22:01:22Z","article_number":"e68238","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-04-14T07:43:46Z","_id":"10116","department":[{"_id":"MaDe"}],"citation":{"short":"T. Vuong-Brender, S. Flynn, Y. Vallis, M. de Bono, ELife 10 (2021).","chicago":"Vuong-Brender, Thanh, Sean Flynn, Yvonne Vallis, and Mario de Bono. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.68238\">https://doi.org/10.7554/eLife.68238</a>.","apa":"Vuong-Brender, T., Flynn, S., Vallis, Y., &#38; de Bono, M. (2021). Neuronal calmodulin levels are controlled by CAMTA transcription factors. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68238\">https://doi.org/10.7554/eLife.68238</a>","ieee":"T. Vuong-Brender, S. Flynn, Y. Vallis, and M. de Bono, “Neuronal calmodulin levels are controlled by CAMTA transcription factors,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ista":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. 2021. Neuronal calmodulin levels are controlled by CAMTA transcription factors. eLife. 10, e68238.","ama":"Vuong-Brender T, Flynn S, Vallis Y, de Bono M. Neuronal calmodulin levels are controlled by CAMTA transcription factors. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.68238\">10.7554/eLife.68238</a>","mla":"Vuong-Brender, Thanh, et al. “Neuronal Calmodulin Levels Are Controlled by CAMTA Transcription Factors.” <i>ELife</i>, vol. 10, e68238, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.68238\">10.7554/eLife.68238</a>."},"status":"public","ec_funded":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"file_date_updated":"2021-10-11T14:15:07Z","title":"Neuronal calmodulin levels are controlled by CAMTA transcription factors","isi":1,"doi":"10.7554/eLife.68238","date_published":"2021-09-17T00:00:00Z","author":[{"last_name":"Vuong-Brender","id":"D389312E-10C4-11EA-ABF4-A4B43DDC885E","first_name":"Thanh","full_name":"Vuong-Brender, Thanh"},{"last_name":"Flynn","first_name":"Sean","full_name":"Flynn, Sean"},{"full_name":"Vallis, Yvonne","first_name":"Yvonne","last_name":"Vallis","id":"05A2795C-31B5-11EA-83A7-7DA23DDC885E"},{"full_name":"De Bono, Mario","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","last_name":"De Bono"}],"file":[{"file_name":"2021_eLife_VuongBrender.pdf","access_level":"open_access","file_id":"10122","file_size":1774624,"content_type":"application/pdf","checksum":"b465e172d2b1f57aa26a2571a085d052","date_updated":"2021-10-11T14:15:07Z","relation":"main_file","date_created":"2021-10-11T14:15:07Z","success":1,"creator":"cchlebak"}],"pmid":1,"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"abstract":[{"lang":"eng","text":"The ubiquitous Ca2+ sensor calmodulin (CaM) binds and regulates many proteins, including ion channels, CaM kinases, and calcineurin, according to Ca2+-CaM levels. What regulates neuronal CaM levels, is, however, unclear. CaM-binding transcription activators (CAMTAs) are ancient proteins expressed broadly in nervous systems and whose loss confers pleiotropic behavioral defects in flies, mice, and humans. Using Caenorhabditis elegans and Drosophila, we show that CAMTAs control neuronal CaM levels. The behavioral and neuronal Ca2+ signaling defects in mutants lacking camt-1, the sole C. elegans CAMTA, can be rescued by supplementing neuronal CaM. CAMT-1 binds multiple sites in the CaM promoter and deleting these sites phenocopies camt-1. Our data suggest CAMTAs mediate a conserved and general mechanism that controls neuronal CaM levels, thereby regulating Ca2+ signaling, physiology, and behavior."}],"scopus_import":"1","day":"17","volume":10,"acknowledgement":"The authors thank the MRC-LMB Flow Cytometry facility and Imaging Service for support, the Cancer Research UK Cambridge Institute Genomics Core for Next Generation Sequencing, Julie Ahringer and Alex Appert for advice and technical help for ChIP-seq experiments, Paula Freire-Pritchett, Tim Stevens, and Gurpreet Ghattaoraya for RNA-seq and ChIP-seq analyses, Nikos Chronis for the TN-XL plasmid, Hong-Sheng Li and Daisuke Yamamoto for generously sending the tes2 and cro mutants, Daria Siekhaus for hosting the fly work, Michaela Misova for technical assistance. The authors are very grateful to Salihah Ece Sönmez for teaching us how to dissect, mount and stain Drosophila retinae. This work was supported by an Advanced ERC grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB, and an IST Plus Fellowship to TV-B (Marie Sklodowska-Curie Agreement no 754411).","has_accepted_license":"1","ddc":["610"],"publisher":"eLife Sciences Publications","oa":1,"article_processing_charge":"No","external_id":{"pmid":["34499028"],"isi":["000695716100001"]},"publication":"eLife","month":"09","type":"journal_article","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"fulldoi":"https://doi.org/10.7554/eLife.68238","year":"2021"},{"month":"09","publication":"Journal of Biological Chemistry","external_id":{"isi":["000706409200006"]},"article_processing_charge":"Yes","oa":1,"publisher":"Elsevier","ddc":["612"],"has_accepted_license":"1","acknowledgement":"We thank de Bono lab members for helpful comments on the manuscript, IST Austria and University of Vienna Mass Spec Facilities for invaluable discussions and comments for the optimization of mass spec analyses of worm samples. The biotin auxotropic E. coli strain MG1655bioB:kan was gift from John Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3′UTR entry vector were kindly shared by Dr Dominique Glauser (University of Fribourg). Codon-optimized mScarlet vector was a generous gift from Dr Manuel Zimmer (University of Vienna).","volume":297,"day":"01","scopus_import":"1","abstract":[{"lang":"eng","text":"Proximity labeling provides a powerful in vivo tool to characterize the proteome of subcellular structures and the interactome of specific proteins. The nematode Caenorhabditis elegans is one of the most intensely studied organisms in biology, offering many advantages for biochemistry. Using the highly active biotin ligase TurboID, we optimize here a proximity labeling protocol for C. elegans. An advantage of TurboID is that biotin's high affinity for streptavidin means biotin-labeled proteins can be affinity-purified under harsh denaturing conditions. By combining extensive sonication with aggressive denaturation using SDS and urea, we achieved near-complete solubilization of worm proteins. We then used this protocol to characterize the proteomes of the worm gut, muscle, skin, and nervous system. Neurons are among the smallest C. elegans cells. To probe the method's sensitivity, we expressed TurboID exclusively in the two AFD neurons and showed that the protocol could identify known and previously unknown proteins expressed selectively in AFD. The active zones of synapses are composed of a protein matrix that is difficult to solubilize and purify. To test if our protocol could solubilize active zone proteins, we knocked TurboID into the endogenous elks-1 gene, which encodes a presynaptic active zone protein. We identified many known ELKS-1-interacting active zone proteins, as well as previously uncharacterized synaptic proteins. Versatile vectors and the inherent advantages of using C. elegans, including fast growth and the ability to rapidly make and functionally test knock-ins, make proximity labeling a valuable addition to the armory of this model organism."}],"publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"year":"2021","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"fulldoi":"https://doi.org/10.1016/J.JBC.2021.101094","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"3","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","ec_funded":1,"status":"public","citation":{"short":"M. Artan, S. Barratt, S.M. Flynn, F. Begum, M. Skehel, A. Nicolas, M. de Bono, Journal of Biological Chemistry 297 (2021).","apa":"Artan, M., Barratt, S., Flynn, S. M., Begum, F., Skehel, M., Nicolas, A., &#38; de Bono, M. (2021). Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. Elsevier. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>","chicago":"Artan, Murat, Stephen Barratt, Sean M. Flynn, Farida Begum, Mark Skehel, Armel Nicolas, and Mario de Bono. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">https://doi.org/10.1016/J.JBC.2021.101094</a>.","ieee":"M. Artan <i>et al.</i>, “Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling,” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3. Elsevier, 2021.","ama":"Artan M, Barratt S, Flynn SM, et al. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. <i>Journal of Biological Chemistry</i>. 2021;297(3). doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>","ista":"Artan M, Barratt S, Flynn SM, Begum F, Skehel M, Nicolas A, de Bono M. 2021. Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling. Journal of Biological Chemistry. 297(3), 101094.","mla":"Artan, Murat, et al. “Interactome Analysis of Caenorhabditis Elegans Synapses by TurboID-Based Proximity Labeling.” <i>Journal of Biological Chemistry</i>, vol. 297, no. 3, 101094, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/J.JBC.2021.101094\">10.1016/J.JBC.2021.101094</a>."},"department":[{"_id":"MaDe"},{"_id":"LifeSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-04-14T07:43:46Z","_id":"10117","article_number":"101094","quality_controlled":"1","date_created":"2021-10-10T22:01:23Z","intvolume":"       297","file":[{"access_level":"open_access","file_id":"10121","file_name":"2021_JBC_Artan.pdf","relation":"main_file","date_updated":"2021-10-11T12:20:58Z","checksum":"19e39d36c5b9387c6dc0e89c9ae856ab","creator":"cchlebak","success":1,"date_created":"2021-10-11T12:20:58Z","content_type":"application/pdf","file_size":1680010}],"author":[{"full_name":"Artan, Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","last_name":"Artan","orcid":"0000-0001-8945-6992","first_name":"Murat"},{"last_name":"Barratt","id":"57740d2b-2a88-11ec-97cf-d9e6d1b39677","first_name":"Stephen","full_name":"Barratt, Stephen"},{"last_name":"Flynn","first_name":"Sean M.","full_name":"Flynn, Sean M."},{"full_name":"Begum, Farida","last_name":"Begum","first_name":"Farida"},{"last_name":"Skehel","first_name":"Mark","full_name":"Skehel, Mark"},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"orcid":"0000-0001-8347-0443","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"De Bono, Mario"}],"publication_status":"published","date_published":"2021-09-01T00:00:00Z","doi":"10.1016/J.JBC.2021.101094","isi":1,"file_date_updated":"2021-10-11T12:20:58Z","title":"Interactome analysis of Caenorhabditis elegans synapses by TurboID-based proximity labeling"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","fulldoi":"https://doi.org/10.1021/acsnano.1c02777 ","year":"2021","type":"journal_article","title":"Durotaxis of passive nanoparticles on elastic membranes","doi":"10.1021/acsnano.1c02777 ","article_type":"original","pmid":1,"publication_status":"published","date_published":"2021-09-22T00:00:00Z","author":[{"full_name":"Palaia, Ivan","last_name":"Palaia","first_name":"Ivan"},{"last_name":"Paraschiv","first_name":"Alexandru","full_name":"Paraschiv, Alexandru"},{"first_name":"Vincent","last_name":"Debets","full_name":"Debets, Vincent"},{"full_name":"Storm, Cornelis","first_name":"Cornelis","last_name":"Storm"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"publication":"ACS Nano","external_id":{"pmid":["34550677 "]},"status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.04.01.438065"}],"article_processing_charge":"No","citation":{"ieee":"I. Palaia, A. Paraschiv, V. Debets, C. Storm, and A. Šarić, “Durotaxis of passive nanoparticles on elastic membranes,” <i>ACS Nano</i>. American Chemical Society, 2021.","mla":"Palaia, Ivan, et al. “Durotaxis of Passive Nanoparticles on Elastic Membranes.” <i>ACS Nano</i>, American Chemical Society, 2021, doi:<a href=\"https://doi.org/10.1021/acsnano.1c02777 \">10.1021/acsnano.1c02777 </a>.","ista":"Palaia I, Paraschiv A, Debets V, Storm C, Šarić A. 2021. Durotaxis of passive nanoparticles on elastic membranes. ACS Nano.","ama":"Palaia I, Paraschiv A, Debets V, Storm C, Šarić A. Durotaxis of passive nanoparticles on elastic membranes. <i>ACS Nano</i>. 2021. doi:<a href=\"https://doi.org/10.1021/acsnano.1c02777 \">10.1021/acsnano.1c02777 </a>","short":"I. Palaia, A. Paraschiv, V. Debets, C. Storm, A. Šarić, ACS Nano (2021).","chicago":"Palaia, Ivan, Alexandru Paraschiv, Vincent Debets, Cornelis Storm, and Anđela Šarić. “Durotaxis of Passive Nanoparticles on Elastic Membranes.” <i>ACS Nano</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsnano.1c02777 \">https://doi.org/10.1021/acsnano.1c02777 </a>.","apa":"Palaia, I., Paraschiv, A., Debets, V., Storm, C., &#38; Šarić, A. (2021). Durotaxis of passive nanoparticles on elastic membranes. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.1c02777 \">https://doi.org/10.1021/acsnano.1c02777 </a>"},"extern":"1","language":[{"iso":"eng"}],"month":"09","oa_version":"Preprint","day":"22","quality_controlled":"1","_id":"10124","date_updated":"2021-10-12T09:50:19Z","abstract":[{"lang":"eng","text":"The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in non-uniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically non-uniform elastic membrane. We observe a non-monotonic affinity of the particle to the membrane as a function of the membrane’s rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties."}],"date_created":"2021-10-12T07:31:21Z","publisher":"American Chemical Society","acknowledgement":"We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the Royal Society (A.Š.) and the European Research Council (I.P. and A.Š.)."},{"fulldoi":"https://doi.org/10.1101/2021.03.23.436559","year":"2021","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Harker-Kirschneck","first_name":"L.","full_name":"Harker-Kirschneck, L."},{"full_name":"Hafner, A. E.","last_name":"Hafner","first_name":"A. E."},{"last_name":"Yao","first_name":"T.","full_name":"Yao, T."},{"full_name":"Pulschen, A.","last_name":"Pulschen","first_name":"A."},{"first_name":"F.","last_name":"Hurtig","full_name":"Hurtig, F."},{"full_name":"Vanhille-Campos, C.","first_name":"C.","last_name":"Vanhille-Campos"},{"full_name":"Hryniuk, D.","first_name":"D.","last_name":"Hryniuk"},{"full_name":"Culley, S.","first_name":"S.","last_name":"Culley"},{"first_name":"R.","last_name":"Henriques","full_name":"Henriques, R."},{"full_name":"Baum, B.","first_name":"B.","last_name":"Baum"},{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"date_published":"2021-03-23T00:00:00Z","publication_status":"submitted","type":"preprint","title":"Physical mechanisms of ESCRT-III-driven cell division in archaea","doi":"10.1101/2021.03.23.436559","extern":"1","language":[{"iso":"eng"}],"month":"03","oa_version":"Preprint","publication":"bioRxiv","status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.03.23.436559"}],"article_processing_charge":"No","citation":{"mla":"Harker-Kirschneck, L., et al. “Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>.","ama":"Harker-Kirschneck L, Hafner AE, Yao T, et al. Physical mechanisms of ESCRT-III-driven cell division in archaea. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>","ista":"Harker-Kirschneck L, Hafner AE, Yao T, Pulschen A, Hurtig F, Vanhille-Campos C, Hryniuk D, Culley S, Henriques R, Baum B, Šarić A. Physical mechanisms of ESCRT-III-driven cell division in archaea. bioRxiv, <a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>.","ieee":"L. Harker-Kirschneck <i>et al.</i>, “Physical mechanisms of ESCRT-III-driven cell division in archaea,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","chicago":"Harker-Kirschneck, L., A. E. Hafner, T. Yao, A. Pulschen, F. Hurtig, C. Vanhille-Campos, D. Hryniuk, et al. “Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.03.23.436559\">https://doi.org/10.1101/2021.03.23.436559</a>.","apa":"Harker-Kirschneck, L., Hafner, A. E., Yao, T., Pulschen, A., Hurtig, F., Vanhille-Campos, C., … Šarić, A. (n.d.). Physical mechanisms of ESCRT-III-driven cell division in archaea. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.03.23.436559\">https://doi.org/10.1101/2021.03.23.436559</a>","short":"L. Harker-Kirschneck, A.E. Hafner, T. Yao, A. Pulschen, F. Hurtig, C. Vanhille-Campos, D. Hryniuk, S. Culley, R. Henriques, B. Baum, A. Šarić, BioRxiv (n.d.)."},"publisher":"Cold Spring Harbor Laboratory","acknowledgement":"We acknowledge support from the Biotechnology and Biological Sciences Research Council (L.H.K.), EPSRC (A.E.H), UCL IPLS (T.Y and D. H.), Wellcome Trust (203276/Z/16/Z, A.P., S.C., R. H., B.B.), Volkswagen Foundation (Az 96727, A.P., B.B., A.Š.), MRC (MC CF1226, R.H., B.B., A.Š.), the ERC grant (”NEPA” 802960, A.Š.), the Royal Society (C.V.-H., A.Š.), the UK Materials and Molecular Modelling Hub for computational resources (EP/P020194/1).","day":"23","date_updated":"2021-10-12T09:50:26Z","_id":"10125","date_created":"2021-10-12T07:45:07Z","abstract":[{"text":"Living systems propagate by undergoing rounds of cell growth and division. Cell division is at heart a physical process that requires mechanical forces, usually exerted by protein assemblies. Here we developed the first physical model for the division of archaeal cells, which despite their structural simplicity share machinery and evolutionary origins with eukaryotes. We show how active geometry changes of elastic ESCRT-III filaments, coupled to filament disassembly, are sufficient to efficiently split the cell. We explore how the non-equilibrium processes that govern the filament behaviour impact the resulting cell division. We show how a quantitative comparison between our simulations and dynamic data for ESCRTIII-mediated division in Sulfolobus acidocaldarius, the closest archaeal relative to eukaryotic cells that can currently be cultured in the lab, and reveal the most likely physical mechanism behind its division.","lang":"eng"}]},{"year":"2021","fulldoi":"https://doi.org/10.26508/lsa.202101100","issue":"11","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_type":"original","type":"journal_article","month":"09","publication":"Life Science Alliance","external_id":{"pmid":["34548382"]},"article_processing_charge":"Yes","oa":1,"corr_author":"1","publisher":"Life Science Alliance","ddc":["576"],"has_accepted_license":"1","acknowledgement":"We thank Connor Richterich and Patricia Reinert, ETH Zurich, for invaluable experimental help; Manuela Pérez Berlanga, University Zurich, for help with the confocal imaging; Lukas Fischer for help with electrical engineering; Thomas Hennek, Sol Taguinod, and Dr. Stephan Sonntag, EPIC Phenomics Center, ETH Zürich, for the generation and maintenance of K14-OptoR2 mice; and Dr. Petra Boukamp, Leibniz Institute, Düsseldorf, Germany, for early-passage HaCaT keratinocytes. This work was supported by the ETH Zurich (grant ETH-06 15-1 to S Werner and L Maddaluno), the Swiss National Science Foundation (grant 31003B-189364 to S Werner), and a Marie Curie postdoctoral fellowship from the European Union (to L Maddaluno).","volume":4,"day":"21","scopus_import":"1","abstract":[{"text":"FGFs and their high-affinity receptors (FGFRs) play key roles in development, tissue repair, and disease. Because FGFRs bind overlapping sets of ligands, their individual functions cannot be determined using ligand stimulation. Here, we generated a light-activated FGFR2 variant (OptoR2) to selectively activate signaling by the major FGFR in keratinocytes. Illumination of OptoR2-expressing HEK 293T cells activated FGFR signaling with remarkable temporal precision and promoted cell migration and proliferation. In murine and human keratinocytes, OptoR2 activation rapidly induced the classical FGFR signaling pathways and expression of FGF target genes. Surprisingly, multi-level counter-regulation occurred in keratinocytes in vitro and in transgenic mice in vivo, including OptoR2 down-regulation and loss of responsiveness to light activation. These results demonstrate unexpected cell type-specific limitations of optogenetic FGFRs in long-term in vitro and in vivo settings and highlight the complex consequences of transferring optogenetic cell signaling tools into their relevant cellular contexts.","lang":"eng"}],"publication_identifier":{"eissn":["2575-1077"]},"publication_status":"published","pmid":1,"date_published":"2021-09-21T00:00:00Z","author":[{"full_name":"Rauschendorfer, Theresa","first_name":"Theresa","last_name":"Rauschendorfer"},{"last_name":"Gurri","first_name":"Selina","full_name":"Gurri, Selina"},{"first_name":"Irina","last_name":"Heggli","full_name":"Heggli, Irina"},{"full_name":"Maddaluno, Luigi","first_name":"Luigi","last_name":"Maddaluno"},{"full_name":"Meyer, Michael","first_name":"Michael","last_name":"Meyer"},{"full_name":"Inglés Prieto, Álvaro","first_name":"Álvaro","orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak"},{"full_name":"Werner, Sabine","first_name":"Sabine","last_name":"Werner"}],"file":[{"file_name":"2021_LifeScAlliance_Rauschendorfer.pdf","access_level":"open_access","file_id":"10152","file_size":2055981,"content_type":"application/pdf","relation":"main_file","checksum":"89fb95b211dbe8678809e7cca4626952","date_updated":"2021-10-18T14:48:06Z","creator":"cchlebak","date_created":"2021-10-18T14:48:06Z","success":1}],"doi":"10.26508/lsa.202101100","file_date_updated":"2021-10-18T14:48:06Z","title":"Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice","language":[{"iso":"eng"}],"extern":"1","oa_version":"Published Version","status":"public","citation":{"short":"T. Rauschendorfer, S. Gurri, I. Heggli, L. Maddaluno, M. Meyer, Á. Inglés Prieto, H.L. Janovjak, S. Werner, Life Science Alliance 4 (2021).","apa":"Rauschendorfer, T., Gurri, S., Heggli, I., Maddaluno, L., Meyer, M., Inglés Prieto, Á., … Werner, S. (2021). Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. <i>Life Science Alliance</i>. Life Science Alliance. <a href=\"https://doi.org/10.26508/lsa.202101100\">https://doi.org/10.26508/lsa.202101100</a>","chicago":"Rauschendorfer, Theresa, Selina Gurri, Irina Heggli, Luigi Maddaluno, Michael Meyer, Álvaro Inglés Prieto, Harald L Janovjak, and Sabine Werner. “Acute and Chronic Effects of a Light-Activated FGF Receptor in Keratinocytes in Vitro and in Mice.” <i>Life Science Alliance</i>. Life Science Alliance, 2021. <a href=\"https://doi.org/10.26508/lsa.202101100\">https://doi.org/10.26508/lsa.202101100</a>.","ieee":"T. Rauschendorfer <i>et al.</i>, “Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice,” <i>Life Science Alliance</i>, vol. 4, no. 11. Life Science Alliance, 2021.","ama":"Rauschendorfer T, Gurri S, Heggli I, et al. Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. <i>Life Science Alliance</i>. 2021;4(11). doi:<a href=\"https://doi.org/10.26508/lsa.202101100\">10.26508/lsa.202101100</a>","ista":"Rauschendorfer T, Gurri S, Heggli I, Maddaluno L, Meyer M, Inglés Prieto Á, Janovjak HL, Werner S. 2021. Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. Life Science Alliance. 4(11), e202101100.","mla":"Rauschendorfer, Theresa, et al. “Acute and Chronic Effects of a Light-Activated FGF Receptor in Keratinocytes in Vitro and in Mice.” <i>Life Science Alliance</i>, vol. 4, no. 11, e202101100, Life Science Alliance, 2021, doi:<a href=\"https://doi.org/10.26508/lsa.202101100\">10.26508/lsa.202101100</a>."},"date_updated":"2024-10-09T21:01:02Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"10144","quality_controlled":"1","article_number":"e202101100","date_created":"2021-10-17T22:01:16Z","intvolume":"         4"}]