[{"intvolume":" 286","month":"01","main_file_link":[{"url":"https://doi.org/10.1016/j.jfa.2024.110320","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15]."}],"ec_funded":1,"volume":286,"issue":"7","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0022-1236"],"eissn":["1096--0783"]},"status":"public","article_type":"original","type":"journal_article","_id":"14931","department":[{"_id":"RoSe"}],"date_updated":"2024-03-28T10:54:02Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","date_created":"2024-02-04T23:00:53Z","doi":"10.1016/j.jfa.2024.110320","date_published":"2024-01-24T00:00:00Z","publication":"Journal of Functional Analysis","day":"24","year":"2024","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427"}],"article_number":"110320","title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2301.04894"]},"author":[{"first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis, vol. 286, no. 7. Elsevier, 2024.","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).","apa":"Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 2024;286(7). doi:10.1016/j.jfa.2024.110320","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320."}},{"page":"183-205","date_created":"2023-01-29T23:00:58Z","doi":"10.1007/978-1-0716-2887-4_12","date_published":"2023-01-19T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"Cell Migration in Three Dimensions","day":"19","oa":1,"quality_controlled":"1","publisher":"Springer Nature","external_id":{"pmid":["36653709"]},"article_processing_charge":"No","author":[{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"first_name":"Colinda L.G.J.","last_name":"Scheele","full_name":"Scheele, Colinda L.G.J."}],"editor":[{"last_name":"Margadant","full_name":"Margadant, Coert","first_name":"Coert"}],"title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","citation":{"chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12","apa":"Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature. https://doi.org/10.1007/978-1-0716-2887-4_12"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2608,"publication_status":"published","publication_identifier":{"eisbn":["9781071628874"],"eissn":["1940-6029"],"isbn":["9781071628867"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2023-02-03T10:56:39Z","file_name":"2023_MIMB_Hannezo.pdf","date_updated":"2023-02-03T10:56:39Z","file_size":826598,"creator":"dernst","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","file_id":"12500","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","intvolume":" 2608","month":"01","abstract":[{"lang":"eng","text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis."}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"EdHa"}],"file_date_updated":"2023-02-03T10:56:39Z","date_updated":"2023-02-03T10:58:56Z","ddc":["570"],"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":"book_chapter","status":"public","_id":"12428","series_title":"MIMB"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (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."},"title":"Dissipative dynamics of an impurity with spin-orbit coupling","article_processing_charge":"No","author":[{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"full_name":"Cappellaro, Alberto","orcid":"0000-0001-6110-2359","last_name":"Cappellaro","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev"}],"article_number":"013029","project":[{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"}],"publication":"Physical Review Research","day":"20","year":"2023","has_accepted_license":"1","date_created":"2023-02-10T09:02:26Z","doi":"10.1103/physrevresearch.5.013029","date_published":"2023-01-20T00:00:00Z","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).","oa":1,"publisher":"American Physical Society","quality_controlled":"1","ddc":["530"],"date_updated":"2023-02-20T07:02:00Z","file_date_updated":"2023-02-13T10:38:10Z","department":[{"_id":"MiLe"}],"_id":"12534","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","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2023-02-13T10:38:10Z","file_size":865150,"date_created":"2023-02-13T10:38:10Z","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"6068b62874c0099628a108bb9c5c6bd2","file_id":"12546","success":1}],"publication_status":"published","publication_identifier":{"issn":["2643-1564"]},"ec_funded":1,"issue":"1","volume":5,"oa_version":"Published Version","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."}],"intvolume":" 5","month":"01","scopus_import":"1"},{"citation":{"short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Peter","full_name":"Zeller, Peter","last_name":"Zeller"},{"last_name":"Yeung","full_name":"Yeung, Jake","orcid":"0000-0003-1732-1559","first_name":"Jake","id":"123012b2-db30-11eb-b4d8-a35840c0551b"},{"last_name":"Viñas Gaza","full_name":"Viñas Gaza, Helena","first_name":"Helena"},{"first_name":"Buys Anton","last_name":"de Barbanson","full_name":"de Barbanson, Buys Anton"},{"first_name":"Vivek","last_name":"Bhardwaj","full_name":"Bhardwaj, Vivek"},{"first_name":"Maria","full_name":"Florescu, Maria","last_name":"Florescu"},{"last_name":"van der Linden","full_name":"van der Linden, Reinier","first_name":"Reinier"},{"first_name":"Alexander","full_name":"van Oudenaarden, Alexander","last_name":"van Oudenaarden"}],"article_processing_charge":"No","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Nature Genetics","page":"333-345","doi":"10.1038/s41588-022-01260-3","date_published":"2023-02-01T00:00:00Z","date_created":"2023-01-12T12:09:09Z","_id":"12158","type":"journal_article","article_type":"review","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","keyword":["Genetics"],"date_updated":"2023-02-27T07:48:24Z","ddc":["570","000"],"file_date_updated":"2023-02-27T07:46:45Z","department":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages."}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 55","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"publication_status":"published","file":[{"creator":"dernst","file_size":21484855,"date_updated":"2023-02-27T07:46:45Z","file_name":"2023_NatureGenetics_Zeller.pdf","date_created":"2023-02-27T07:46:45Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"12688","checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e"}],"language":[{"iso":"eng"}],"volume":55},{"type":"conference","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2023-01-22","end_date":"2023-01-25","location":"Florence, Italy"},"status":"public","_id":"12676","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"date_updated":"2023-02-27T09:01:16Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611977554.ch173"}],"month":"02","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","ec_funded":1,"publication_identifier":{"isbn":["9781611977554"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","last_name":"Svoboda"}],"article_processing_charge":"No","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","citation":{"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.","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.","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.","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.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","page":"4590-4605","date_published":"2023-02-01T00:00:00Z","doi":"10.1137/1.9781611977554.ch173","date_created":"2023-02-24T12:20:47Z","year":"2023","day":"01","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms"},{"year":"2023","publication":"DNA Manipulation and Analysis","day":"01","page":"33-44","date_created":"2023-03-12T23:01:02Z","doi":"10.1007/978-1-0716-3004-4_3","date_published":"2023-03-01T00:00:00Z","quality_controlled":"1","publisher":"Springer Nature","citation":{"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","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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"pmid":["36853454"]},"author":[{"first_name":"Sandra","full_name":"Arroyo-Urea, Sandra","last_name":"Arroyo-Urea"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","last_name":"Watson","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"last_name":"García-Nafría","full_name":"García-Nafría, Javier","first_name":"Javier"}],"editor":[{"first_name":"Garry","full_name":"Scarlett, Garry","last_name":"Scarlett"}],"title":"Molecular Cloning Using In Vivo DNA Assembly","publication_status":"published","publication_identifier":{"eisbn":["978-1-0716-3004-4"],"issn":["1064-3745"],"isbn":["978-1-0716-3003-7"],"eissn":["1940-6029"]},"language":[{"iso":"eng"}],"volume":2633,"abstract":[{"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.","lang":"eng"}],"oa_version":"None","pmid":1,"scopus_import":"1","alternative_title":["Methods in Molecular Biology"],"intvolume":" 2633","month":"03","place":"New York, NY, United States","date_updated":"2023-03-16T08:34:24Z","department":[{"_id":"PeJo"}],"series_title":"MIMB","_id":"12720","type":"book_chapter","status":"public"},{"_id":"12735","status":"public","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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","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."},"department":[{"_id":"DaAl"}],"title":"Fast and scalable channels in Kotlin Coroutines","author":[{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","last_name":"Koval"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"Roman","full_name":"Elizarov, Roman","last_name":"Elizarov"}],"article_processing_charge":"No","external_id":{"arxiv":["2211.04986"]},"oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"month":"02","publisher":"Association for Computing Machinery","scopus_import":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04986","open_access":"1"}],"oa":1,"day":"25","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","publication_identifier":{"isbn":["9798400700156"]},"publication_status":"published","year":"2023","doi":"10.1145/3572848.3577481","date_published":"2023-02-25T00:00:00Z","date_created":"2023-03-19T23:00:58Z","page":"107-118"},{"citation":{"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","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.","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.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","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."},"date_updated":"2023-03-20T07:57:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vitaly","full_name":"Aksenov, Vitaly","last_name":"Aksenov"},{"last_name":"Brown","full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A"},{"last_name":"Fedorov","full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander"},{"first_name":"Ilya","last_name":"Kokorin","full_name":"Kokorin, Ilya"}],"article_processing_charge":"No","title":"Unexpected scaling in path copying trees","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"_id":"12736","type":"conference_poster","conference":{"start_date":"2023-02-25","location":"Montreal, QB, Canada","end_date":"2023-03-01","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"status":"public","publication_identifier":{"isbn":["9798400700156"]},"year":"2023","publication_status":"published","day":"25","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","page":"438-440","doi":"10.1145/3572848.3577512","date_published":"2023-02-25T00:00:00Z","date_created":"2023-03-19T23:00:58Z","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"}],"oa_version":"Published Version","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.","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"main_file_link":[{"url":"https://doi.org/10.1145/3572848.3577512","open_access":"1"}],"month":"02"},{"article_number":"36","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","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","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","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."},"title":"Dynamic maintenance of monotone dynamic programs and applications","author":[{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Stefan","full_name":"Neumann, Stefan","last_name":"Neumann"},{"first_name":"Harald","full_name":"Räcke, Harald","last_name":"Räcke"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"article_processing_charge":"No","external_id":{"arxiv":["2301.01744"]},"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.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"day":"01","publication":"40th International Symposium on Theoretical Aspects of Computer Science","has_accepted_license":"1","year":"2023","doi":"10.4230/LIPIcs.STACS.2023.36","date_published":"2023-03-01T00:00:00Z","date_created":"2023-03-26T22:01:07Z","_id":"12760","status":"public","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":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","start_date":"2023-03-07","location":"Hamburg, Germany","end_date":"2023-03-09"},"ddc":["000"],"date_updated":"2023-03-27T06:46:27Z","file_date_updated":"2023-03-27T06:37:22Z","department":[{"_id":"MoHe"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"03","intvolume":" 254","alternative_title":["LIPIcs"],"scopus_import":"1","file":[{"success":1,"file_id":"12769","checksum":"22141ab8bc55188e2dfff665e5daecbd","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_LIPICS_HenzingerM.pdf","date_created":"2023-03-27T06:37:22Z","creator":"dernst","file_size":872706,"date_updated":"2023-03-27T06:37:22Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"publication_status":"published","volume":254},{"year":"2023","has_accepted_license":"1","day":"10","page":"178","date_created":"2023-03-08T15:19:45Z","date_published":"2023-03-10T00:00:00Z","doi":"10.15479/at:ista:12716","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"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.","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.","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.","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"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Burnett, Laura","orcid":"0000-0002-8937-410X","last_name":"Burnett"}],"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","project":[{"call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","name":"Circuits of Visual Attention"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","file_id":"12717","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2023-03-08T15:08:46Z","file_name":"Burnett_Thesis_2023.docx","creator":"lburnett","date_updated":"2023-03-08T15:08:46Z","file_size":23029260},{"success":1,"checksum":"cebc77705288bf4382db9b3541483cd0","file_id":"12718","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Burnett_Thesis_2023_pdfA.pdf","date_created":"2023-03-08T15:08:46Z","creator":"lburnett","file_size":11959869,"date_updated":"2023-03-08T15:08:46Z"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","date_updated":"2023-04-05T10:59:04Z","supervisor":[{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","last_name":"Jösch"}],"ddc":["599","573"],"file_date_updated":"2023-03-08T15:08:46Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"_id":"12716","type":"dissertation","status":"public"},{"doi":"10.1007/978-3-031-30820-8_32","date_published":"2023-04-20T00:00:00Z","date_created":"2023-04-20T08:22:53Z","page":"535-540","day":"20","publication":"Tools and Algorithms for the Construction and Analysis of Systems","has_accepted_license":"1","year":"2023","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","title":"Bubaak: Runtime monitoring of program verifiers","author":[{"first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 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."},"project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"volume":13994,"ec_funded":1,"file":[{"file_name":"2023_LNCS_Chalupa.pdf","date_created":"2023-04-25T06:58:36Z","creator":"dernst","file_size":16096413,"date_updated":"2023-04-25T06:58:36Z","success":1,"checksum":"120d2c2a38384058ad0630fdf8288312","file_id":"12864","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9783031308208"],"eissn":["1611-3349"],"isbn":["9783031308192"],"issn":["0302-9743"]},"publication_status":"published","month":"04","intvolume":" 13994","alternative_title":["LNCS"],"oa_version":"Published Version","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."}],"department":[{"_id":"ToHe"}],"file_date_updated":"2023-04-25T06:58:36Z","ddc":["000"],"date_updated":"2023-04-25T07:02:43Z","status":"public","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","location":"Paris, France","end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"_id":"12854"},{"type":"preprint","project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"status":"public","_id":"12846","article_number":"2303.14555","article_processing_charge":"No","external_id":{"arxiv":["2303.14555"]},"author":[{"first_name":"Albert","full_name":"Chern, Albert","last_name":"Chern"},{"first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","full_name":"Ishida, Sadashige"}],"title":"Area formula for spherical polygons via prequantization","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"citation":{"mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","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","short":"A. Chern, S. Ishida, ArXiv (n.d.).","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. .","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555."},"date_updated":"2023-04-25T06:51:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.14555"}],"month":"03","abstract":[{"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.","lang":"eng"}],"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).","oa_version":"Preprint","date_created":"2023-04-18T19:16:06Z","doi":"10.48550/arXiv.2303.14555","date_published":"2023-03-25T00:00:00Z","publication_status":"submitted","year":"2023","publication":"arXiv","language":[{"iso":"eng"}],"day":"25"},{"page":"260-281","doi":"10.1007/978-3-031-30826-0_15","date_published":"2023-04-20T00:00:00Z","date_created":"2023-04-20T08:29:42Z","has_accepted_license":"1","year":"2023","day":"20","publication":"Fundamental Approaches to Software Engineering","publisher":"Springer Nature","quality_controlled":"1","oa":1,"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.","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek"},{"first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian","last_name":"Mühlböck"},{"last_name":"Muroya Lei","full_name":"Muroya Lei, Stefanie","first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"article_processing_charge":"No","title":"Vamos: Middleware for best-effort third-party monitoring","citation":{"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.","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.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"volume":13991,"related_material":{"record":[{"relation":"earlier_version","id":"12407","status":"public"}]},"ec_funded":1,"publication_identifier":{"eisbn":["9783031308260"],"issn":["0302-9743"],"isbn":["9783031308253"],"eissn":["1611-3349"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"17a7c8e08be609cf2408d37ea55e322c","file_id":"12865","success":1,"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"}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"month":"04","intvolume":" 13991","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\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"}],"oa_version":"Published Version","department":[{"_id":"ToHe"}],"file_date_updated":"2023-04-25T07:16:36Z","date_updated":"2023-04-25T07:19:07Z","ddc":["000"],"type":"conference","conference":{"start_date":"2023-04-22","end_date":"2023-04-27","location":"Paris, France","name":"FASE: Fundamental Approaches to Software Engineering"},"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":"12856"},{"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.","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2023","day":"27","page":"38","date_published":"2023-01-27T00:00:00Z","doi":"10.15479/AT:ISTA:12407","date_created":"2023-01-27T03:18:08Z","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"citation":{"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.","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","last_name":"Mühlböck"},{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","first_name":"Stefanie","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"}],"article_processing_charge":"No","title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","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"}],"oa_version":"Published Version","alternative_title":["IST Austria Technical Report"],"month":"01","publication_identifier":{"eissn":["2664-1690"]},"publication_status":"published","file":[{"success":1,"checksum":"55426e463fdeafe9777fc3ff635154c7","file_id":"12408","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"main.pdf","date_created":"2023-01-27T03:18:34Z","creator":"fmuehlbo","file_size":662409,"date_updated":"2023-01-27T03:18:34Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","id":"12856","status":"public"}]},"ec_funded":1,"_id":"12407","type":"technical_report","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","keyword":["runtime monitoring","best effort","third party"],"date_updated":"2023-04-25T07:19:06Z","ddc":["005"],"file_date_updated":"2023-01-27T03:18:34Z","department":[{"_id":"ToHe"}]},{"type":"book_chapter","status":"public","_id":"12866","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"},{"first_name":"Chad","full_name":"Beyer, Chad","last_name":"Beyer"}],"department":[{"_id":"TiVo"}],"editor":[{"first_name":"Bonnie","full_name":"Halpern-Felsher, Bonnie","last_name":"Halpern-Felsher"}],"title":"Altered childhood brain development in autism and epilepsy","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.","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.","short":"C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.","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","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","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."},"date_updated":"2023-04-25T09:25:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","edition":"1","quality_controlled":"1","alternative_title":["Vol. 1: Biological Development and Physical Health"],"publisher":"Elsevier","month":"02","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","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","publication_status":"published","year":"2023","publication_identifier":{"isbn":["9780128188736"]},"language":[{"iso":"eng"}],"publication":"Encyclopedia of Child and Adolescent Health","day":"01"},{"file":[{"date_created":"2023-04-07T06:16:06Z","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","date_updated":"2023-04-07T06:16:06Z","file_size":9881969,"creator":"cchlebak","file_id":"12814","checksum":"35b5997d2b0acb461f9d33d073da0df5","embargo":"2024-04-07","content_type":"application/pdf","embargo_to":"open_access","access_level":"closed","relation":"main_file"},{"content_type":"application/pdf","relation":"source_file","access_level":"closed","file_id":"12815","checksum":"81198f63c294890f6d58e8b29782efdc","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"},{"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,"file_id":"12816","checksum":"0317bf7f457bb585f99d453ffa69eb53","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"month":"04","alternative_title":["ISTA Thesis"],"ddc":["570"],"supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"}],"date_updated":"2023-04-26T12:16:56Z","file_date_updated":"2023-04-07T06:18:05Z","department":[{"_id":"GradSch"},{"_id":"RySh"}],"_id":"12809","status":"public","type":"dissertation","day":"06","has_accepted_license":"1","year":"2023","date_published":"2023-04-06T00:00:00Z","doi":"10.15479/at:ista:12809","date_created":"2023-04-06T07:54:09Z","page":"115","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi: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.","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.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","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."},"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","author":[{"first_name":"Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","last_name":"Alcarva","full_name":"Alcarva, Catarina"}],"article_processing_charge":"No","project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}]},{"extern":"1","date_updated":"2023-05-08T10:52:49Z","department":[{"_id":"XiFe"}],"_id":"12668","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1474-760X"]},"publication_status":"published","volume":24,"oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"month":"01","intvolume":" 24","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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)."},"title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","author":[{"first_name":"Long","full_name":"Zhao, Long","last_name":"Zhao"},{"first_name":"Yiman","last_name":"Yang","full_name":"Yang, Yiman"},{"first_name":"Jinchao","full_name":"Chen, Jinchao","last_name":"Chen"},{"first_name":"Xuelei","last_name":"Lin","full_name":"Lin, Xuelei"},{"first_name":"Hao","full_name":"Zhang, Hao","last_name":"Zhang"},{"last_name":"Wang","full_name":"Wang, Hao","first_name":"Hao"},{"full_name":"Wang, Hongzhe","last_name":"Wang","first_name":"Hongzhe"},{"first_name":"Xiaomin","last_name":"Bie","full_name":"Bie, Xiaomin"},{"first_name":"Jiafu","full_name":"Jiang, Jiafu","last_name":"Jiang"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"},{"last_name":"Fu","full_name":"Fu, Xiangdong","first_name":"Xiangdong"},{"first_name":"Xiansheng","last_name":"Zhang","full_name":"Zhang, Xiansheng"},{"first_name":"Zhuo","full_name":"Du, Zhuo","last_name":"Du"},{"full_name":"Xiao, Jun","last_name":"Xiao","first_name":"Jun"}],"article_processing_charge":"No","external_id":{"pmid":["36639687"]},"article_number":"7","day":"13","publication":"Genome Biology","year":"2023","date_published":"2023-01-13T00:00:00Z","doi":"10.1186/s13059-022-02844-2","date_created":"2023-02-23T09:13:49Z","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","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.","page":"1768-1776","date_created":"2023-05-22T08:02:02Z","date_published":"2023-06-02T00:00:00Z","doi":"10.1145/3564246.3585113","year":"2023","publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","day":"02","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","grant_number":"M03073","name":"Learning and triangulating manifolds via collapses"}],"article_processing_charge":"No","external_id":{"arxiv":["2303.04014"]},"author":[{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"},{"last_name":"Wintraecken","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","citation":{"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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/2303.04014","open_access":"1"}],"month":"06","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"}],"oa_version":"Preprint","ec_funded":1,"publication_status":"published","publication_identifier":{"isbn":["9781450399135"]},"language":[{"iso":"eng"}],"conference":{"name":"STOC: Symposium on Theory of Computing","location":"Orlando, FL, United States","end_date":"2023-06-23","start_date":"2023-06-20"},"type":"conference","status":"public","_id":"13048","department":[{"_id":"HeEd"}],"date_updated":"2023-05-22T08:15:19Z"},{"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","main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=_eTZBs-yedr"}],"oa":1,"quality_controlled":"1","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":[{"id":"13074","status":"public","relation":"dissertation_contains"}]},"date_published":"2023-05-01T00:00:00Z","_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","location":"Kigali, Rwanda ","end_date":"2023-05-05","start_date":"2023-05-01"},"type":"conference","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.","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 .","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 .","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 .","short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations ."},"title":"CrAM: A Compression-Aware Minimizer","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"external_id":{"arxiv":["2207.14200"]},"article_processing_charge":"No","author":[{"first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra","last_name":"Peste"},{"full_name":"Vladu, Adrian","last_name":"Vladu","first_name":"Adrian"},{"id":"47beb3a5-07b5-11eb-9b87-b108ec578218","first_name":"Eldar","full_name":"Kurtic, Eldar","last_name":"Kurtic"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}]},{"department":[{"_id":"KrPi"}],"date_updated":"2023-06-19T08:03:37Z","status":"public","conference":{"name":"PKC: Public-Key Cryptography","start_date":"2023-05-07","location":"Atlanta, GA, United States","end_date":"2023-05-10"},"type":"conference","_id":"13143","volume":13940,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031313677"]},"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":[{"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.","lang":"eng"}],"title":"Certifying giant nonprimes","article_processing_charge":"No","author":[{"first_name":"Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","full_name":"Hoffmann, Charlotte","last_name":"Hoffmann"},{"first_name":"Pavel","last_name":"Hubáček","full_name":"Hubáček, Pavel"},{"last_name":"Kamath","full_name":"Kamath, Chethan","first_name":"Chethan"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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."},"date_created":"2023-06-18T22:00:47Z","date_published":"2023-05-02T00:00:00Z","doi":"10.1007/978-3-031-31368-4_19","page":"530-553","publication":"Public-Key Cryptography - PKC 2023","day":"02","year":"2023","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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."}]