[{"_id":"12534","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-02-20T07:02:00Z","ddc":["530"],"file_date_updated":"2023-02-13T10:38:10Z","department":[{"_id":"MiLe"}],"abstract":[{"lang":"eng","text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics."}],"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 5","publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","file":[{"creator":"dernst","file_size":865150,"date_updated":"2023-02-13T10:38:10Z","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","date_created":"2023-02-13T10:38:10Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"12546","checksum":"6068b62874c0099628a108bb9c5c6bd2"}],"language":[{"iso":"eng"}],"issue":"1","volume":5,"ec_funded":1,"article_number":"013029","project":[{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 2023;5(1). doi:10.1103/physrevresearch.5.013029","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” Physical Review Research, vol. 5, no. 1. American Physical Society, 2023.","mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:10.1103/physrevresearch.5.013029.","ista":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029.","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/physrevresearch.5.013029."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543"},{"full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359","last_name":"Cappellaro","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev"}],"article_processing_charge":"No","title":"Dissipative dynamics of an impurity with spin-orbit coupling","acknowledgement":"We thank Rafael Barfknecht for help at the initial stages of this project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","publisher":"American Physical Society","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2023","day":"20","publication":"Physical Review Research","date_published":"2023-01-20T00:00:00Z","doi":"10.1103/physrevresearch.5.013029","date_created":"2023-02-10T09:02:26Z"},{"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","oa":1,"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","year":"2023","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","page":"4590-4605","date_created":"2023-02-24T12:20:47Z","date_published":"2023-02-01T00:00:00Z","doi":"10.1137/1.9781611977554.ch173","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"citation":{"short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605.","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:10.1137/1.9781611977554.ch173.","ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605.","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch173."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias"},{"orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","first_name":"Raimundo J"},{"full_name":"Svoboda, Jakub","last_name":"Svoboda","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"}],"title":"Faster algorithm for turn-based stochastic games with bounded treewidth","abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611977554.ch173"}],"month":"02","publication_status":"published","publication_identifier":{"isbn":["9781611977554"]},"language":[{"iso":"eng"}],"ec_funded":1,"_id":"12676","conference":{"location":"Florence, Italy","end_date":"2023-01-25","start_date":"2023-01-22","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","status":"public","date_updated":"2023-02-27T09:01:16Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}]},{"date_published":"2023-03-01T00:00:00Z","doi":"10.1007/978-1-0716-3004-4_3","date_created":"2023-03-12T23:01:02Z","page":"33-44","day":"01","publication":"DNA Manipulation and Analysis","year":"2023","quality_controlled":"1","publisher":"Springer Nature","editor":[{"first_name":"Garry","full_name":"Scarlett, Garry","last_name":"Scarlett"}],"title":"Molecular Cloning Using In Vivo DNA Assembly","author":[{"first_name":"Sandra","full_name":"Arroyo-Urea, Sandra","last_name":"Arroyo-Urea"},{"first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake"},{"last_name":"García-Nafría","full_name":"García-Nafría, Javier","first_name":"Javier"}],"external_id":{"pmid":["36853454"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” DNA Manipulation and Analysis, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:10.1007/978-1-0716-3004-4_3.","short":"S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023, pp. 33–44.","ieee":"S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using In Vivo DNA Assembly,” in DNA Manipulation and Analysis, vol. 2633, G. Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44.","apa":"Arroyo-Urea, S., Watson, J., & García-Nafría, J. (2023). Molecular Cloning Using In Vivo DNA Assembly. In G. Scarlett (Ed.), DNA Manipulation and Analysis (Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. https://doi.org/10.1007/978-1-0716-3004-4_3","ama":"Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. In: Scarlett G, ed. DNA Manipulation and Analysis. Vol 2633. MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:10.1007/978-1-0716-3004-4_3","chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In DNA Manipulation and Analysis, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3004-4_3.","ista":"Arroyo-Urea S, Watson J, García-Nafría J. 2023.Molecular Cloning Using In Vivo DNA Assembly. In: DNA Manipulation and Analysis. Methods in Molecular Biology, vol. 2633, 33–44."},"volume":2633,"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["978-1-0716-3004-4"],"isbn":["978-1-0716-3003-7"],"eissn":["1940-6029"],"issn":["1064-3745"]},"publication_status":"published","place":"New York, NY, United States","month":"03","intvolume":" 2633","scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","pmid":1,"abstract":[{"lang":"eng","text":"Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues."}],"department":[{"_id":"PeJo"}],"date_updated":"2023-03-16T08:34:24Z","status":"public","type":"book_chapter","series_title":"MIMB","_id":"12720"},{"author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","full_name":"Koval, Nikita","last_name":"Koval"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"first_name":"Roman","last_name":"Elizarov","full_name":"Elizarov, Roman"}],"article_processing_charge":"No","external_id":{"arxiv":["2211.04986"]},"title":"Fast and scalable channels in Kotlin Coroutines","department":[{"_id":"DaAl"}],"date_updated":"2023-03-20T07:29:28Z","citation":{"ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 107–18. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577481.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481","ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2023:107-118. doi:10.1145/3572848.3577481","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118.","mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–18, doi:10.1145/3572848.3577481."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","conference":{"end_date":"2023-03-01","location":"Montreal, QC, Canada","start_date":"2023-02-25","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"status":"public","_id":"12735","page":"107-118","doi":"10.1145/3572848.3577481","date_published":"2023-02-25T00:00:00Z","date_created":"2023-03-19T23:00:58Z","publication_identifier":{"isbn":["9798400700156"]},"publication_status":"published","year":"2023","day":"25","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","publisher":"Association for Computing Machinery","scopus_import":"1","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04986"}],"oa":1,"month":"02","abstract":[{"text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations.","lang":"eng"}],"oa_version":"Preprint"},{"page":"438-440","date_created":"2023-03-19T23:00:58Z","doi":"10.1145/3572848.3577512","date_published":"2023-02-25T00:00:00Z","publication_status":"published","year":"2023","publication_identifier":{"isbn":["9798400700156"]},"language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","day":"25","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"publisher":"Association for Computing Machinery","quality_controlled":"1","month":"02","abstract":[{"text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al.","lang":"eng"}],"acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Aksenov","full_name":"Aksenov, Vitaly","first_name":"Vitaly"},{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","full_name":"Brown, Trevor A"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"full_name":"Kokorin, Ilya","last_name":"Kokorin","first_name":"Ilya"}],"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"title":"Unexpected scaling in path copying trees","citation":{"chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577512.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512.","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512"},"date_updated":"2023-03-20T07:57:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","start_date":"2023-02-25","end_date":"2023-03-01","location":"Montreal, QB, Canada"},"type":"conference_poster","status":"public","_id":"12736"},{"abstract":[{"lang":"eng","text":"Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However,\r\nmany DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity.\r\nIn this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce\r\na novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting, and with polylogarithmic update times when the DP entries change\r\ndynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time.\r\nWe further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack."}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LIPIcs"],"intvolume":" 254","month":"03","publication_status":"published","publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"22141ab8bc55188e2dfff665e5daecbd","file_id":"12769","success":1,"date_updated":"2023-03-27T06:37:22Z","file_size":872706,"creator":"dernst","date_created":"2023-03-27T06:37:22Z","file_name":"2023_LIPICS_HenzingerM.pdf"}],"volume":254,"_id":"12760","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2023-03-07","location":"Hamburg, Germany","end_date":"2023-03-09","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"type":"conference","status":"public","date_updated":"2023-03-27T06:46:27Z","ddc":["000"],"file_date_updated":"2023-03-27T06:37:22Z","department":[{"_id":"MoHe"}],"acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science Fund (FWF) project I 5025-N (DELTA), 2020-2024.","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2023","has_accepted_license":"1","publication":"40th International Symposium on Theoretical Aspects of Computer Science","day":"01","date_created":"2023-03-26T22:01:07Z","date_published":"2023-03-01T00:00:00Z","doi":"10.4230/LIPIcs.STACS.2023.36","article_number":"36","citation":{"ista":"Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36.","chicago":"Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In 40th International Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36.","apa":"Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In 40th International Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36","ama":"Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: 40th International Symposium on Theoretical Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36","short":"M.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ieee":"M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in 40th International Symposium on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.","mla":"Henzinger, Monika H., et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” 40th International Symposium on Theoretical Aspects of Computer Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.STACS.2023.36."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2301.01744"]},"author":[{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger"},{"first_name":"Stefan","full_name":"Neumann, Stefan","last_name":"Neumann"},{"full_name":"Räcke, Harald","last_name":"Räcke","first_name":"Harald"},{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"}],"title":"Dynamic maintenance of monotone dynamic programs and applications"},{"publisher":"Institute of Science and Technology Austria","oa":1,"day":"10","has_accepted_license":"1","year":"2023","doi":"10.15479/at:ista:12716","date_published":"2023-03-10T00:00:00Z","date_created":"2023-03-08T15:19:45Z","page":"178","project":[{"name":"Circuits of Visual Attention","grant_number":"756502","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716.","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria."},"title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","author":[{"id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X","last_name":"Burnett"}],"article_processing_charge":"No","oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"abstract":[{"text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.","lang":"eng"}],"month":"03","alternative_title":["ISTA Thesis"],"file":[{"file_id":"12717","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","date_created":"2023-03-08T15:08:46Z","file_name":"Burnett_Thesis_2023.docx","date_updated":"2023-03-08T15:08:46Z","file_size":23029260,"creator":"lburnett"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12718","checksum":"cebc77705288bf4382db9b3541483cd0","file_size":11959869,"date_updated":"2023-03-08T15:08:46Z","creator":"lburnett","file_name":"Burnett_Thesis_2023_pdfA.pdf","date_created":"2023-03-08T15:08:46Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","ec_funded":1,"_id":"12716","status":"public","type":"dissertation","ddc":["599","573"],"supervisor":[{"last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"}],"date_updated":"2023-04-05T10:59:04Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"file_date_updated":"2023-03-08T15:08:46Z"},{"_id":"12854","conference":{"start_date":"2023-04-22","end_date":"2023-04-27","location":"Paris, France","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","date_updated":"2023-04-25T07:02:43Z","ddc":["000"],"file_date_updated":"2023-04-25T06:58:36Z","department":[{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition."}],"oa_version":"Published Version","alternative_title":["LNCS"],"intvolume":" 13994","month":"04","publication_status":"published","publication_identifier":{"eisbn":["9783031308208"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308192"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-04-25T06:58:36Z","file_size":16096413,"creator":"dernst","date_created":"2023-04-25T06:58:36Z","file_name":"2023_LNCS_Chalupa.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"120d2c2a38384058ad0630fdf8288312","file_id":"12864","success":1}],"ec_funded":1,"volume":13994,"project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"citation":{"chicago":"Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” In Tools and Algorithms for the Construction and Analysis of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32.","ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540.","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32.","apa":"Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32","ama":"Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540.","ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 535–540."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"title":"Bubaak: Runtime monitoring of program verifiers","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2023","has_accepted_license":"1","publication":"Tools and Algorithms for the Construction and Analysis of Systems","day":"20","page":"535-540","date_created":"2023-04-20T08:22:53Z","doi":"10.1007/978-3-031-30820-8_32","date_published":"2023-04-20T00:00:00Z"},{"date_updated":"2023-04-25T06:51:21Z","citation":{"ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","short":"A. Chern, S. Ishida, ArXiv (n.d.).","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chern","full_name":"Chern, Albert","first_name":"Albert"},{"last_name":"Ishida","full_name":"Ishida, Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige"}],"article_processing_charge":"No","external_id":{"arxiv":["2303.14555"]},"title":"Area formula for spherical polygons via prequantization","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"_id":"12846","article_number":"2303.14555","type":"preprint","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"status":"public","year":"2023","publication_status":"submitted","day":"25","language":[{"iso":"eng"}],"publication":"arXiv","date_published":"2023-03-25T00:00:00Z","doi":"10.48550/arXiv.2303.14555","date_created":"2023-04-18T19:16:06Z","abstract":[{"lang":"eng","text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons."}],"oa_version":"Preprint","acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","main_file_link":[{"url":"https://arxiv.org/abs/2303.14555","open_access":"1"}],"oa":1,"month":"03"},{"title":"Vamos: Middleware for best-effort third-party monitoring","article_processing_charge":"No","author":[{"last_name":"Chalupa","full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek"},{"orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian","last_name":"Mühlböck","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian"},{"first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei"},{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in Fundamental Approaches to Software Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: Fundamental Approaches to Software Engineering. Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30826-0_15","mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15."},"project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"date_created":"2023-04-20T08:29:42Z","doi":"10.1007/978-3-031-30826-0_15","date_published":"2023-04-20T00:00:00Z","page":"260-281","publication":"Fundamental Approaches to Software Engineering","day":"20","year":"2023","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","department":[{"_id":"ToHe"}],"file_date_updated":"2023-04-25T07:16:36Z","ddc":["000"],"date_updated":"2023-04-25T07:19:07Z","status":"public","conference":{"name":"FASE: Fundamental Approaches to Software Engineering","start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"12856","ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"12407"}]},"volume":13991,"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-04-25T07:16:36Z","file_size":580828,"creator":"dernst","date_created":"2023-04-25T07:16:36Z","file_name":"2023_LNCS_ChalupaM.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"17a7c8e08be609cf2408d37ea55e322c","file_id":"12865","success":1}],"publication_status":"published","publication_identifier":{"eisbn":["9783031308260"],"eissn":["1611-3349"],"isbn":["9783031308253"],"issn":["0302-9743"]},"intvolume":" 13991","month":"04","alternative_title":["LNCS"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}]},{"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","date_created":"2023-01-27T03:18:08Z","date_published":"2023-01-27T00:00:00Z","doi":"10.15479/AT:ISTA:12407","page":"38","day":"27","year":"2023","has_accepted_license":"1","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","article_processing_charge":"No","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"last_name":"Mühlböck","orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian"},{"first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","last_name":"Muroya Lei","full_name":"Muroya Lei, Stefanie"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407.","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 2023.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria; 2023. doi:10.15479/AT:ISTA:12407","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 38p."},"month":"01","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\n\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"12856","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"file_size":662409,"date_updated":"2023-01-27T03:18:34Z","creator":"fmuehlbo","file_name":"main.pdf","date_created":"2023-01-27T03:18:34Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12408","checksum":"55426e463fdeafe9777fc3ff635154c7"}],"publication_status":"published","publication_identifier":{"eissn":["2664-1690"]},"keyword":["runtime monitoring","best effort","third party"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"technical_report","_id":"12407","file_date_updated":"2023-01-27T03:18:34Z","department":[{"_id":"ToHe"}],"ddc":["005"],"date_updated":"2023-04-25T07:19:06Z"},{"abstract":[{"lang":"eng","text":"Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation.\r\nDecades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain."}],"oa_version":"None","edition":"1","quality_controlled":"1","publisher":"Elsevier","alternative_title":["Vol. 1: Biological Development and Physical Health"],"month":"02","publication_status":"published","year":"2023","publication_identifier":{"isbn":["9780128188736"]},"publication":"Encyclopedia of Child and Adolescent Health","language":[{"iso":"eng"}],"day":"01","page":"86-98","date_created":"2023-04-25T07:52:43Z","date_published":"2023-02-01T00:00:00Z","doi":"10.1016/b978-0-12-818872-9.00129-1","_id":"12866","type":"book_chapter","status":"public","date_updated":"2023-04-25T09:25:40Z","citation":{"ista":"Currin C, Beyer C. 2023.Altered childhood brain development in autism and epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological Development and Physical Health, , 86–98.","chicago":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” In Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-818872-9.00129-1.","apa":"Currin, C., & Beyer, C. (2023). Altered childhood brain development in autism and epilepsy. In B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health (1st ed., pp. 86–98). Elsevier. https://doi.org/10.1016/b978-0-12-818872-9.00129-1","ama":"Currin C, Beyer C. Altered childhood brain development in autism and epilepsy. In: Halpern-Felsher B, ed. Encyclopedia of Child and Adolescent Health. 1st ed. Elsevier; 2023:86-98. doi:10.1016/b978-0-12-818872-9.00129-1","short":"C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.","ieee":"C. Currin and C. Beyer, “Altered childhood brain development in autism and epilepsy,” in Encyclopedia of Child and Adolescent Health, 1st ed., B. Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.","mla":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:10.1016/b978-0-12-818872-9.00129-1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Currin","orcid":"0000-0002-4809-5059","full_name":"Currin, Christopher","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","first_name":"Christopher"},{"full_name":"Beyer, Chad","last_name":"Beyer","first_name":"Chad"}],"editor":[{"last_name":"Halpern-Felsher","full_name":"Halpern-Felsher, Bonnie","first_name":"Bonnie"}],"title":"Altered childhood brain development in autism and epilepsy","department":[{"_id":"TiVo"}]},{"_id":"12809","status":"public","type":"dissertation","ddc":["570"],"date_updated":"2023-04-26T12:16:56Z","supervisor":[{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"RySh"}],"file_date_updated":"2023-04-07T06:18:05Z","oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"month":"04","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"access_level":"closed","relation":"main_file","content_type":"application/pdf","embargo_to":"open_access","file_id":"12814","checksum":"35b5997d2b0acb461f9d33d073da0df5","embargo":"2024-04-07","creator":"cchlebak","date_updated":"2023-04-07T06:16:06Z","file_size":9881969,"date_created":"2023-04-07T06:16:06Z","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf"},{"file_size":44201583,"date_updated":"2023-04-07T06:17:11Z","creator":"cchlebak","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","date_created":"2023-04-07T06:17:11Z","content_type":"application/pdf","relation":"source_file","access_level":"closed","checksum":"81198f63c294890f6d58e8b29782efdc","file_id":"12815"},{"file_id":"12816","checksum":"0317bf7f457bb585f99d453ffa69eb53","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-04-07T06:18:05Z","file_name":"Thesis_CatarinaAlcarva_final.docx","creator":"cchlebak","date_updated":"2023-04-07T06:18:05Z","file_size":84731244}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023."},"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","article_processing_charge":"No","author":[{"last_name":"Alcarva","full_name":"Alcarva, Catarina","first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","day":"06","year":"2023","has_accepted_license":"1","date_created":"2023-04-06T07:54:09Z","date_published":"2023-04-06T00:00:00Z","doi":"10.15479/at:ista:12809","page":"115"},{"month":"01","intvolume":" 24","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis."}],"volume":24,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1474-760X"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"12668","department":[{"_id":"XiFe"}],"extern":"1","date_updated":"2023-05-08T10:52:49Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"doi":"10.1186/s13059-022-02844-2","date_published":"2023-01-13T00:00:00Z","date_created":"2023-02-23T09:13:49Z","day":"13","publication":"Genome Biology","year":"2023","article_number":"7","title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","author":[{"last_name":"Zhao","full_name":"Zhao, Long","first_name":"Long"},{"first_name":"Yiman","last_name":"Yang","full_name":"Yang, Yiman"},{"full_name":"Chen, Jinchao","last_name":"Chen","first_name":"Jinchao"},{"first_name":"Xuelei","last_name":"Lin","full_name":"Lin, Xuelei"},{"first_name":"Hao","last_name":"Zhang","full_name":"Zhang, Hao"},{"full_name":"Wang, Hao","last_name":"Wang","first_name":"Hao"},{"last_name":"Wang","full_name":"Wang, Hongzhe","first_name":"Hongzhe"},{"first_name":"Xiaomin","full_name":"Bie, Xiaomin","last_name":"Bie"},{"first_name":"Jiafu","full_name":"Jiang, Jiafu","last_name":"Jiang"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"last_name":"Fu","full_name":"Fu, Xiangdong","first_name":"Xiangdong"},{"first_name":"Xiansheng","full_name":"Zhang, Xiansheng","last_name":"Zhang"},{"first_name":"Zhuo","full_name":"Du, Zhuo","last_name":"Du"},{"last_name":"Xiao","full_name":"Xiao, Jun","first_name":"Jun"}],"article_processing_charge":"No","external_id":{"pmid":["36639687"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023, doi:10.1186/s13059-022-02844-2.","ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7."}},{"oa_version":"Preprint","abstract":[{"text":"In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis.","lang":"eng"}],"month":"06","main_file_link":[{"url":"https://arxiv.org/abs/2303.04014","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450399135"]},"publication_status":"published","ec_funded":1,"_id":"13048","status":"public","type":"conference","conference":{"name":"STOC: Symposium on Theory of Computing","start_date":"2023-06-20","location":"Orlando, FL, United States","end_date":"2023-06-23"},"date_updated":"2023-05-22T08:15:19Z","department":[{"_id":"HeEd"}],"acknowledgement":"We are greatly indebted to Erin Chambers for posing a number of questions that eventually led to this paper. We would also like to thank the other organizers of the workshop on ‘Algorithms\r\nfor the medial axis’. We are also indebted to Tatiana Ezubova for helping with the search for and translation of Russian literature. The second author thanks all members of the Edelsbrunner and Datashape groups for the atmosphere in which the research was conducted.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073.","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"day":"02","publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","year":"2023","date_published":"2023-06-02T00:00:00Z","doi":"10.1145/3564246.3585113","date_created":"2023-05-22T08:02:02Z","page":"1768-1776","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Learning and triangulating manifolds via collapses","grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” In Proceedings of the 55th Annual ACM Symposium on Theory of Computing, 1768–76. Association for Computing Machinery, 2023. https://doi.org/10.1145/3564246.3585113.","ista":"Lieutier A, Wintraecken M. 2023. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. Proceedings of the 55th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 1768–1776.","mla":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–76, doi:10.1145/3564246.3585113.","short":"A. Lieutier, M. Wintraecken, in:, Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–1776.","ieee":"A. Lieutier and M. Wintraecken, “Hausdorff and Gromov-Hausdorff stable subsets of the medial axis,” in Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Orlando, FL, United States, 2023, pp. 1768–1776.","ama":"Lieutier A, Wintraecken M. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In: Proceedings of the 55th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2023:1768-1776. doi:10.1145/3564246.3585113","apa":"Lieutier, A., & Wintraecken, M. (2023). Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In Proceedings of the 55th Annual ACM Symposium on Theory of Computing (pp. 1768–1776). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3564246.3585113"},"title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","author":[{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"},{"orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2303.04014"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-06-01T12:54:45Z","citation":{"ista":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","chicago":"Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations , n.d.","ama":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations .","apa":"Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda .","short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","ieee":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda .","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations ."},"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"title":"CrAM: A Compression-Aware Minimizer","article_processing_charge":"No","external_id":{"arxiv":["2207.14200"]},"author":[{"first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","last_name":"Peste","full_name":"Peste, Elena-Alexandra"},{"first_name":"Adrian","last_name":"Vladu","full_name":"Vladu, Adrian"},{"last_name":"Kurtic","full_name":"Kurtic, Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","first_name":"Eldar"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"_id":"13053","status":"public","project":[{"grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2023-05-05","location":"Kigali, Rwanda ","start_date":"2023-05-01"},"type":"conference","language":[{"iso":"eng"}],"publication":"11th International Conference on Learning Representations ","year":"2023","publication_status":"accepted","ec_funded":1,"date_created":"2023-05-23T11:36:18Z","related_material":{"record":[{"status":"public","id":"13074","relation":"dissertation_contains"}]},"date_published":"2023-05-01T00:00:00Z","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)-","oa_version":"Preprint","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL .","lang":"eng"}],"month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=_eTZBs-yedr"}],"quality_controlled":"1"},{"volume":13940,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031313677"],"issn":["0302-9743"]},"intvolume":" 13940","month":"05","main_file_link":[{"url":"https://eprint.iacr.org/2023/238","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.\r\nIn this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.\r\nOur approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality."}],"department":[{"_id":"KrPi"}],"date_updated":"2023-06-19T08:03:37Z","status":"public","conference":{"start_date":"2023-05-07","location":"Atlanta, GA, United States","end_date":"2023-05-10","name":"PKC: Public-Key Cryptography"},"type":"conference","_id":"13143","date_created":"2023-06-18T22:00:47Z","doi":"10.1007/978-3-031-31368-4_19","date_published":"2023-05-02T00:00:00Z","page":"530-553","publication":"Public-Key Cryptography - PKC 2023","day":"02","year":"2023","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We are grateful to Pavel Atnashev for clarifying via e-mail several aspects of the primality tests implementated in the PrimeGrid project. Pavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, ISF grants 484/18 and 1789/19, and ERC StG project SPP: Secrecy Preserving Proofs.","title":"Certifying giant nonprimes","article_processing_charge":"No","author":[{"first_name":"Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","last_name":"Hoffmann","full_name":"Hoffmann, Charlotte"},{"first_name":"Pavel","full_name":"Hubáček, Pavel","last_name":"Hubáček"},{"first_name":"Chethan","last_name":"Kamath","full_name":"Kamath, Chethan"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Krzysztof Z Pietrzak. “Certifying Giant Nonprimes.” In Public-Key Cryptography - PKC 2023, 13940:530–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-31368-4_19.","ista":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. 2023. Certifying giant nonprimes. Public-Key Cryptography - PKC 2023. PKC: Public-Key Cryptography, LNCS, vol. 13940, 530–553.","mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” Public-Key Cryptography - PKC 2023, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:10.1007/978-3-031-31368-4_19.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Pietrzak, K. Z. (2023). Certifying giant nonprimes. In Public-Key Cryptography - PKC 2023 (Vol. 13940, pp. 530–553). Atlanta, GA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-31368-4_19","ama":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. Certifying giant nonprimes. In: Public-Key Cryptography - PKC 2023. Vol 13940. Springer Nature; 2023:530-553. doi:10.1007/978-3-031-31368-4_19","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and K. Z. Pietrzak, “Certifying giant nonprimes,” in Public-Key Cryptography - PKC 2023, Atlanta, GA, United States, 2023, vol. 13940, pp. 530–553.","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553."}},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","page":"3-25","date_created":"2023-06-18T22:00:47Z","date_published":"2023-04-22T00:00:00Z","doi":"10.1007/978-3-031-30823-9_1","year":"2023","has_accepted_license":"1","publication":"Tools and Algorithms for the Construction and Analysis of Systems ","day":"22","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"article_processing_charge":"No","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","last_name":"Zikelic"}],"title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","citation":{"apa":"Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). A learner-verifier framework for neural network controllers and certificates of stochastic systems. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13993, pp. 3–25). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30823-9_1","ama":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. A learner-verifier framework for neural network controllers and certificates of stochastic systems. In: Tools and Algorithms for the Construction and Analysis of Systems . Vol 13993. Springer Nature; 2023:3-25. doi:10.1007/978-3-031-30823-9_1","ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in Tools and Algorithms for the Construction and Analysis of Systems , Paris, France, 2023, vol. 13993, pp. 3–25.","short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25.","mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” Tools and Algorithms for the Construction and Analysis of Systems , vol. 13993, Springer Nature, 2023, pp. 3–25, doi:10.1007/978-3-031-30823-9_1.","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In Tools and Algorithms for the Construction and Analysis of Systems , 13993:3–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30823-9_1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 13993","month":"04","abstract":[{"lang":"eng","text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions."}],"oa_version":"Published Version","ec_funded":1,"volume":13993,"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031308222"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"13150","checksum":"3d8a8bb24d211bc83360dfc2fd744307","file_size":528455,"date_updated":"2023-06-19T08:29:30Z","creator":"dernst","file_name":"2023_LNCS_Chatterjee.pdf","date_created":"2023-06-19T08:29:30Z"}],"conference":{"start_date":"2023-04-22","end_date":"2023-04-27","location":"Paris, France","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","status":"public","_id":"13142","file_date_updated":"2023-06-19T08:29:30Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-06-19T08:30:54Z","ddc":["000"]},{"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308192"]},"publication_status":"published","file":[{"file_id":"13151","checksum":"60dcafc1b4f6f070be43bad3fe877974","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-06-19T08:43:21Z","file_name":"2023_LNCS_Anand.pdf","creator":"dernst","date_updated":"2023-06-19T08:43:21Z","file_size":521425}],"language":[{"iso":"eng"}],"volume":13994,"abstract":[{"lang":"eng","text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive."}],"oa_version":"Published Version","scopus_import":"1","alternative_title":["LNCS"],"month":"04","intvolume":" 13994","date_updated":"2023-06-19T08:49:46Z","ddc":["000"],"file_date_updated":"2023-06-19T08:43:21Z","department":[{"_id":"ToHe"}],"_id":"13141","type":"conference","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2023-04-22","end_date":"2023-04-27","location":"Paris, France"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2023","day":"20","publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","page":"211-228","doi":"10.1007/978-3-031-30820-8_15","date_published":"2023-04-20T00:00:00Z","date_created":"2023-06-18T22:00:47Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:10.1007/978-3-031-30820-8_15.","apa":"Anand, A., Mallik, K., Nayak, S. P., & Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_15","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:211-228. doi:10.1007/978-3-031-30820-8_15","short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228.","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 211–228.","chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, 13994:211–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_15.","ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ashwani","last_name":"Anand","full_name":"Anand, Ashwani"},{"last_name":"Mallik","full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475","first_name":"Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598"},{"first_name":"Satya Prakash","last_name":"Nayak","full_name":"Nayak, Satya Prakash"},{"first_name":"Anne Kathrin","last_name":"Schmuck","full_name":"Schmuck, Anne Kathrin"}],"article_processing_charge":"No","title":"Computing adequately permissive assumptions for synthesis"},{"department":[{"_id":"MaJö"},{"_id":"GradSch"}],"file_date_updated":"2023-04-20T09:26:51Z","ddc":["570","571"],"supervisor":[{"last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"}],"date_updated":"2023-06-23T09:47:36Z","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12826","ec_funded":1,"file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"12857","checksum":"5f589a9af025f7eeebfd0c186209913e","file_size":14507243,"date_updated":"2023-04-20T09:26:51Z","creator":"vpokusae","file_name":"Thesis_Pokusaeva.docx","date_created":"2023-04-20T09:14:38Z"},{"file_id":"12858","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-04-20T09:14:44Z","file_name":"Thesis_Pokusaeva.pdf","creator":"vpokusae","date_updated":"2023-04-20T09:14:44Z","file_size":10090711}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","month":"04","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"abstract":[{"text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.","lang":"eng"}],"title":"Neural control of optic flow-based navigation in Drosophila melanogaster","author":[{"orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826.","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826"},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_published":"2023-04-18T00:00:00Z","doi":"10.15479/at:ista:12826","date_created":"2023-04-14T14:56:04Z","page":"106","day":"18","has_accepted_license":"1","year":"2023","publisher":"Institute of Science and Technology Austria","oa":1},{"_id":"12086","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_updated":"2023-06-27T12:53:43Z","department":[{"_id":"HeEd"}],"file_date_updated":"2023-01-20T10:02:48Z","oa_version":"Published Version","abstract":[{"text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets.","lang":"eng"}],"month":"01","intvolume":" 85","scopus_import":"1","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"12322","checksum":"71685ca5121f4c837f40c3f8eb50c915","success":1,"date_updated":"2023-01-20T10:02:48Z","file_size":911017,"creator":"dernst","date_created":"2023-01-20T10:02:48Z","file_name":"2023_Algorithmica_Edelsbrunner.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"publication_status":"published","volume":85,"ec_funded":1,"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","grant_number":"Z00342","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6."},"title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Osang, Georg F","last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000846967100001"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"day":"01","publication":"Algorithmica","has_accepted_license":"1","isi":1,"year":"2023","date_published":"2023-01-01T00:00:00Z","doi":"10.1007/s00453-022-01027-6","date_created":"2022-09-11T22:01:57Z","page":"277-295"},{"date_created":"2023-01-08T23:00:53Z","doi":"10.1007/s00028-022-00859-7","date_published":"2023-01-01T00:00:00Z","year":"2023","has_accepted_license":"1","isi":1,"publication":"Journal of Evolution Equations","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000906214600004"]},"author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","last_name":"Dello Schiavo","full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870"},{"id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","first_name":"Melchior","orcid":"0000-0002-0519-4241","full_name":"Wirth, Melchior","last_name":"Wirth"}],"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","citation":{"ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7.","apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7","ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"name":"Configuration Spaces over Non-Smooth Spaces","grant_number":"E208","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"},{"grant_number":"ESP156_N","name":"Gradient flow techniques for quantum Markov semigroups","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833"}],"article_number":"9","ec_funded":1,"issue":"1","volume":23,"publication_status":"published","publication_identifier":{"issn":["1424-3199"],"eissn":["1424-3202"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"1f34f3e2cb521033de6154f274ea3a4e","file_id":"12325","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","date_created":"2023-01-20T10:45:06Z","creator":"dernst","file_size":422612,"date_updated":"2023-01-20T10:45:06Z"}],"scopus_import":"1","intvolume":" 23","month":"01","abstract":[{"text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"JaMa"}],"file_date_updated":"2023-01-20T10:45:06Z","date_updated":"2023-06-28T11:54:35Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"12104"},{"article_type":"original","type":"journal_article","status":"public","_id":"11434","department":[{"_id":"CaMu"}],"date_updated":"2023-06-28T11:49:58Z","scopus_import":"1","intvolume":" 60","month":"01","abstract":[{"lang":"eng","text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall."}],"oa_version":"None","volume":60,"related_material":{"link":[{"relation":"erratum","url":" https://doi.org/10.1007/s00382-022-06401-2"}]},"publication_status":"published","publication_identifier":{"eissn":["1432-0894"],"issn":["0930-7575"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"isi":["000803119400002"]},"author":[{"first_name":"Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","last_name":"Goswami","full_name":"Goswami, Bidyut B"}],"title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","citation":{"ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” Climate Dynamics, vol. 60. Springer Nature, pp. 427–442, 2023.","short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442.","apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. Springer Nature. https://doi.org/10.1007/s00382-022-06337-7","ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 2023;60:427-442. doi:10.1007/s00382-022-06337-7","mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics, vol. 60, Springer Nature, 2023, pp. 427–42, doi:10.1007/s00382-022-06337-7.","ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442.","chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics. Springer Nature, 2023. https://doi.org/10.1007/s00382-022-06337-7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","page":"427-442","date_created":"2022-06-05T22:01:50Z","date_published":"2023-01-01T00:00:00Z","doi":"10.1007/s00382-022-06337-7","year":"2023","isi":1,"publication":"Climate Dynamics","day":"01"},{"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"file_date_updated":"2023-06-19T10:28:09Z","date_updated":"2023-07-14T11:20:27Z","ddc":["000"],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2023-04-22","end_date":"2023-04-27","location":"Paris, France","name":"FOSSACS: Foundations of Software Science and Computation Structures"},"status":"public","_id":"12467","volume":13992,"ec_funded":1,"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308284"],"issn":["0302-9743"]},"publication_status":"published","file":[{"file_id":"12468","checksum":"981025aed580b6b27c426cb8856cf63e","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-01-31T07:22:21Z","file_name":"qsl.pdf","date_updated":"2023-01-31T07:22:21Z","file_size":449027,"creator":"esarac"},{"success":1,"file_id":"13153","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_LNCS_HenzingerT.pdf","date_created":"2023-06-19T10:28:09Z","creator":"dernst","file_size":1048171,"date_updated":"2023-06-19T10:28:09Z"}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":"1","month":"04","intvolume":" 13992","abstract":[{"text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E","last_name":"Sarac"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.11175"]},"title":"Quantitative safety and liveness","citation":{"ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"page":"349-370","date_published":"2023-04-21T00:00:00Z","doi":"10.1007/978-3-031-30829-1_17","date_created":"2023-01-31T07:23:56Z","has_accepted_license":"1","year":"2023","day":"21","publication":"26th International Conference Foundations of Software Science and Computation Structures","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093."},{"publication":"Proceedings of the ACM on Programming Languages","day":"06","year":"2023","has_accepted_license":"1","date_created":"2023-07-02T22:00:43Z","doi":"10.1145/3591230","date_published":"2023-06-06T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"N. Koval, D. Khalanskiy, D.-A. Alistarh, Proceedings of the ACM on Programming Languages 7 (2023).","ieee":"N. Koval, D. Khalanskiy, and D.-A. Alistarh, “CQS: A formally-verified framework for fair and abortable synchronization,” Proceedings of the ACM on Programming Languages, vol. 7. Association for Computing Machinery , 2023.","apa":"Koval, N., Khalanskiy, D., & Alistarh, D.-A. (2023). CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. Association for Computing Machinery . https://doi.org/10.1145/3591230","ama":"Koval N, Khalanskiy D, Alistarh D-A. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 2023;7. doi:10.1145/3591230","mla":"Koval, Nikita, et al. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages, vol. 7, 116, Association for Computing Machinery , 2023, doi:10.1145/3591230.","ista":"Koval N, Khalanskiy D, Alistarh D-A. 2023. CQS: A formally-verified framework for fair and abortable synchronization. Proceedings of the ACM on Programming Languages. 7, 116.","chicago":"Koval, Nikita, Dmitry Khalanskiy, and Dan-Adrian Alistarh. “CQS: A Formally-Verified Framework for Fair and Abortable Synchronization.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery , 2023. https://doi.org/10.1145/3591230."},"title":"CQS: A formally-verified framework for fair and abortable synchronization","article_processing_charge":"No","author":[{"last_name":"Koval","full_name":"Koval, Nikita","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry","last_name":"Khalanskiy","full_name":"Khalanskiy, Dmitry"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"article_number":"116","language":[{"iso":"eng"}],"file":[{"file_name":"2023_ACMProgram.Lang._Koval.pdf","date_created":"2023-07-03T13:09:39Z","creator":"alisjak","file_size":1266773,"date_updated":"2023-07-03T13:09:39Z","success":1,"checksum":"5dba6e73f0ed79adbdae14d165bc2f68","file_id":"13187","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2475-1421"]},"volume":7,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Writing concurrent code that is both correct and efficient is notoriously difficult. Thus, programmers often prefer to use synchronization abstractions, which render code simpler and easier to reason about. Despite a wealth of work on this topic, there is still a gap between the rich semantics provided by synchronization abstractions in modern programming languages—specifically, fair FIFO ordering of synchronization requests and support for abortable operations—and frameworks for implementing it correctly and efficiently. Supporting such semantics is critical given the rising popularity of constructs for asynchronous programming, such as coroutines, which abort frequently and are cheaper to suspend and resume compared to native threads.\r\n\r\nThis paper introduces a new framework called CancellableQueueSynchronizer (CQS), which enables simple yet efficient implementations of a wide range of fair and abortable synchronization primitives: mutexes, semaphores, barriers, count-down latches, and blocking pools. Our main contribution is algorithmic, as implementing both fairness and abortability efficiently at this level of generality is non-trivial. Importantly, all our algorithms, including the CQS framework and the primitives built on top of it, come with formal proofs in the Iris framework for Coq for many of their properties. These proofs are modular, so it is easy to show correctness for new primitives implemented on top of CQS. From a practical perspective, implementation of CQS for native threads on the JVM improves throughput by up to two orders of magnitude over Java’s AbstractQueuedSynchronizer, the only practical abstraction offering similar semantics. Further, we successfully integrated CQS as a core component of the popular Kotlin Coroutines library, validating the framework’s practical impact and expressiveness in a real-world environment. In sum, CancellableQueueSynchronizer is the first framework to combine expressiveness with formal guarantees and solid practical performance. Our approach should be extensible to other languages and families of synchronization primitives."}],"intvolume":" 7","month":"06","scopus_import":"1","ddc":["000"],"date_updated":"2023-07-17T08:43:19Z","department":[{"_id":"DaAl"}],"file_date_updated":"2023-07-03T13:09:39Z","_id":"13179","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original"},{"status":"public","article_type":"original","type":"journal_article","_id":"13180","department":[{"_id":"TiBr"}],"date_updated":"2023-07-17T08:39:19Z","month":"05","intvolume":" 16","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2203.06881","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study the density of everywhere locally soluble diagonal quadric surfaces, parameterised by rational points that lie on a split quadric surface"}],"volume":16,"issue":"2","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1944-4176"],"eissn":["1944-4184"]},"publication_status":"published","title":"Local solubility for a family of quadrics over a split quadric surface","author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"},{"last_name":"Lyczak","full_name":"Lyczak, Julian","id":"3572849A-F248-11E8-B48F-1D18A9856A87","first_name":"Julian"},{"first_name":"Roman","full_name":"Sarapin, Roman","last_name":"Sarapin"}],"article_processing_charge":"No","external_id":{"arxiv":["2203.06881"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Browning, Timothy D., et al. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve, vol. 16, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–42, doi:10.2140/involve.2023.16.331.","ieee":"T. D. Browning, J. Lyczak, and R. Sarapin, “Local solubility for a family of quadrics over a split quadric surface,” Involve, vol. 16, no. 2. Mathematical Sciences Publishers, pp. 331–342, 2023.","short":"T.D. Browning, J. Lyczak, R. Sarapin, Involve 16 (2023) 331–342.","ama":"Browning TD, Lyczak J, Sarapin R. Local solubility for a family of quadrics over a split quadric surface. Involve. 2023;16(2):331-342. doi:10.2140/involve.2023.16.331","apa":"Browning, T. D., Lyczak, J., & Sarapin, R. (2023). Local solubility for a family of quadrics over a split quadric surface. Involve. Mathematical Sciences Publishers. https://doi.org/10.2140/involve.2023.16.331","chicago":"Browning, Timothy D, Julian Lyczak, and Roman Sarapin. “Local Solubility for a Family of Quadrics over a Split Quadric Surface.” Involve. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/involve.2023.16.331.","ista":"Browning TD, Lyczak J, Sarapin R. 2023. Local solubility for a family of quadrics over a split quadric surface. Involve. 16(2), 331–342."},"quality_controlled":"1","publisher":"Mathematical Sciences Publishers","oa":1,"doi":"10.2140/involve.2023.16.331","date_published":"2023-05-26T00:00:00Z","date_created":"2023-07-02T22:00:43Z","page":"331-342","day":"26","publication":"Involve","year":"2023"},{"project":[{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","ieee":"Y. Wei et al., “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” The Journal of Physical Chemistry Letters, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023.","apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., & Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01158","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 2023;14(27):6309-6314. doi:10.1021/acs.jpclett.3c01158","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:10.1021/acs.jpclett.3c01158.","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” The Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01158."},"title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","author":[{"orcid":"0000-0001-8913-9719","full_name":"Wei, Yujing","last_name":"Wei","first_name":"Yujing","id":"0c5ff007-2600-11ee-b896-98bd8d663294"},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lorenc, Dusan","last_name":"Lorenc","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan"},{"full_name":"Zhumekenov, Ayan A.","last_name":"Zhumekenov","first_name":"Ayan A."},{"first_name":"Osman M.","full_name":"Bakr, Osman M.","last_name":"Bakr"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"},{"orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek","last_name":"Alpichshev","first_name":"Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["2304.14198"],"isi":["001022811500001"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","quality_controlled":"1","publisher":"American Chemical Society","oa":1,"day":"05","publication":"The Journal of Physical Chemistry Letters","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-07-05T00:00:00Z","doi":"10.1021/acs.jpclett.3c01158","date_created":"2023-07-18T11:13:17Z","page":"6309-6314","_id":"13251","status":"public","keyword":["General Materials Science","Physical and Theoretical Chemistry"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_updated":"2023-07-19T06:59:19Z","file_date_updated":"2023-07-19T06:55:39Z","department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy."}],"month":"07","intvolume":" 14","file":[{"file_size":2121252,"date_updated":"2023-07-19T06:55:39Z","creator":"dernst","file_name":"2023_JourPhysChemistry_Wei.pdf","date_created":"2023-07-19T06:55:39Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"c0c040063f06a51b9c463adc504f1a23","file_id":"13253"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1948-7185"]},"publication_status":"published","issue":"27","volume":14,"ec_funded":1},{"ec_funded":1,"volume":261,"language":[{"iso":"eng"}],"file":[{"file_name":"icalp23.pdf","date_created":"2023-07-24T15:11:05Z","creator":"esarac","file_size":859379,"date_updated":"2023-07-24T15:11:05Z","success":1,"checksum":"5d4c8932ef3450615a53b9bb15d92eb2","file_id":"13293","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]},"intvolume":" 261","month":"07","alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time.","lang":"eng"}],"file_date_updated":"2023-07-24T15:11:05Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-07-31T08:38:38Z","status":"public","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2023-07-10","location":"Paderborn, Germany","end_date":"2023-07-14"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"13292","date_created":"2023-07-24T15:11:41Z","doi":"10.4230/LIPIcs.ICALP.2023.129","date_published":"2023-07-05T00:00:00Z","page":"129:1--129:20","publication":"50th International Colloquium on Automata, Languages, and Programming","day":"05","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","title":"Regular methods for operator precedence languages","article_processing_charge":"Yes","external_id":{"arxiv":["2305.03447"]},"author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Kebis","full_name":"Kebis, Pavol","first_name":"Pavol"},{"first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","full_name":"Sarac, Naci E"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129."},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}]},{"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":523236,"date_updated":"2023-07-31T09:02:27Z","file_name":"2023_SciPostPhysCore_Tucci.pdf","date_created":"2023-07-31T09:02:27Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"b472bc82108747eda5d52adf9e2ac7f3","file_id":"13329"}],"publication_status":"published","publication_identifier":{"issn":["2666-9366"]},"ec_funded":1,"issue":"2","volume":6,"oa_version":"Published Version","abstract":[{"text":"Recent experimental advances have inspired the development of theoretical tools to describe the non-equilibrium dynamics of quantum systems. Among them an exact representation of quantum spin systems in terms of classical stochastic processes has been proposed. Here we provide first steps towards the extension of this stochastic approach to bosonic systems by considering the one-dimensional quantum quartic oscillator. We show how to exactly parameterize the time evolution of this prototypical model via the dynamics of a set of classical variables. We interpret these variables as stochastic processes, which allows us to propose a novel way to numerically simulate the time evolution of the system. We benchmark our findings by considering analytically solvable limits and providing alternative derivations of known results.","lang":"eng"}],"intvolume":" 6","month":"04","ddc":["530"],"date_updated":"2023-07-31T09:03:28Z","file_date_updated":"2023-07-31T09:02:27Z","department":[{"_id":"MaSe"}],"_id":"13277","keyword":["Statistical and Nonlinear Physics","Atomic and Molecular Physics","and Optics","Nuclear and High Energy Physics","Condensed Matter Physics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"SciPost Physics Core","day":"14","year":"2023","has_accepted_license":"1","date_created":"2023-07-24T10:47:46Z","doi":"10.21468/scipostphyscore.6.2.029","date_published":"2023-04-14T00:00:00Z","acknowledgement":"S. De Nicola acknowledges funding from the Institute of Science and Technology Austria (ISTA), and from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. S. De Nicola also acknowledges funding from the EPSRC Center for Doctoral Training in Cross-Disciplinary Approaches to NonEquilibrium Systems (CANES) under Grant EP/L015854/1. ","oa":1,"publisher":"SciPost Foundation","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Tucci, Gennaro, et al. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core, vol. 6, no. 2, 029, SciPost Foundation, 2023, doi:10.21468/scipostphyscore.6.2.029.","ama":"Tucci G, De Nicola S, Wald S, Gambassi A. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 2023;6(2). doi:10.21468/scipostphyscore.6.2.029","apa":"Tucci, G., De Nicola, S., Wald, S., & Gambassi, A. (2023). Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. SciPost Foundation. https://doi.org/10.21468/scipostphyscore.6.2.029","short":"G. Tucci, S. De Nicola, S. Wald, A. Gambassi, SciPost Physics Core 6 (2023).","ieee":"G. Tucci, S. De Nicola, S. Wald, and A. Gambassi, “Stochastic representation of the quantum quartic oscillator,” SciPost Physics Core, vol. 6, no. 2. SciPost Foundation, 2023.","chicago":"Tucci, Gennaro, Stefano De Nicola, Sascha Wald, and Andrea Gambassi. “Stochastic Representation of the Quantum Quartic Oscillator.” SciPost Physics Core. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscore.6.2.029.","ista":"Tucci G, De Nicola S, Wald S, Gambassi A. 2023. Stochastic representation of the quantum quartic oscillator. SciPost Physics Core. 6(2), 029."},"title":"Stochastic representation of the quantum quartic oscillator","external_id":{"arxiv":["2211.01923"]},"article_processing_charge":"No","author":[{"first_name":"Gennaro","full_name":"Tucci, Gennaro","last_name":"Tucci"},{"last_name":"De Nicola","orcid":"0000-0002-4842-6671","full_name":"De Nicola, Stefano","id":"42832B76-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"},{"first_name":"Sascha","last_name":"Wald","full_name":"Wald, Sascha"},{"first_name":"Andrea","last_name":"Gambassi","full_name":"Gambassi, Andrea"}],"article_number":"029","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}]},{"related_material":{"record":[{"status":"public","id":"13275","relation":"research_data"}]},"ec_funded":1,"publication_identifier":{"issn":["2949-804X"]},"publication_status":"published","file":[{"checksum":"f583a70fe915d2208c803f5afb426daa","file_id":"13330","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-07-31T09:09:23Z","file_name":"2023_SciPostPhysCodebase_Rammelmueller.pdf","creator":"dernst","date_updated":"2023-07-31T09:09:23Z","file_size":551418}],"language":[{"iso":"eng"}],"month":"04","abstract":[{"text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2023-07-31T09:09:23Z","department":[{"_id":"MiLe"}],"date_updated":"2023-07-31T09:16:02Z","ddc":["530"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"13276","date_published":"2023-04-19T00:00:00Z","doi":"10.21468/scipostphyscodeb.12","date_created":"2023-07-24T10:47:15Z","has_accepted_license":"1","year":"2023","day":"19","publication":"SciPost Physics Codebases","quality_controlled":"1","publisher":"SciPost Foundation","oa":1,"acknowledgement":"We acknowledge fruitful discussions with Hans-Werner Hammer and thank Gerhard Zürn and\r\nPietro Massignan for sending us their data. We thank Fabian Brauneis for beta-testing the\r\nprovided code-package, and comments on the manuscript.\r\nL.R. is supported by FP7/ERC Consolidator Grant QSIMCORR, No.\r\n771891, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under\r\nGermany’s Excellence Strategy –EXC–2111–390814868. A.G.V. acknowledges support\r\nby European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.","author":[{"last_name":"Rammelmüller","full_name":"Rammelmüller, Lukas","first_name":"Lukas"},{"last_name":"Huber","full_name":"Huber, David","first_name":"David"},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2202.04603"]},"title":"A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D","citation":{"mla":"Rammelmüller, Lukas, et al. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases, 12, SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12.","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D,” SciPost Physics Codebases. SciPost Foundation, 2023.","short":"L. Rammelmüller, D. Huber, A. Volosniev, SciPost Physics Codebases (2023).","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12","ama":"Rammelmüller L, Huber D, Volosniev A. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases. 2023. doi:10.21468/scipostphyscodeb.12","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “A Modular Implementation of an Effective Interaction Approach for Harmonically Trapped Fermions in 1D.” SciPost Physics Codebases. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12.","ista":"Rammelmüller L, Huber D, Volosniev A. 2023. A modular implementation of an effective interaction approach for harmonically trapped fermions in 1D. SciPost Physics Codebases., 12."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"12"},{"type":"research_data_reference","status":"public","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"_id":"13275","article_processing_charge":"No","author":[{"first_name":"Lukas","last_name":"Rammelmüller","full_name":"Rammelmüller, Lukas"},{"first_name":"David","full_name":"Huber, David","last_name":"Huber"},{"last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"MiLe"}],"title":"Codebase release 1.0 for FermiFCI","citation":{"ista":"Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, 10.21468/scipostphyscodeb.12-r1.0.","chicago":"Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12-r1.0.","apa":"Rammelmüller, L., Huber, D., & Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12-r1.0","ama":"Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:10.21468/scipostphyscodeb.12-r1.0","short":"L. Rammelmüller, D. Huber, A. Volosniev, (2023).","ieee":"L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023.","mla":"Rammelmüller, Lukas, et al. Codebase Release 1.0 for FermiFCI. SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12-r1.0."},"date_updated":"2023-07-31T09:16:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"oa":1,"main_file_link":[{"url":"https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0","open_access":"1"}],"publisher":"SciPost Foundation","month":"04","abstract":[{"text":"We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost.","lang":"eng"}],"oa_version":"Published Version","date_created":"2023-07-24T10:46:23Z","ec_funded":1,"date_published":"2023-04-19T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"13276","status":"public"}]},"doi":"10.21468/scipostphyscodeb.12-r1.0","year":"2023","day":"19"},{"day":"17","publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","has_accepted_license":"1","year":"2023","doi":"10.1145/3558481.3591082","date_published":"2023-06-17T00:00:00Z","date_created":"2023-07-23T22:01:12Z","page":"261-271","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL, United States, 2023, pp. 261–271.","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271."},"title":"Provably-efficient and internally-deterministic parallel Union-Find","author":[{"full_name":"Fedorov, Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander"},{"id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","first_name":"Diba","full_name":"Hashemi, Diba","last_name":"Hashemi"},{"first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2304.09331"]},"file":[{"date_updated":"2023-07-31T10:53:08Z","file_size":2087937,"creator":"dernst","date_created":"2023-07-31T10:53:08Z","file_name":"2023_SPAA_Fedorov.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","file_id":"13334","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450395458"]},"publication_status":"published","oa_version":"Published Version","abstract":[{"text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.","lang":"eng"}],"month":"06","scopus_import":"1","ddc":["000"],"date_updated":"2023-07-31T10:54:32Z","file_date_updated":"2023-07-31T10:53:08Z","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"_id":"13262","status":"public","type":"conference","conference":{"location":"Orlando, FL, United States","end_date":"2023-06-19","start_date":"2023-06-17","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"volume":16,"issue":"2","publication_status":"published","publication_identifier":{"eissn":["1752-4571"]},"language":[{"iso":"eng"}],"file":[{"file_size":2269822,"date_updated":"2023-02-27T07:10:17Z","creator":"dernst","file_name":"2023_EvolutionaryApplications_DeJode.pdf","date_created":"2023-02-27T07:10:17Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12685","checksum":"d4d6fa9ddf36643af994a6a757919afb"}],"scopus_import":"1","intvolume":" 16","month":"02","abstract":[{"text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"file_date_updated":"2023-02-27T07:10:17Z","date_updated":"2023-08-01T12:25:44Z","ddc":["576"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"11479","page":"542-559","date_created":"2022-07-03T22:01:33Z","date_published":"2023-02-01T00:00:00Z","doi":"10.1111/eva.13428","year":"2023","isi":1,"has_accepted_license":"1","publication":"Evolutionary Applications","day":"01","oa":1,"publisher":"Wiley","quality_controlled":"1","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","article_processing_charge":"No","external_id":{"isi":["000815663700001"]},"author":[{"last_name":"De Jode","full_name":"De Jode, Aurélien","first_name":"Aurélien"},{"first_name":"Alan","full_name":"Le Moan, Alan","last_name":"Le Moan"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"title":"Ten years of demographic modelling of divergence and speciation in the sea","citation":{"ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications. Wiley, 2023. https://doi.org/10.1111/eva.13428.","ieee":"A. De Jode et al., “Ten years of demographic modelling of divergence and speciation in the sea,” Evolutionary Applications, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. Wiley. https://doi.org/10.1111/eva.13428","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 2023;16(2):542-559. doi:10.1111/eva.13428","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” Evolutionary Applications, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:10.1111/eva.13428."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"Gonçalo Oliveira is supported by the NOMIS Foundation, Fundação Serrapilheira 1812-27395, by CNPq grants 428959/2018-0 and 307475/2018-2, and by FAPERJ through the grant Jovem Cientista do Nosso Estado E-26/202.793/2019.","date_published":"2023-01-10T00:00:00Z","doi":"10.1038/s41598-022-19827-9","date_created":"2023-01-22T23:00:55Z","day":"10","publication":"Scientific Reports","has_accepted_license":"1","isi":1,"year":"2023","article_number":"468","title":"New approaches to epidemic modeling on networks","author":[{"full_name":"Gómez, Arturo","last_name":"Gómez","first_name":"Arturo"},{"last_name":"Oliveira","full_name":"Oliveira, Goncalo","id":"58abbde8-f455-11eb-a497-98c8fd71b905","first_name":"Goncalo"}],"external_id":{"isi":["001003345000051"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Gómez A, Oliveira G. New approaches to epidemic modeling on networks. Scientific Reports. 2023;13. doi:10.1038/s41598-022-19827-9","apa":"Gómez, A., & Oliveira, G. (2023). New approaches to epidemic modeling on networks. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-19827-9","ieee":"A. Gómez and G. Oliveira, “New approaches to epidemic modeling on networks,” Scientific Reports, vol. 13. Springer Nature, 2023.","short":"A. Gómez, G. Oliveira, Scientific Reports 13 (2023).","mla":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports, vol. 13, 468, Springer Nature, 2023, doi:10.1038/s41598-022-19827-9.","ista":"Gómez A, Oliveira G. 2023. New approaches to epidemic modeling on networks. Scientific Reports. 13, 468.","chicago":"Gómez, Arturo, and Goncalo Oliveira. “New Approaches to Epidemic Modeling on Networks.” Scientific Reports. Springer Nature, 2023. https://doi.org/10.1038/s41598-022-19827-9."},"month":"01","intvolume":" 13","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"In this article, we develop two independent and new approaches to model epidemic spread in a network. Contrary to the most studied models, those developed here allow for contacts with different probabilities of transmitting the disease (transmissibilities). We then examine each of these models using some mean field type approximations. The first model looks at the late-stage effects of an epidemic outbreak and allows for the computation of the probability that a given vertex was infected. This computation is based on a mean field approximation and only depends on the number of contacts and their transmissibilities. This approach shares many similarities with percolation models in networks. The second model we develop is a dynamic model which we analyze using a mean field approximation which highly reduces the dimensionality of the system. In particular, the original system which individually analyses each vertex of the network is reduced to one with as many equations as different transmissibilities. Perhaps the greatest contribution of this article is the observation that, in both these models, the existence and size of an epidemic outbreak are linked to the properties of a matrix which we call the R-matrix. This is a generalization of the basic reproduction number which more precisely characterizes the main routes of infection.","lang":"eng"}],"volume":13,"file":[{"date_created":"2023-01-23T07:53:23Z","file_name":"2023_ScientificReports_Gomez.pdf","creator":"dernst","date_updated":"2023-01-23T07:53:23Z","file_size":2167792,"checksum":"a8b83739f4a951e83e0b2a778f03b327","file_id":"12336","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2045-2322"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12329","department":[{"_id":"TaHa"}],"file_date_updated":"2023-01-23T07:53:23Z","ddc":["510"],"date_updated":"2023-08-01T12:31:40Z"},{"title":"Integral points of bounded height on a log Fano threefold","author":[{"first_name":"Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425","orcid":"0000-0001-7302-8256","full_name":"Wilsch, Florian Alexander","last_name":"Wilsch"}],"external_id":{"isi":["000773116000001"],"arxiv":["1901.08503"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023.","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808.","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048."},"publisher":"Oxford Academic","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","date_published":"2023-04-01T00:00:00Z","doi":"10.1093/imrn/rnac048","date_created":"2021-01-22T09:31:09Z","page":"6780-6808","day":"01","publication":"International Mathematics Research Notices","isi":1,"year":"2023","status":"public","article_type":"original","type":"journal_article","_id":"9034","department":[{"_id":"TiBr"}],"date_updated":"2023-08-01T12:23:55Z","month":"04","intvolume":" 2023","main_file_link":[{"url":"https://arxiv.org/abs/1901.08503","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors."}],"issue":"8","volume":2023,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"publication_status":"published"},{"day":"16","publication":"Frontiers in Microbiology","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.3389/fmicb.2023.1119002","date_published":"2023-03-16T00:00:00Z","date_created":"2023-01-31T08:13:40Z","acknowledgement":"We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad, B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz, E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25 to MAF) and the Academy of Finland (343022 to LV). ","quality_controlled":"1","publisher":"Frontiers","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1119002.","ista":"Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 14, 1119002.","mla":"Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” Frontiers in Microbiology, vol. 14, 1119002, Frontiers, 2023, doi:10.3389/fmicb.2023.1119002.","apa":"Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1119002","ama":"Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1119002","short":"L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T. Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).","ieee":"L. Viljakainen et al., “Antiviral immune response reveals host-specific virus infections in natural ant populations,” Frontiers in Microbiology, vol. 14. Frontiers, 2023."},"title":"Antiviral immune response reveals host-specific virus infections in natural ant populations","author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Fürst","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V"},{"last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana","first_name":"Jaana"},{"id":"403169A4-080F-11EA-9993-BF3F3DDC885E","first_name":"Jinook","full_name":"Oh, Jinook","orcid":"0000-0001-7425-2372","last_name":"Oh"},{"full_name":"Tolonen, Lassi","last_name":"Tolonen","first_name":"Lassi"},{"first_name":"Thomas","last_name":"Eder","full_name":"Eder, Thomas"},{"first_name":"Thomas","full_name":"Rattei, Thomas","last_name":"Rattei"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000961542100001"],"pmid":["PPR559293 "]},"article_number":"1119002","project":[{"name":"Viral pathogens and social immunity in ants","grant_number":"M02076","call_identifier":"FWF","_id":"25DF61D8-B435-11E9-9278-68D0E5697425"}],"file":[{"file_id":"12843","checksum":"cd52292963acce1111634d9fac08c699","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-04-17T07:49:09Z","file_name":"2023_FrontMicrobiology_Viljakainen.pdf","date_updated":"2023-04-17T07:49:09Z","file_size":4866332,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664-302X"]},"publication_status":"published","volume":14,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Hosts can carry many viruses in their bodies, but not all of them cause disease. We studied ants as a social host to determine both their overall viral repertoire and the subset of actively infecting viruses across natural populations of three subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae). We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response. This approach led to the discovery of 41 novel viruses in ants and revealed a host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species. The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the virus and the respective ant species, but not its population. Overall, we found the highest virus abundance and diversity per population in Li. humile, followed by La. neglectus and M. rubra. Argentine ants also shared a high proportion of viruses between populations, whilst overlap was nearly absent in M. rubra. Only one of the 59 viruses was found to infect two of the ant species as hosts, revealing high host-specificity in active infections. In contrast, six viruses actively infected one ant species, but were found as contaminants only in the others. Disentangling spillover of disease-causing infection from non-infecting contamination across species is providing relevant information for disease ecology and ecosystem management.","lang":"eng"}],"month":"03","intvolume":" 14","scopus_import":"1","ddc":["570"],"date_updated":"2023-08-01T12:39:58Z","department":[{"_id":"SyCr"}],"file_date_updated":"2023-04-17T07:49:09Z","_id":"12469","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"}],"citation":{"ama":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 2023;69:156-191. doi:10.1007/s00454-022-00431-7","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., & Wintraecken, M. (2023). Local criteria for triangulating general manifolds. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00431-7","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, M. Wintraecken, Discrete & Computational Geometry 69 (2023) 156–191.","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, and M. Wintraecken, “Local criteria for triangulating general manifolds,” Discrete & Computational Geometry, vol. 69. Springer Nature, pp. 156–191, 2023.","mla":"Boissonnat, Jean-Daniel, et al. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry, vol. 69, Springer Nature, 2023, pp. 156–91, doi:10.1007/s00454-022-00431-7.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Wintraecken M. 2023. Local criteria for triangulating general manifolds. Discrete & Computational Geometry. 69, 156–191.","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, and Mathijs Wintraecken. “Local Criteria for Triangulating General Manifolds.” Discrete & Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00431-7."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"isi":["000862193600001"]},"author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"full_name":"Dyer, Ramsay","last_name":"Dyer","first_name":"Ramsay"},{"full_name":"Ghosh, Arijit","last_name":"Ghosh","first_name":"Arijit"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken"}],"title":"Local criteria for triangulating general manifolds","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). Arijit Ghosh is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015). Part of this work was done when Arijit Ghosh was a Researcher at Max-Planck-Institute for Informatics, Germany, supported by the IndoGerman Max Planck Center for Computer Science (IMPECS). Mathijs Wintraecken also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Austrian Science Fund (FWF): M-3073. A part of the results described in this paper were presented at SoCG 2018 and in [3]. \r\nOpen access funding provided by the Austrian Science Fund (FWF).","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2023","isi":1,"has_accepted_license":"1","publication":"Discrete & Computational Geometry","day":"01","page":"156-191","date_created":"2023-01-16T10:04:06Z","date_published":"2023-01-01T00:00:00Z","doi":"10.1007/s00454-022-00431-7","_id":"12287","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Computational Theory and Mathematics","Discrete Mathematics and Combinatorics","Geometry and Topology","Theoretical Computer Science"],"status":"public","date_updated":"2023-08-01T12:47:32Z","ddc":["510"],"file_date_updated":"2023-02-02T11:01:10Z","department":[{"_id":"HeEd"}],"abstract":[{"text":"We present criteria for establishing a triangulation of a manifold. Given a manifold M, a simplicial complex A, and a map H from the underlying space of A to M, our criteria are presented in local coordinate charts for M, and ensure that H is a homeomorphism. These criteria do not require a differentiable structure, or even an explicit metric on M. No Delaunay property of A is assumed. The result provides a triangulation guarantee for algorithms that construct a simplicial complex by working in local coordinate patches. Because the criteria are easily verified in such a setting, they are expected to be of general use.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 69","month":"01","publication_status":"published","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12488","checksum":"46352e0ee71e460848f88685ca852681","file_size":582850,"date_updated":"2023-02-02T11:01:10Z","creator":"dernst","file_name":"2023_DiscreteCompGeometry_Boissonnat.pdf","date_created":"2023-02-02T11:01:10Z"}],"ec_funded":1,"volume":69},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-022-00539-y.","ista":"Hof B. 2023. Directed percolation and the transition to turbulence. Nature Reviews Physics. 5, 62–72.","mla":"Hof, Björn. “Directed Percolation and the Transition to Turbulence.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 62–72, doi:10.1038/s42254-022-00539-y.","ieee":"B. Hof, “Directed percolation and the transition to turbulence,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 62–72, 2023.","short":"B. Hof, Nature Reviews Physics 5 (2023) 62–72.","apa":"Hof, B. (2023). Directed percolation and the transition to turbulence. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-022-00539-y","ama":"Hof B. Directed percolation and the transition to turbulence. Nature Reviews Physics. 2023;5:62-72. doi:10.1038/s42254-022-00539-y"},"title":"Directed percolation and the transition to turbulence","author":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"external_id":{"isi":["000890148700002"]},"article_processing_charge":"No","day":"01","publication":"Nature Reviews Physics","isi":1,"year":"2023","doi":"10.1038/s42254-022-00539-y","date_published":"2023-01-01T00:00:00Z","date_created":"2023-01-12T12:10:18Z","page":"62-72","publisher":"Springer Nature","quality_controlled":"1","date_updated":"2023-08-01T12:50:48Z","department":[{"_id":"BjHo"}],"_id":"12165","status":"public","keyword":["General Physics and Astronomy"],"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2522-5820"]},"publication_status":"published","volume":5,"oa_version":"None","abstract":[{"text":"It may come as a surprise that a phenomenon as ubiquitous and prominent as the transition from laminar to turbulent flow has resisted combined efforts by physicists, engineers and mathematicians, and remained unresolved for almost one and a half centuries. In recent years, various studies have proposed analogies to directed percolation, a well-known universality class in statistical mechanics, which describes a non-equilibrium phase transition from a fluctuating active phase into an absorbing state. It is this unlikely relation between the multiscale, high-dimensional dynamics that signify the transition process in virtually all flows of practical relevance, and the arguably most basic non-equilibrium phase transition, that so far has mainly been the subject of model studies, which I review in this Perspective.","lang":"eng"}],"month":"01","intvolume":" 5","scopus_import":"1"},{"date_updated":"2023-08-01T12:55:32Z","ddc":["570"],"file_date_updated":"2023-03-16T07:58:16Z","department":[{"_id":"FlSc"}],"_id":"12421","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Biochemistry"],"status":"public","publication_status":"published","publication_identifier":{"issn":["0300-5127"],"eissn":["1470-8752"]},"language":[{"iso":"eng"}],"file":[{"file_id":"12728","checksum":"4e7069845e3dad22bb44fb71ec624c60","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-03-16T07:58:16Z","file_name":"2023_BioChemicalSocietyTransactions_Faessler.pdf","creator":"dernst","date_updated":"2023-03-16T07:58:16Z","file_size":10045006}],"issue":"1","volume":51,"abstract":[{"text":"The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 51","month":"02","citation":{"ama":"Fäßler F, Javoor M, Schur FK. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 2023;51(1):87-99. doi:10.1042/bst20220221","apa":"Fäßler, F., Javoor, M., & Schur, F. K. (2023). Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/bst20220221","ieee":"F. Fäßler, M. Javoor, and F. K. Schur, “Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM,” Biochemical Society Transactions, vol. 51, no. 1. Portland Press, pp. 87–99, 2023.","short":"F. Fäßler, M. Javoor, F.K. Schur, Biochemical Society Transactions 51 (2023) 87–99.","mla":"Fäßler, Florian, et al. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions, vol. 51, no. 1, Portland Press, 2023, pp. 87–99, doi:10.1042/bst20220221.","ista":"Fäßler F, Javoor M, Schur FK. 2023. Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochemical Society Transactions. 51(1), 87–99.","chicago":"Fäßler, Florian, Manjunath Javoor, and Florian KM Schur. “Deciphering the Molecular Mechanisms of Actin Cytoskeleton Regulation in Cell Migration Using Cryo-EM.” Biochemical Society Transactions. Portland Press, 2023. https://doi.org/10.1042/bst20220221."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000926043100001"]},"article_processing_charge":"No","author":[{"first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian","last_name":"Fäßler"},{"full_name":"Javoor, Manjunath","last_name":"Javoor","first_name":"Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"title":"Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"year":"2023","isi":1,"has_accepted_license":"1","publication":"Biochemical Society Transactions","day":"01","page":"87-99","date_created":"2023-01-27T10:08:19Z","doi":"10.1042/bst20220221","date_published":"2023-02-01T00:00:00Z","acknowledgement":"We apologize for not being able to mention and cite additional excellent work that would have fit the scope of this review, due to space restraints. We thank Jesse Hansen for comments on the manuscript. We acknowledge support from the Austrian Science Fund (FWF): P33367 and the Institute of Science and Technology Austria.","oa":1,"quality_controlled":"1","publisher":"Portland Press"},{"title":"Symmetry-reduced dynamic mode decomposition of near-wall turbulence","author":[{"last_name":"Marensi","full_name":"Marensi, Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","first_name":"Elena"},{"first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","full_name":"Yalniz, Gökhan","orcid":"0000-0002-8490-9312","last_name":"Yalniz"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000903336600001"],"arxiv":["2101.07516"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Marensi, Elena, Gökhan Yalniz, Björn Hof, and Nazmi B Budanur. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2022.1001.","ista":"Marensi E, Yalniz G, Hof B, Budanur NB. 2023. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 954, A10.","mla":"Marensi, Elena, et al. “Symmetry-Reduced Dynamic Mode Decomposition of near-Wall Turbulence.” Journal of Fluid Mechanics, vol. 954, A10, Cambridge University Press, 2023, doi:10.1017/jfm.2022.1001.","ama":"Marensi E, Yalniz G, Hof B, Budanur NB. Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. 2023;954. doi:10.1017/jfm.2022.1001","apa":"Marensi, E., Yalniz, G., Hof, B., & Budanur, N. B. (2023). Symmetry-reduced dynamic mode decomposition of near-wall turbulence. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2022.1001","ieee":"E. Marensi, G. Yalniz, B. Hof, and N. B. Budanur, “Symmetry-reduced dynamic mode decomposition of near-wall turbulence,” Journal of Fluid Mechanics, vol. 954. Cambridge University Press, 2023.","short":"E. Marensi, G. Yalniz, B. Hof, N.B. Budanur, Journal of Fluid Mechanics 954 (2023)."},"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"article_number":"A10","doi":"10.1017/jfm.2022.1001","date_published":"2023-01-10T00:00:00Z","date_created":"2023-01-08T23:00:53Z","day":"10","publication":"Journal of Fluid Mechanics","isi":1,"has_accepted_license":"1","year":"2023","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"acknowledgement":"E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge\r\na grant from the Simons Foundation (662960, BH).","file_date_updated":"2023-02-02T12:34:54Z","department":[{"_id":"BjHo"}],"ddc":["530"],"date_updated":"2023-08-01T12:53:23Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"12105","volume":954,"file":[{"date_updated":"2023-02-02T12:34:54Z","file_size":1931647,"creator":"dernst","date_created":"2023-02-02T12:34:54Z","file_name":"2023_JourFluidMechanics_Marensi.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"9224f987caefe5dd85a70814d3cce65c","file_id":"12489","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"publication_status":"published","month":"01","intvolume":" 954","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Data-driven dimensionality reduction methods such as proper orthogonal decomposition and dynamic mode decomposition have proven to be useful for exploring complex phenomena within fluid dynamics and beyond. A well-known challenge for these techniques is posed by the continuous symmetries, e.g. translations and rotations, of the system under consideration, as drifts in the data dominate the modal expansions without providing an insight into the dynamics of the problem. In the present study, we address this issue for fluid flows in rectangular channels by formulating a continuous symmetry reduction method that eliminates the translations in the streamwise and spanwise directions simultaneously. We demonstrate our method by computing the symmetry-reduced dynamic mode decomposition (SRDMD) of sliding windows of data obtained from the transitional plane-Couette and turbulent plane-Poiseuille flow simulations. In the former setting, SRDMD captures the dynamics in the vicinity of the invariant solutions with translation symmetries, i.e. travelling waves and relative periodic orbits, whereas in the latter, our calculations reveal episodes of turbulent time evolution that can be approximated by a low-dimensional linear expansion.","lang":"eng"}]},{"department":[{"_id":"NiBa"}],"date_updated":"2023-08-01T12:58:30Z","status":"public","article_type":"original","type":"journal_article","_id":"12514","issue":"1","volume":77,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1558-5646"]},"intvolume":" 77","month":"01","main_file_link":[{"url":"https://doi.org/10.1093/evolut/qpac004","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model."}],"title":"A multivariate view of the speciation continuum","article_processing_charge":"No","external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"author":[{"first_name":"Daniel I.","full_name":"Bolnick, Daniel I.","last_name":"Bolnick"},{"full_name":"Hund, Amanda K.","last_name":"Hund","first_name":"Amanda K."},{"first_name":"Patrik","last_name":"Nosil","full_name":"Nosil, Patrik"},{"last_name":"Peng","full_name":"Peng, Foen","first_name":"Foen"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"first_name":"Swapna","full_name":"Subramanian, Swapna","last_name":"Subramanian"},{"first_name":"Jochen B.W.","last_name":"Wolf","full_name":"Wolf, Jochen B.W."},{"full_name":"Yukilevich, Roman","last_name":"Yukilevich","first_name":"Roman"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004."},"date_created":"2023-02-05T23:00:59Z","doi":"10.1093/evolut/qpac004","date_published":"2023-01-01T00:00:00Z","page":"318-328","publication":"Evolution: International journal of organic evolution","day":"01","year":"2023","isi":1,"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript."},{"file_date_updated":"2023-02-14T07:58:26Z","department":[{"_id":"HeEd"}],"ddc":["600"],"date_updated":"2023-08-01T13:15:48Z","status":"public","conference":{"location":"Orlando, FL, United States","end_date":"2022-12-01","start_date":"2022-11-28","name":"ICDMW: Conference on Data Mining Workshops"},"type":"conference","_id":"12548","language":[{"iso":"eng"}],"file":[{"creator":"fkarimip","date_updated":"2023-02-14T07:58:26Z","file_size":1183339,"date_created":"2023-02-14T07:58:26Z","file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c253bee25e6dfe484f96662daa119cb6","file_id":"12549","success":1}],"publication_status":"published","publication_identifier":{"eisbn":["9798350346091"],"eissn":["2375-9259"]},"month":"02","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts."}],"title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","external_id":{"isi":["000971492200145"]},"article_processing_charge":"No","author":[{"full_name":"Forghani, Mohammad","last_name":"Forghani","first_name":"Mohammad"},{"first_name":"Christophe","full_name":"Claramunt, Christophe","last_name":"Claramunt"},{"orcid":"0000-0001-6746-4174","full_name":"Karimipour, Farid","last_name":"Karimipour","first_name":"Farid","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425"},{"first_name":"Georg","full_name":"Heiler, Georg","last_name":"Heiler"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093.","apa":"Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023.","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023.","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093."},"article_number":"00093","date_created":"2023-02-14T07:56:21Z","date_published":"2023-02-08T00:00:00Z","doi":"10.1109/icdmw58026.2022.00093","publication":"2022 IEEE International Conference on Data Mining Workshops","day":"08","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial & Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223.","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79.","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial & Applied Mathematics, pp. 38–79, 2023.","ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223","apa":"Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial & Applied Mathematics. https://doi.org/10.1137/20m1378223","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial & Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223.","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79."},"title":"Topology and adjunction in promise constraint satisfaction","article_processing_charge":"No","external_id":{"isi":["000955000000001"],"arxiv":["2003.11351"]},"author":[{"first_name":"Andrei","last_name":"Krokhin","full_name":"Krokhin, Andrei"},{"last_name":"Opršal","full_name":"Opršal, Jakub","orcid":"0000-0003-1245-3456","first_name":"Jakub","id":"ec596741-c539-11ec-b829-c79322a91242"},{"last_name":"Wrochna","full_name":"Wrochna, Marcin","first_name":"Marcin"},{"last_name":"Živný","full_name":"Živný, Stanislav","first_name":"Stanislav"}],"project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"publication":"SIAM Journal on Computing","day":"01","year":"2023","isi":1,"date_created":"2023-02-16T07:03:52Z","date_published":"2023-01-01T00:00:00Z","doi":"10.1137/20m1378223","page":"38-79","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","oa":1,"publisher":"Society for Industrial & Applied Mathematics","quality_controlled":"1","date_updated":"2023-08-01T13:11:30Z","department":[{"_id":"UlWa"}],"_id":"12563","keyword":["General Mathematics","General Computer Science"],"status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"ec_funded":1,"issue":"1","volume":52,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems."}],"intvolume":" 52","month":"01","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2003.11351"}],"scopus_import":"1"},{"publisher":"American Mathematical Society","quality_controlled":"1","oa":1,"doi":"10.1090/proc/15239","date_published":"2023-01-01T00:00:00Z","date_created":"2023-01-29T23:00:58Z","page":"907-914","day":"01","publication":"Proceedings of the American Mathematical Society","isi":1,"year":"2023","title":"Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups","author":[{"id":"3ACCD756-F248-11E8-B48F-1D18A9856A87","first_name":"Francesca","full_name":"Balestrieri, Francesca","last_name":"Balestrieri"}],"external_id":{"isi":["000898440000001"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Balestrieri F. 2023. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 151(3), 907–914.","chicago":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/15239.","apa":"Balestrieri, F. (2023). Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/15239","ama":"Balestrieri F. Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups. Proceedings of the American Mathematical Society. 2023;151(3):907-914. doi:10.1090/proc/15239","short":"F. Balestrieri, Proceedings of the American Mathematical Society 151 (2023) 907–914.","ieee":"F. Balestrieri, “Some remarks on strong approximation and applications to homogeneous spaces of linear algebraic groups,” Proceedings of the American Mathematical Society, vol. 151, no. 3. American Mathematical Society, pp. 907–914, 2023.","mla":"Balestrieri, Francesca. “Some Remarks on Strong Approximation and Applications to Homogeneous Spaces of Linear Algebraic Groups.” Proceedings of the American Mathematical Society, vol. 151, no. 3, American Mathematical Society, 2023, pp. 907–14, doi:10.1090/proc/15239."},"month":"01","intvolume":" 151","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://hal.science/hal-03013498/"}],"oa_version":"Preprint","abstract":[{"text":"Let k be a number field and X a smooth, geometrically integral quasi-projective variety over k. For any linear algebraic group G over k and any G-torsor g : Z → X, we observe that if the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for all twists of Z by elements in H^1(k, G), then the étale-Brauer obstruction is the only one for strong approximation off a finite set of places S for X. As an application, we show that any homogeneous space of the form G/H with G a connected linear algebraic group over k satisfies strong approximation off the infinite places with étale-Brauer obstruction, under some compactness assumptions when k is totally real. We also prove more refined strong approximation results for homogeneous spaces of the form G/H with G semisimple simply connected and H finite, using the theory of torsors and descent.","lang":"eng"}],"issue":"3","volume":151,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1088-6826"],"issn":["0002-9939"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"12427","department":[{"_id":"TiBr"}],"date_updated":"2023-08-01T13:03:32Z"},{"volume":111,"issue":"3","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1097-4199"]},"publication_status":"published","month":"02","intvolume":" 111","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo."}],"department":[{"_id":"SiHi"}],"date_updated":"2023-08-01T13:10:27Z","status":"public","type":"journal_article","article_type":"letter_note","_id":"12542","date_published":"2023-02-01T00:00:00Z","doi":"10.1016/j.neuron.2023.01.006","date_created":"2023-02-12T23:00:58Z","page":"291-293","day":"01","publication":"Neuron","isi":1,"year":"2023","quality_controlled":"1","publisher":"Elsevier","title":"Going back in time with TEMPO","author":[{"orcid":"0000-0002-5615-5277","full_name":"Villalba Requena, Ana","last_name":"Villalba Requena","first_name":"Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"article_processing_charge":"No","external_id":{"isi":["000994473300001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:10.1016/j.neuron.2023.01.006.","ama":"Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. Neuron. 2023;111(3):291-293. doi:10.1016/j.neuron.2023.01.006","apa":"Villalba Requena, A., & Hippenmeyer, S. (2023). Going back in time with TEMPO. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.01.006","ieee":"A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” Neuron, vol. 111, no. 3. Elsevier, pp. 291–293, 2023.","short":"A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293.","chicago":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron. Elsevier, 2023. https://doi.org/10.1016/j.neuron.2023.01.006.","ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293."}},{"title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","article_processing_charge":"No","external_id":{"isi":["000930324700001"]},"author":[{"full_name":"Mrestani, Achmed","last_name":"Mrestani","first_name":"Achmed"},{"id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","first_name":"Katharina","full_name":"Lichter, Katharina","last_name":"Lichter"},{"first_name":"Anna Leena","full_name":"Sirén, Anna Leena","last_name":"Sirén"},{"first_name":"Manfred","full_name":"Heckmann, Manfred","last_name":"Heckmann"},{"first_name":"Mila M.","full_name":"Paul, Mila M.","last_name":"Paul"},{"first_name":"Martin","full_name":"Pauli, Martin","last_name":"Pauli"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023.","ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128.","ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128."},"article_number":"2128","date_created":"2023-02-19T23:00:56Z","date_published":"2023-01-21T00:00:00Z","doi":"10.3390/ijms24032128","publication":"International Journal of Molecular Sciences","day":"21","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"MDPI","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program.","department":[{"_id":"PeJo"}],"file_date_updated":"2023-02-20T07:09:27Z","ddc":["570"],"date_updated":"2023-08-01T13:16:36Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"12567","issue":"3","volume":24,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"69a35dcd3e0249f902ab881b06ee2e58","file_id":"12569","success":1,"date_updated":"2023-02-20T07:09:27Z","file_size":2823025,"creator":"dernst","date_created":"2023-02-20T07:09:27Z","file_name":"2023_IJMS_Mrestani.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1422-0067"]},"intvolume":" 24","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations."}]},{"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"},{"_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"840605","name":"Coordination in constrained and natural distributed systems"}],"article_number":"113733","external_id":{"isi":["000934262700001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Faith","last_name":"Ellen","full_name":"Ellen, Faith"},{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","last_name":"Rybicki"}],"title":"Wait-free approximate agreement on graphs","citation":{"ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733","apa":"Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023).","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023.","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","date_created":"2023-02-19T23:00:55Z","doi":"10.1016/j.tcs.2023.113733","date_published":"2023-02-28T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Theoretical Computer Science","day":"28","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"12566","file_date_updated":"2023-02-20T07:30:20Z","department":[{"_id":"DaAl"}],"date_updated":"2023-08-01T13:17:20Z","ddc":["000"],"scopus_import":"1","intvolume":" 948","month":"02","abstract":[{"text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"2","volume":948,"publication_status":"published","publication_identifier":{"issn":["0304-3975"]},"language":[{"iso":"eng"}],"file":[{"checksum":"b27c5290f2f1500c403494364ee39c9f","file_id":"12570","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-02-20T07:30:20Z","file_name":"2023_TheoreticalCompScience_Alistarh.pdf","creator":"dernst","date_updated":"2023-02-20T07:30:20Z","file_size":602333}]},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"12681","file_date_updated":"2023-02-27T09:23:02Z","department":[{"_id":"BjHo"}],"ddc":["530"],"date_updated":"2023-08-01T13:19:47Z","intvolume":" 55","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The dissolution of minute concentration of polymers in wall-bounded flows is well-known for its unparalleled ability to reduce turbulent friction drag. Another phenomenon, elasto-inertial turbulence (EIT), has been far less studied even though elastic instabilities have already been observed in dilute polymer solutions before the discovery of polymer drag reduction. EIT is a chaotic state driven by polymer dynamics that is observed across many orders of magnitude in Reynolds number. It involves energy transfer from small elastic scales to large flow scales. The investigation of the mechanisms of EIT offers the possibility to better understand other complex phenomena such as elastic turbulence and maximum drag reduction. In this review, we survey recent research efforts that are advancing the understanding of the dynamics of EIT. We highlight the fundamental differences between EIT and Newtonian/inertial turbulence from the perspective of experiments, numerical simulations, instabilities, and coherent structures. Finally, we discuss the possible links between EIT and elastic turbulence and polymer drag reduction, as well as the remaining challenges in unraveling the self-sustaining mechanism of EIT."}],"volume":55,"issue":"1","language":[{"iso":"eng"}],"file":[{"file_name":"2023_AnnReviewFluidMech_Dubief.pdf","date_created":"2023-02-27T09:23:02Z","creator":"dernst","file_size":4036706,"date_updated":"2023-02-27T09:23:02Z","success":1,"checksum":"2666aa3af2a25252d35eb8681d3edff7","file_id":"12690","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1545-4479"],"issn":["0066-4189"]},"title":"Elasto-inertial turbulence","article_processing_charge":"No","external_id":{"isi":["000915418100026"]},"author":[{"full_name":"Dubief, Yves","last_name":"Dubief","first_name":"Yves"},{"first_name":"Vincent E.","full_name":"Terrapon, Vincent E.","last_name":"Terrapon"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Dubief, Yves, et al. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics, vol. 55, no. 1, Annual Reviews, 2023, pp. 675–705, doi:10.1146/annurev-fluid-032822-025933.","short":"Y. Dubief, V.E. Terrapon, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 675–705.","ieee":"Y. Dubief, V. E. Terrapon, and B. Hof, “Elasto-inertial turbulence,” Annual Review of Fluid Mechanics, vol. 55, no. 1. Annual Reviews, pp. 675–705, 2023.","ama":"Dubief Y, Terrapon VE, Hof B. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 2023;55(1):675-705. doi:10.1146/annurev-fluid-032822-025933","apa":"Dubief, Y., Terrapon, V. E., & Hof, B. (2023). Elasto-inertial turbulence. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-032822-025933","chicago":"Dubief, Yves, Vincent E. Terrapon, and Björn Hof. “Elasto-Inertial Turbulence.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-032822-025933.","ista":"Dubief Y, Terrapon VE, Hof B. 2023. Elasto-inertial turbulence. Annual Review of Fluid Mechanics. 55(1), 675–705."},"oa":1,"publisher":"Annual Reviews","quality_controlled":"1","acknowledgement":"Part of the material presented here is based upon work supported by the National Science Foundation CBET (Chemical, Bioengineering, Environmental and Transport Systems) award 1805636 (to Y.D.), the Binational Science Foundation award 2016145 (to Y.D. and Victor Steinberg), a FRIA (Fund for Research Training in Industry and Agriculture) grant of the Belgian F.R.S.-FNRS (National Fund for Scientific Research) (to V.E.T.), the Marie Curie FP7 Career Integration grant PCIG10-GA-2011-304073 (to V.E.T.), and the Fonds spéciaux pour la recherche grant C-13/19 of the University of Liege (to V.E.T.). Computational resources have been provided by the Consortium des Équipements de Calcul Intensif (CECI) funded by the Belgian F.R.S.-FNRS, the Vermont Advanced Computing Center (VACC), the Partnership for Advanced Computing in Europe (PRACE), and the Tier-1 supercomputer of the Fédération Wallonie-Bruxelles funded by the Walloon Region (grant agreement 117545).","date_created":"2023-02-26T23:01:01Z","date_published":"2023-01-19T00:00:00Z","doi":"10.1146/annurev-fluid-032822-025933","page":"675-705","publication":"Annual Review of Fluid Mechanics","day":"19","year":"2023","isi":1,"has_accepted_license":"1"},{"file_date_updated":"2023-02-27T09:35:52Z","department":[{"_id":"BjHo"}],"ddc":["530"],"date_updated":"2023-08-01T13:20:30Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"12682","volume":55,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12691","checksum":"f99ef30f76cabc9e5e1946b380c16db4","file_size":4769537,"date_updated":"2023-02-27T09:35:52Z","creator":"dernst","file_name":"2023_AnnReviewFluidMech_Avila.pdf","date_created":"2023-02-27T09:35:52Z"}],"publication_status":"published","publication_identifier":{"issn":["0066-4189"]},"intvolume":" 55","month":"01","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Since the seminal studies by Osborne Reynolds in the nineteenth century, pipe flow has served as a primary prototype for investigating the transition to turbulence in wall-bounded flows. Despite the apparent simplicity of this flow, various facets of this problem have occupied researchers for more than a century. Here we review insights from three distinct perspectives: (a) stability and susceptibility of laminar flow, (b) phase transition and spatiotemporal dynamics, and (c) dynamical systems analysis of the Navier—Stokes equations. We show how these perspectives have led to a profound understanding of the onset of turbulence in pipe flow. Outstanding open points, applications to flows of complex fluids, and similarities with other wall-bounded flows are discussed.","lang":"eng"}],"title":"Transition to turbulence in pipe flow","external_id":{"isi":["000915418100023"]},"article_processing_charge":"No","author":[{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"first_name":"Dwight","last_name":"Barkley","full_name":"Barkley, Dwight"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Avila, Marc, Dwight Barkley, and Björn Hof. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics. Annual Reviews, 2023. https://doi.org/10.1146/annurev-fluid-120720-025957.","ista":"Avila M, Barkley D, Hof B. 2023. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 55, 575–602.","mla":"Avila, Marc, et al. “Transition to Turbulence in Pipe Flow.” Annual Review of Fluid Mechanics, vol. 55, Annual Reviews, 2023, pp. 575–602, doi:10.1146/annurev-fluid-120720-025957.","ama":"Avila M, Barkley D, Hof B. Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. 2023;55:575-602. doi:10.1146/annurev-fluid-120720-025957","apa":"Avila, M., Barkley, D., & Hof, B. (2023). Transition to turbulence in pipe flow. Annual Review of Fluid Mechanics. Annual Reviews. https://doi.org/10.1146/annurev-fluid-120720-025957","short":"M. Avila, D. Barkley, B. Hof, Annual Review of Fluid Mechanics 55 (2023) 575–602.","ieee":"M. Avila, D. Barkley, and B. Hof, “Transition to turbulence in pipe flow,” Annual Review of Fluid Mechanics, vol. 55. Annual Reviews, pp. 575–602, 2023."},"project":[{"grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows","_id":"238598C6-32DE-11EA-91FC-C7463DDC885E"}],"date_created":"2023-02-26T23:01:01Z","doi":"10.1146/annurev-fluid-120720-025957","date_published":"2023-01-19T00:00:00Z","page":"575-602","publication":"Annual Review of Fluid Mechanics","day":"19","year":"2023","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Annual Reviews","quality_controlled":"1","acknowledgement":"The authors are very grateful to Laurette Tuckerman for her helpful comments. This work was supported by grants from the Simons Foundation (grant numbers 662985, D.B., and 662960, B.H.) and the Priority Programme “SPP 1881: Turbulent Superstructures” of the Deutsche Forschungsgemeinschaft (grant number AV120/3-2 to M.A.)."},{"_id":"12708","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["540"],"date_updated":"2023-08-01T13:28:39Z","file_date_updated":"2023-03-07T09:19:41Z","department":[{"_id":"AnSa"}],"oa_version":"Published Version","abstract":[{"text":"Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.","lang":"eng"}],"intvolume":" 19","month":"02","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12711","checksum":"af95aa18b9b01e32fb8f13477c0e2687","file_size":3581939,"date_updated":"2023-03-07T09:19:41Z","creator":"cchlebak","file_name":"2023_SoftMatter_Araujo.pdf","date_created":"2023-03-07T09:19:41Z"}],"publication_status":"published","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"ec_funded":1,"volume":19,"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e.","ieee":"N. A. M. Araújo et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e","chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e.","ista":"Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704."},"title":"Steering self-organisation through confinement","external_id":{"isi":["000940388100001"],"arxiv":["2204.10059"]},"article_processing_charge":"No","author":[{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"full_name":"Janssen, Liesbeth M.C.","last_name":"Janssen","first_name":"Liesbeth M.C."},{"last_name":"Barois","full_name":"Barois, Thomas","first_name":"Thomas"},{"first_name":"Guido","last_name":"Boffetta","full_name":"Boffetta, Guido"},{"first_name":"Itai","last_name":"Cohen","full_name":"Cohen, Itai"},{"full_name":"Corbetta, Alessandro","last_name":"Corbetta","first_name":"Alessandro"},{"full_name":"Dauchot, Olivier","last_name":"Dauchot","first_name":"Olivier"},{"last_name":"Dijkstra","full_name":"Dijkstra, Marjolein","first_name":"Marjolein"},{"first_name":"William M.","last_name":"Durham","full_name":"Durham, William M."},{"full_name":"Dussutour, Audrey","last_name":"Dussutour","first_name":"Audrey"},{"full_name":"Garnier, Simon","last_name":"Garnier","first_name":"Simon"},{"last_name":"Gelderblom","full_name":"Gelderblom, Hanneke","first_name":"Hanneke"},{"first_name":"Ramin","full_name":"Golestanian, Ramin","last_name":"Golestanian"},{"first_name":"Lucio","full_name":"Isa, Lucio","last_name":"Isa"},{"full_name":"Koenderink, Gijsje H.","last_name":"Koenderink","first_name":"Gijsje H."},{"first_name":"Hartmut","last_name":"Löwen","full_name":"Löwen, Hartmut"},{"last_name":"Metzler","full_name":"Metzler, Ralf","first_name":"Ralf"},{"first_name":"Marco","full_name":"Polin, Marco","last_name":"Polin"},{"last_name":"Royall","full_name":"Royall, C. Patrick","first_name":"C. Patrick"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Anupam","last_name":"Sengupta","full_name":"Sengupta, Anupam"},{"last_name":"Sykes","full_name":"Sykes, Cécile","first_name":"Cécile"},{"first_name":"Vito","last_name":"Trianni","full_name":"Trianni, Vito"},{"first_name":"Idan","full_name":"Tuval, Idan","last_name":"Tuval"},{"first_name":"Nicolas","last_name":"Vogel","full_name":"Vogel, Nicolas"},{"first_name":"Julia M.","full_name":"Yeomans, Julia M.","last_name":"Yeomans"},{"first_name":"Iker","last_name":"Zuriguel","full_name":"Zuriguel, Iker"},{"first_name":"Alvaro","last_name":"Marin","full_name":"Marin, Alvaro"},{"last_name":"Volpe","full_name":"Volpe, Giorgio","first_name":"Giorgio"}],"acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","oa":1,"publisher":"Royal Society of Chemistry","quality_controlled":"1","publication":"Soft Matter","day":"06","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2023-03-05T23:01:06Z","date_published":"2023-02-06T00:00:00Z","doi":"10.1039/d2sm01562e","page":"1695-1704"}]