[{"volume":527,"date_created":"2024-01-22T08:22:17Z","date_updated":"2024-01-23T12:33:50Z","author":[{"full_name":"Kramarenko, Ivan","id":"9a9394cb-3200-11ee-973b-f5ba2a8b16e4","first_name":"Ivan","last_name":"Kramarenko"},{"last_name":"Kerutt","first_name":"J","full_name":"Kerutt, J"},{"last_name":"Verhamme","first_name":"A","full_name":"Verhamme, A"},{"last_name":"Oesch","first_name":"P A","full_name":"Oesch, P A"},{"first_name":"L","last_name":"Barrufet","full_name":"Barrufet, L"},{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"last_name":"Kusakabe","first_name":"H","full_name":"Kusakabe, H"},{"full_name":"Goovaerts, I","first_name":"I","last_name":"Goovaerts"},{"first_name":"T T","last_name":"Thai","full_name":"Thai, T T"}],"publisher":"Oxford University Press","department":[{"_id":"GradSch"},{"_id":"JoMa"}],"publication_status":"published","acknowledgement":"We thank the anonymous referee for the constructive feedback that helped to improve the manuscript. We thank Michael Maseda, Daniel Schaerer, Charlotte Simmonds, and Rashmi Gottumukkala for useful comments and productive discussions. We also thank the organizers and participants of the 24th MUSE Science Busy Week in Leiden. IGK acknowledges an Excellence Master Fellowship granted by the Faculty of Science of the University of Geneva. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant number 200020_207349 and SNSF Professorship grant number 190079. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant number 140. This paper is based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 094.A-0289(B), 095.A-0010(A), 096.A-0045(A), 096.A-0045(B), 094.A-0205, 095.A-0240, 096.A-0090, 097.A-0160, and 098.A-0017. We made extensive use of several open-source software packages and we are thankful to the respective authors for sharing their work: NUMPY (Harris et al. 2020), ASTROPY (Astropy Collaboration 2022), MATPLOTLIB (Hunter 2007), IPYTHON (Perez & Granger 2007), and TOPCAT (Taylor 2005).","year":"2024","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2024-01-23T12:30:45Z","language":[{"iso":"eng"}],"doi":"10.1093/mnras/stad3853","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.07044"]},"publication_identifier":{"issn":["0035-8711"],"eissn":["1365-2966"]},"month":"02","oa_version":"Published Version","file":[{"file_id":"14879","relation":"main_file","success":1,"checksum":"9d02df4035c4951cf63dee0db1e462e9","date_created":"2024-01-23T12:30:45Z","date_updated":"2024-01-23T12:30:45Z","access_level":"open_access","file_name":"2024_MNAstronomSoc_Kramarenko.pdf","creator":"dernst","content_type":"application/pdf","file_size":4521738}],"intvolume":" 527","title":"Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape","status":"public","ddc":["520"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14852","issue":"4","abstract":[{"lang":"eng","text":"The physical conditions giving rise to high escape fractions of ionizing radiation (LyC fesc) in star-forming galaxies – most likely protagonists of cosmic reionization – are not yet fully understood. Using the VLT/MUSE observations of ∼1400 Ly α emitters at 2.9 < z < 6.7, we compare stacked rest-frame UV spectra of candidates for LyC leakers and non-leakers selected based on their Ly α profiles. We find that the stacks of potential LyC leakers, i.e. galaxies with narrow, symmetric Ly α profiles with small peak separation, generally show (i) strong nebular O iii]λ1666, [Si iii]λ1883, and [C iii]λ1907 +C iii]λ1909 emission, indicating a high-ionization state of the interstellar medium (ISM); (ii) high equivalent widths of He iiλ1640 (∼1 − 3 Å), suggesting the presence of hard ionizing radiation fields; (iii) Si ii*λ1533 emission, revealing substantial amounts of neutral hydrogen off the line of sight; (iv) high C ivλλ1548,1550 to [C iii]λ1907 +C iii]λ1909 ratios (C iv/C iii] ≳0.75) , signalling the presence of low column density channels in the ISM. In contrast, the stacks with broad, asymmetric Ly α profiles with large peak separation show weak nebular emission lines, low He iiλ1640 equivalent widths (≲1 Å), and low C iv/C iii] (≲0.25), implying low-ionization states and high-neutral hydrogen column densities. Our results suggest that C iv/C iii] might be sensitive to the physical conditions that govern LyC photon escape, providing a promising tool for identification of ionizing sources among star-forming galaxies in the epoch of reionization."}],"type":"journal_article","date_published":"2024-02-01T00:00:00Z","page":"9853-9871","article_type":"original","citation":{"ieee":"I. Kramarenko et al., “Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape,” Monthly Notices of the Royal Astronomical Society, vol. 527, no. 4. Oxford University Press, pp. 9853–9871, 2024.","apa":"Kramarenko, I., Kerutt, J., Verhamme, A., Oesch, P. A., Barrufet, L., Matthee, J. J., … Thai, T. T. (2024). Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stad3853","ista":"Kramarenko I, Kerutt J, Verhamme A, Oesch PA, Barrufet L, Matthee JJ, Kusakabe H, Goovaerts I, Thai TT. 2024. Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 527(4), 9853–9871.","ama":"Kramarenko I, Kerutt J, Verhamme A, et al. Linking UV spectral properties of MUSE Ly α emitters at z ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 2024;527(4):9853-9871. doi:10.1093/mnras/stad3853","chicago":"Kramarenko, Ivan, J Kerutt, A Verhamme, P A Oesch, L Barrufet, Jorryt J Matthee, H Kusakabe, I Goovaerts, and T T Thai. “Linking UV Spectral Properties of MUSE Ly α Emitters at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stad3853.","short":"I. Kramarenko, J. Kerutt, A. Verhamme, P.A. Oesch, L. Barrufet, J.J. Matthee, H. Kusakabe, I. Goovaerts, T.T. Thai, Monthly Notices of the Royal Astronomical Society 527 (2024) 9853–9871.","mla":"Kramarenko, Ivan, et al. “Linking UV Spectral Properties of MUSE Ly α Emitters at z ≳ 3 to Lyman Continuum Escape.” Monthly Notices of the Royal Astronomical Society, vol. 527, no. 4, Oxford University Press, 2024, pp. 9853–71, doi:10.1093/mnras/stad3853."},"publication":"Monthly Notices of the Royal Astronomical Society","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","keyword":["Space and Planetary Science","Astronomy and Astrophysics"]},{"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896","name":"Causes and consequences of population fragmentation"},{"name":"Polygenic Adaptation in a Metapopulation","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","grant_number":"26380"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Polechova, Jitka","first_name":"Jitka","last_name":"Polechova"},{"last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"}],"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14711","month":"01","publication_identifier":{"issn":["2663 - 337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"year":"2024","date_created":"2023-12-26T22:49:53Z","date_updated":"2024-01-26T12:00:54Z","author":[{"full_name":"Olusanya, Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314","first_name":"Oluwafunmilola O","last_name":"Olusanya"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10658"},{"relation":"part_of_dissertation","status":"public","id":"10787"},{"relation":"part_of_dissertation","status":"public","id":"14732"}]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2024-01-03T18:31:34Z","ec_funded":1,"page":"183","citation":{"ama":"Olusanya OO. Local adaptation, genetic load and extinction in metapopulations. 2024. doi:10.15479/at:ista:14711","apa":"Olusanya, O. O. (2024). Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14711","ieee":"O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,” Institute of Science and Technology Austria, 2024.","ista":"Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations. Institute of Science and Technology Austria.","short":"O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations, Institute of Science and Technology Austria, 2024.","mla":"Olusanya, Oluwafunmilola O. Local Adaptation, Genetic Load and Extinction in Metapopulations. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14711.","chicago":"Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction in Metapopulations.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14711."},"date_published":"2024-01-19T00:00:00Z","day":"19","has_accepted_license":"1","article_processing_charge":"No","title":"Local adaptation, genetic load and extinction in metapopulations","status":"public","ddc":["576"],"_id":"14711","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"date_created":"2024-01-03T18:30:13Z","date_updated":"2024-01-03T18:30:13Z","checksum":"de179b1c6758f182ff0c70d8b38c1501","file_id":"14730","relation":"source_file","creator":"oolusany","file_size":16986244,"content_type":"application/zip","file_name":"FinalSubmission_Thesis_OLUSANYA.zip","access_level":"closed"},{"access_level":"open_access","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","content_type":"application/pdf","file_size":6460403,"creator":"oolusany","relation":"main_file","file_id":"14731","checksum":"0e331585e3cd4823320aab4e69e64ccf","success":1,"date_created":"2024-01-03T18:31:34Z","date_updated":"2024-01-03T18:31:34Z"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.","lang":"eng"}]},{"publication_identifier":{"issn":["2663 - 337X"]},"month":"01","doi":"10.15479/at:ista:14821","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"ec_funded":1,"file_date_updated":"2024-01-19T11:04:05Z","author":[{"full_name":"Chiossi, Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","last_name":"Chiossi","first_name":"Heloisa"}],"date_updated":"2024-02-01T09:50:29Z","date_created":"2024-01-16T14:25:21Z","year":"2024","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"19","date_published":"2024-01-19T00:00:00Z","citation":{"chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14821.","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","mla":"Chiossi, Heloisa S. C. Adaptive Hierarchical Representations in the Hippocampus. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14821.","apa":"Chiossi, H. S. C. (2024). Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14821","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:10.15479/at:ista:14821"},"page":"89","type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"file_id":"14838","relation":"source_file","checksum":"d3fa3de1abd5af5204c13e9d55375615","date_updated":"2024-01-19T11:04:05Z","date_created":"2024-01-19T11:04:05Z","access_level":"closed","file_name":"PhD_Thesis_190124.docx","creator":"hchiossi","file_size":8656268,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","date_created":"2024-01-19T11:03:59Z","date_updated":"2024-01-19T11:03:59Z","file_id":"14839","embargo":"2025-01-19","relation":"main_file","creator":"hchiossi","content_type":"application/pdf","file_size":6567275,"access_level":"closed","file_name":"PhD_Thesis_190124.pdf","embargo_to":"open_access"}],"_id":"14821","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Adaptive hierarchical representations in the hippocampus","ddc":["570"],"status":"public"},{"file_date_updated":"2024-02-05T10:06:35Z","author":[{"full_name":"Nomura, Keiko","last_name":"Nomura","first_name":"Keiko"},{"first_name":"Simon","last_name":"Rella","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon"},{"full_name":"Merritt, Haily","first_name":"Haily","last_name":"Merritt"},{"full_name":"Baltussen, Mathieu","last_name":"Baltussen","first_name":"Mathieu"},{"first_name":"Darcy","last_name":"Bird","full_name":"Bird, Darcy"},{"full_name":"Tjuka, Annika","last_name":"Tjuka","first_name":"Annika"},{"full_name":"Falk, Dan","first_name":"Dan","last_name":"Falk"}],"date_created":"2024-01-30T11:58:02Z","date_updated":"2024-02-05T10:10:27Z","volume":18,"acknowledgement":"The authors would like to thank the special issue co-editors, Marco Janssen and Xiao-Shan Yap, and the anonymous reviewers for their comments that helped improve the manuscript. The paper also benefited from suggestions by other author participants in this special issue. We would also like to thank the 2022 Santa Fe Institute Complex Systems Summer School for providing space to initiate this study.","year":"2024","publication_status":"published","publisher":"Ubiquity Press","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"month":"01","publication_identifier":{"issn":["1875-0281"]},"doi":"10.5334/ijc.1275","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"Global services like navigation, communication, and Earth observation have increased dramatically in the 21st century due to advances in outer space industries. But as orbits become increasingly crowded with both satellites and inevitable space debris pollution, continued operations become endangered by the heightened risks of debris collisions in orbit. Kessler Syndrome is the term for when a critical threshold of orbiting debris triggers a runaway positive feedback loop of debris collisions, creating debris congestion that can render orbits unusable. As this potential tipping point becomes more widely recognized, there have been renewed calls for debris mitigation and removal. Here, we combine complex systems and social-ecological systems approaches to study how these efforts may affect space debris accumulation and the likelihood of reaching Kessler Syndrome. Specifically, we model how debris levels are affected by future launch rates, cleanup activities, and collisions between extant debris. We contextualize and interpret our dynamic model within a discussion of existing space debris governance and other social, economic, and geopolitical factors that may influence effective collective management of the orbital commons. In line with previous studies, our model finds that debris congestion may be reached in less than 200 years, though a holistic management strategy combining removal and mitigation actions can avoid such outcomes while continuing space activities. Moreover, although active debris removal may be particularly effective, the current lack of market and governance support may impede its implementation. Research into these critical dynamics and the multi-faceted variables that influence debris outcomes can support policymakers in curating impactful governance strategies and realistic transition pathways to sustaining debris-free orbits. Overall, our study is useful for communicating about space debris sustainability in policy and education settings by providing an exploration of policy portfolio options supported by a simple and clear social-ecological modeling approach."}],"issue":"1","type":"journal_article","file":[{"relation":"main_file","file_id":"14939","date_updated":"2024-02-05T10:06:35Z","date_created":"2024-02-05T10:06:35Z","checksum":"b80ebc889033c365d8f8c05a0c655382","success":1,"file_name":"2023_IntJourCommons_Nomura.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1305786,"creator":"dernst"}],"oa_version":"Published Version","_id":"14901","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Tipping points of space debris in low earth orbit","ddc":["550"],"intvolume":" 18","day":"11","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","keyword":["Sociology and Political Science"],"date_published":"2024-01-11T00:00:00Z","publication":"International Journal of the Commons","citation":{"ista":"Nomura K, Rella S, Merritt H, Baltussen M, Bird D, Tjuka A, Falk D. 2024. Tipping points of space debris in low earth orbit. International Journal of the Commons. 18(1).","ieee":"K. Nomura et al., “Tipping points of space debris in low earth orbit,” International Journal of the Commons, vol. 18, no. 1. Ubiquity Press, 2024.","apa":"Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., & Falk, D. (2024). Tipping points of space debris in low earth orbit. International Journal of the Commons. Ubiquity Press. https://doi.org/10.5334/ijc.1275","ama":"Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low earth orbit. International Journal of the Commons. 2024;18(1). doi:10.5334/ijc.1275","chicago":"Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird, Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons. Ubiquity Press, 2024. https://doi.org/10.5334/ijc.1275.","mla":"Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons, vol. 18, no. 1, Ubiquity Press, 2024, doi:10.5334/ijc.1275.","short":"K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024)."},"article_type":"original"},{"doi":"10.15479/AT:ISTA:14705","date_published":"2024-01-02T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"short":"M.N. Elkrewi, (2024).","mla":"Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705.","chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14705","ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14705."},"project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction"}],"article_processing_charge":"No","has_accepted_license":"1","day":"02","month":"01","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"related_material":{"record":[{"id":"15009","status":"public","relation":"used_in_publication"}]},"contributor":[{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","contributor_type":"researcher","last_name":"Bett","first_name":"Vincent K"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","contributor_type":"project_member","last_name":"Macon"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","contributor_type":"supervisor"},{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","contributor_type":"researcher","last_name":"Elkrewi","first_name":"Marwan N"}],"author":[{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N"}],"file":[{"checksum":"bdaf1392867786634ec5466d528c36ca","success":1,"date_created":"2023-12-22T13:54:21Z","date_updated":"2023-12-22T13:54:21Z","relation":"main_file","file_id":"14707","content_type":"text/plain","file_size":847,"creator":"melkrewi","access_level":"open_access","file_name":"readme.txt.txt"},{"relation":"main_file","file_id":"14708","date_created":"2023-12-22T14:14:06Z","date_updated":"2023-12-22T14:14:06Z","checksum":"973e1cbdab923a71709782177980829f","success":1,"file_name":"data_artemia_franciscana_genome.zip","access_level":"open_access","content_type":"application/x-zip-compressed","file_size":343632753,"creator":"melkrewi"}],"oa_version":"Published Version","date_created":"2023-12-22T13:40:48Z","date_updated":"2024-02-26T09:59:29Z","_id":"14705","year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"status":"public","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","ddc":["576"],"file_date_updated":"2023-12-22T14:14:06Z","abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"type":"research_data"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step."}],"issue":"6678","status":"public","title":"The genetic basis of a recent transition to live-bearing in marine snails","intvolume":" 383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14796","oa_version":"None","scopus_import":"1","day":"05","article_processing_charge":"No","article_type":"original","page":"114-119","publication":"Science","citation":{"ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982","ieee":"S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024.","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982."},"date_published":"2024-01-05T00:00:00Z","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"publisher":"American Association for the Advancement of Science","acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","year":"2024","pmid":1,"date_updated":"2024-03-05T09:35:25Z","date_created":"2024-01-14T23:00:56Z","volume":383,"author":[{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"first_name":"Martin D.","last_name":"Garlovsky","full_name":"Garlovsky, Martin D."},{"last_name":"Pal","first_name":"Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","full_name":"Pal, Arka"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","first_name":"Daria","last_name":"Shipilina","full_name":"Shipilina, Daria"},{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","last_name":"Garcia Castillo","full_name":"Garcia Castillo, Diego Fernando"},{"full_name":"Lifchitz, Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","last_name":"Lifchitz","first_name":"Hila"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"full_name":"Leder, Erica","last_name":"Leder","first_name":"Erica"},{"full_name":"Reeve, James","last_name":"Reeve","first_name":"James"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","relation":"press_release","description":"News on ISTA Website"}],"record":[{"status":"public","relation":"research_data","id":"14812"}]},"month":"01","publication_identifier":{"eissn":["1095-9203"]},"quality_controlled":"1","external_id":{"pmid":["38175895"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.adi2982"},{"date_published":"2024-02-23T00:00:00Z","page":"158","citation":{"chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020"},"article_processing_charge":"No","has_accepted_license":"1","day":"23","keyword":["Theoretical biology","Optimality","Evolution","Information"],"file":[{"access_level":"open_access","file_name":"hledik thesis pdfa 2b.pdf","content_type":"application/pdf","file_size":7102089,"creator":"mhledik","relation":"main_file","file_id":"15021","checksum":"b2d3da47c98d481577a4baf68944fe41","success":1,"date_updated":"2024-02-23T13:50:53Z","date_created":"2024-02-23T13:50:53Z"},{"file_size":14014790,"content_type":"application/zip","creator":"mhledik","file_name":"hledik thesis source.zip","access_level":"closed","date_created":"2024-02-23T13:50:54Z","date_updated":"2024-02-23T14:20:16Z","checksum":"eda9b9430da2610fee7ce1c1419a479a","relation":"source_file","file_id":"15022"}],"oa_version":"Published Version","status":"public","ddc":["576","519"],"title":"Genetic information and biological optimization","_id":"15020","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"doi":"10.15479/at:ista:15020","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"oa":1,"publication_identifier":{"issn":["2663 - 337X"]},"month":"02","date_updated":"2024-03-06T14:22:52Z","date_created":"2024-02-23T14:02:04Z","related_material":{"record":[{"id":"7553","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"12081"},{"id":"7606","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal","full_name":"Hledik, Michal"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2024","ec_funded":1,"file_date_updated":"2024-02-23T14:20:16Z"},{"day":"11","has_accepted_license":"1","article_processing_charge":"No","date_published":"2024-03-11T00:00:00Z","citation":{"mla":"Chen, JingJing. Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","apa":"Chen, J. (2024). Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101"},"page":"84","type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2024-03-12T07:12:17Z","date_created":"2024-03-11T14:10:58Z","checksum":"db4947474ffa271e66c254b6fe876a55","file_id":"15104","relation":"source_file","creator":"jchen","file_size":11271363,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Jingjing CHEN.docx","access_level":"closed"},{"date_created":"2024-03-11T14:11:06Z","date_updated":"2024-03-11T14:11:06Z","checksum":"a5eeae8b5702cd540f5d03469bc33dde","relation":"main_file","file_id":"15105","embargo":"2024-04-01","file_size":16627311,"content_type":"application/pdf","creator":"jchen","embargo_to":"open_access","file_name":"Thesis_Jingjing CHEN_merged.pdf","access_level":"closed"}],"oa_version":"Published Version","_id":"15101","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","ddc":["570"],"status":"public","month":"03","publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:15101","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2024-03-12T07:12:17Z","ec_funded":1,"author":[{"first_name":"JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, JingJing"}],"related_material":{"record":[{"id":"14843","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2024-03-14T13:14:19Z","date_created":"2024-03-11T10:09:54Z","year":"2024","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"PeJo"}]},{"author":[{"full_name":"Dvorak, Martin","last_name":"Dvorak","first_name":"Martin","orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}],"date_updated":"2024-03-19T08:20:31Z","date_created":"2021-09-27T10:48:23Z","acknowledgement":"We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria).","year":"2024","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"publisher":"Springer Nature","publication_status":"epub_ahead","file_date_updated":"2021-09-27T10:54:51Z","article_number":"2109.10203","doi":"10.1007/s10107-024-02064-5","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2109.10203"]},"oa":1,"quality_controlled":"1","publication_identifier":{"eissn":["1436-4646"],"issn":["0025-5610"]},"month":"03","oa_version":"Preprint","file":[{"relation":"main_file","file_id":"10046","checksum":"e7e83065f7bc18b9c188bf93b5ca5db6","success":1,"date_created":"2021-09-27T10:54:51Z","date_updated":"2021-09-27T10:54:51Z","access_level":"open_access","file_name":"Generalized-0-Ext.pdf","file_size":603672,"content_type":"application/pdf","creator":"mdvorak"}],"_id":"10045","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"title":"Generalized minimum 0-extension problem and discrete convexity","status":"public","abstract":[{"text":"Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n","lang":"eng"}],"type":"journal_article","date_published":"2024-03-07T00:00:00Z","citation":{"ama":"Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5","ieee":"M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and discrete convexity,” Mathematical Programming. Springer Nature, 2024.","apa":"Dvorak, M., & Kolmogorov, V. (2024). Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5","ista":"Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming., 2109.10203.","short":"M. Dvorak, V. Kolmogorov, Mathematical Programming (2024).","mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming, 2109.10203, Springer Nature, 2024, doi:10.1007/s10107-024-02064-5.","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02064-5."},"publication":"Mathematical Programming","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"07","scopus_import":"1","keyword":["minimum 0-extension problem","metric labeling problem","discrete metric spaces","metric extensions","computational complexity","valued constraint satisfaction problems","discrete convex analysis","L-convex functions"]},{"date_published":"2024-03-08T00:00:00Z","page":"108","citation":{"short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.","ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria."},"article_processing_charge":"No","has_accepted_license":"1","day":"08","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Thesis Sebastiano.pdf","file_size":4106872,"content_type":"application/pdf","creator":"scultrer","relation":"main_file","file_id":"15112","checksum":"1e468bfa42a7dcf04d89f4dadc621c87","success":1,"date_updated":"2024-03-14T08:55:07Z","date_created":"2024-03-14T08:55:07Z"},{"date_created":"2024-03-14T08:56:24Z","date_updated":"2024-03-14T14:14:35Z","checksum":"bcbd213490f5a7e68855a092bbce93f1","file_id":"15113","relation":"source_file","creator":"scultrer","content_type":"application/zip","file_size":4746234,"file_name":"Thesis (1).zip","access_level":"closed"}],"status":"public","title":"Persistence and Morse theory for discrete geometric structures","ddc":["514","500","516"],"_id":"15094","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:15094","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887","name":"Discretization in Geometry and Dynamics"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"publication_identifier":{"issn":["2663 - 337X"]},"month":"03","date_updated":"2024-03-20T09:36:57Z","date_created":"2024-03-08T15:28:10Z","related_material":{"record":[{"id":"11660","status":"public","relation":"part_of_dissertation"},{"id":"11658","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"13182"},{"relation":"part_of_dissertation","status":"public","id":"15090"},{"id":"15091","status":"public","relation":"part_of_dissertation"},{"id":"15093","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","last_name":"Cultrera di Montesano"}],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2024","ec_funded":1,"file_date_updated":"2024-03-14T14:14:35Z"},{"ec_funded":1,"date_created":"2023-02-24T12:20:47Z","date_updated":"2023-02-27T09:01:16Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias"},{"first_name":"Raimundo J","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J"},{"first_name":"Jakub","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub"}],"publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"year":"2023","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","month":"02","publication_identifier":{"isbn":["9781611977554"]},"language":[{"iso":"eng"}],"conference":{"name":"SODA: Symposium on Discrete Algorithms","end_date":"2023-01-25","location":"Florence, Italy","start_date":"2023-01-22"},"doi":"10.1137/1.9781611977554.ch173","quality_controlled":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"main_file_link":[{"url":"https://doi.org/10.1137/1.9781611977554.ch173","open_access":"1"}],"oa":1,"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."}],"type":"conference","oa_version":"Published Version","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12676","day":"01","article_processing_charge":"No","date_published":"2023-02-01T00:00:00Z","page":"4590-4605","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","citation":{"short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605.","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.","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.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","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.","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."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12736","year":"2023","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.","title":"Unexpected scaling in path copying trees","publication_status":"published","status":"public","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publisher":"Association for Computing Machinery","author":[{"first_name":"Vitaly","last_name":"Aksenov","full_name":"Aksenov, Vitaly"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","last_name":"Brown","full_name":"Brown, Trevor A"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"full_name":"Kokorin, Ilya","first_name":"Ilya","last_name":"Kokorin"}],"date_updated":"2023-03-20T07:57:27Z","date_created":"2023-03-19T23:00:58Z","oa_version":"Published Version","type":"conference_poster","abstract":[{"lang":"eng","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."}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","citation":{"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.","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.","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","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","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.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"oa":1,"quality_controlled":"1","page":"438-440","conference":{"location":"Montreal, QB, Canada","start_date":"2023-02-25","end_date":"2023-03-01","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"doi":"10.1145/3572848.3577512","date_published":"2023-02-25T00:00:00Z","language":[{"iso":"eng"}],"day":"25","month":"02","article_processing_charge":"No","publication_identifier":{"isbn":["9798400700156"]}},{"month":"03","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12716","project":[{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502","call_identifier":"H2020","name":"Circuits of Visual Attention"}],"oa":1,"file_date_updated":"2023-03-08T15:08:46Z","ec_funded":1,"date_created":"2023-03-08T15:19:45Z","date_updated":"2023-04-05T10:59:04Z","author":[{"full_name":"Burnett, Laura","last_name":"Burnett","first_name":"Laura","orcid":"0000-0002-8937-410X","id":"3B717F68-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","year":"2023","day":"10","has_accepted_license":"1","article_processing_charge":"No","date_published":"2023-03-10T00:00:00Z","page":"178","citation":{"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.","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","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.","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","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.","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.","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."},"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."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"access_level":"closed","file_name":"Burnett_Thesis_2023.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":23029260,"creator":"lburnett","relation":"source_file","file_id":"12717","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z"},{"date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","checksum":"cebc77705288bf4382db9b3541483cd0","success":1,"relation":"main_file","file_id":"12718","content_type":"application/pdf","file_size":11959869,"creator":"lburnett","file_name":"Burnett_Thesis_2023_pdfA.pdf","access_level":"open_access"}],"oa_version":"Published Version","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","status":"public","ddc":["599","573"],"_id":"12716","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"author":[{"full_name":"Chern, Albert","first_name":"Albert","last_name":"Chern"},{"id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","last_name":"Ishida","first_name":"Sadashige","full_name":"Ishida, Sadashige"}],"date_created":"2023-04-18T19:16:06Z","date_updated":"2023-04-25T06:51:21Z","oa_version":"Preprint","_id":"12846","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","title":"Area formula for spherical polygons via prequantization","publication_status":"submitted","status":"public","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"abstract":[{"lang":"eng","text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons."}],"article_number":"2303.14555","type":"preprint","doi":"10.48550/arXiv.2303.14555","date_published":"2023-03-25T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","oa":1,"citation":{"mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","short":"A. Chern, S. Ishida, ArXiv (n.d.).","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. 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","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. 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","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. ."},"main_file_link":[{"url":"https://arxiv.org/abs/2303.14555","open_access":"1"}],"external_id":{"arxiv":["2303.14555"]},"project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}],"month":"03","day":"25","article_processing_charge":"No"},{"file":[{"content_type":"application/pdf","file_size":9881969,"creator":"cchlebak","embargo_to":"open_access","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","access_level":"closed","date_updated":"2023-04-07T06:16:06Z","date_created":"2023-04-07T06:16:06Z","checksum":"35b5997d2b0acb461f9d33d073da0df5","relation":"main_file","embargo":"2024-04-07","file_id":"12814"},{"relation":"source_file","file_id":"12815","checksum":"81198f63c294890f6d58e8b29782efdc","date_updated":"2023-04-07T06:17:11Z","date_created":"2023-04-07T06:17:11Z","access_level":"closed","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","file_size":44201583,"content_type":"application/pdf","creator":"cchlebak"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":84731244,"creator":"cchlebak","file_name":"Thesis_CatarinaAlcarva_final.docx","access_level":"closed","date_updated":"2023-04-07T06:18:05Z","date_created":"2023-04-07T06:18:05Z","checksum":"0317bf7f457bb585f99d453ffa69eb53","relation":"source_file","file_id":"12816"}],"oa_version":"Published Version","_id":"12809","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","ddc":["570"],"status":"public","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. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-04-06T00:00:00Z","citation":{"ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 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.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","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","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.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","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."},"page":"115","day":"06","article_processing_charge":"No","has_accepted_license":"1","author":[{"first_name":"Catarina","last_name":"Alcarva","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","full_name":"Alcarva, Catarina"}],"date_updated":"2023-04-26T12:16:56Z","date_created":"2023-04-06T07:54:09Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"RySh"}],"file_date_updated":"2023-04-07T06:18:05Z","doi":"10.15479/at:ista:12809","supervisor":[{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"project":[{"_id":"267DFB90-B435-11E9-9278-68D0E5697425","name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?"}],"month":"04","publication_identifier":{"issn":["2663 - 337X"]}},{"oa":1,"external_id":{"arxiv":["2207.14200"]},"citation":{"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.","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations .","short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","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.","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 .","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 .","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 ."},"main_file_link":[{"url":"https://openreview.net/pdf?id=_eTZBs-yedr","open_access":"1"}],"publication":"11th International Conference on Learning Representations ","project":[{"call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","date_published":"2023-05-01T00:00:00Z","conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2023-05-05","location":"Kigali, Rwanda ","start_date":"2023-05-01"},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"article_processing_charge":"No","month":"05","_id":"13053","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)-","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"title":"CrAM: A Compression-Aware Minimizer","status":"public","publication_status":"accepted","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13074"}]},"author":[{"full_name":"Peste, Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","last_name":"Peste","first_name":"Elena-Alexandra"},{"last_name":"Vladu","first_name":"Adrian","full_name":"Vladu, Adrian"},{"full_name":"Kurtic, Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218","last_name":"Kurtic","first_name":"Eldar"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"}],"oa_version":"Preprint","date_updated":"2023-06-01T12:54:45Z","date_created":"2023-05-23T11:36:18Z","type":"conference","ec_funded":1,"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"}]},{"date_updated":"2023-06-23T09:47:36Z","date_created":"2023-04-14T14:56:04Z","author":[{"orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","first_name":"Victoria","full_name":"Pokusaeva, Victoria"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"year":"2023","file_date_updated":"2023-04-20T09:26:51Z","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Maximilian A","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12826","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"04","publication_identifier":{"issn":["2663 - 337X"]},"oa_version":"Published Version","file":[{"file_id":"12857","relation":"source_file","checksum":"5f589a9af025f7eeebfd0c186209913e","date_created":"2023-04-20T09:14:38Z","date_updated":"2023-04-20T09:26:51Z","access_level":"closed","file_name":"Thesis_Pokusaeva.docx","creator":"vpokusae","file_size":14507243,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"relation":"main_file","file_id":"12858","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","success":1,"date_updated":"2023-04-20T09:14:44Z","date_created":"2023-04-20T09:14:44Z","access_level":"open_access","file_name":"Thesis_Pokusaeva.pdf","content_type":"application/pdf","file_size":10090711,"creator":"vpokusae"}],"ddc":["570","571"],"status":"public","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12826","abstract":[{"text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2023-04-18T00:00:00Z","page":"106","citation":{"apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826."},"day":"18","article_processing_charge":"No","has_accepted_license":"1"},{"doi":"10.1007/978-3-031-30829-1_17","conference":{"name":"FOSSACS: Foundations of Software Science and Computation Structures","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2301.11175"]},"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308284"]},"month":"04","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","last_name":"Mazzocchi"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"volume":13992,"date_updated":"2023-07-14T11:20:27Z","date_created":"2023-01-31T07:23:56Z","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","year":"2023","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"file_date_updated":"2023-06-19T10:28:09Z","date_published":"2023-04-21T00:00:00Z","citation":{"ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2023. Quantitative safety and liveness. 26th International Conference Foundations of Software Science and Computation Structures. FOSSACS: Foundations of Software Science and Computation Structures, LNCS, vol. 13992, 349–370.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in 26th International Conference Foundations of Software Science and Computation Structures, Paris, France, 2023, vol. 13992, pp. 349–370.","apa":"Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2023). Quantitative safety and liveness. In 26th International Conference Foundations of Software Science and Computation Structures (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30829-1_17","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: 26th International Conference Foundations of Software Science and Computation Structures. Vol 13992. Springer Nature; 2023:349-370. doi:10.1007/978-3-031-30829-1_17","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In 26th International Conference Foundations of Software Science and Computation Structures, 13992:349–70. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30829-1_17.","mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” 26th International Conference Foundations of Software Science and Computation Structures, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:10.1007/978-3-031-30829-1_17.","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370."},"publication":"26th International Conference Foundations of Software Science and Computation Structures","page":"349-370","article_processing_charge":"No","has_accepted_license":"1","day":"21","scopus_import":"1","file":[{"file_size":449027,"content_type":"application/pdf","creator":"esarac","file_name":"qsl.pdf","access_level":"open_access","date_updated":"2023-01-31T07:22:21Z","date_created":"2023-01-31T07:22:21Z","checksum":"981025aed580b6b27c426cb8856cf63e","success":1,"relation":"main_file","file_id":"12468"},{"file_size":1048171,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_LNCS_HenzingerT.pdf","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","success":1,"date_updated":"2023-06-19T10:28:09Z","date_created":"2023-06-19T10:28:09Z","relation":"main_file","file_id":"13153"}],"oa_version":"Published Version","_id":"12467","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 13992","title":"Quantitative safety and liveness","ddc":["000"],"status":"public","abstract":[{"lang":"eng","text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states."}],"type":"conference","alternative_title":["LNCS"]},{"abstract":[{"lang":"eng","text":"The operator precedence languages (OPLs) represent the largest known subclass of the context-free languages which enjoys all desirable closure and decidability properties. This includes the decidability of language inclusion, which is the ultimate verification problem. Operator precedence grammars, automata, and logics have been investigated and used, for example, to verify programs with arithmetic expressions and exceptions (both of which are deterministic pushdown but lie outside the scope of the visibly pushdown languages). In this paper, we complete the picture and give, for the first time, an algebraic characterization of the class of OPLs in the form of a syntactic congruence that has finitely many equivalence classes exactly for the operator precedence languages. This is a generalization of the celebrated Myhill-Nerode theorem for the regular languages to OPLs. As one of the consequences, we show that universality and language inclusion for nondeterministic operator precedence automata can be solved by an antichain algorithm. Antichain algorithms avoid determinization and complementation through an explicit subset construction, by leveraging a quasi-order on words, which allows the pruning of the search space for counterexample words without sacrificing completeness. Antichain algorithms can be implemented symbolically, and these implementations are today the best-performing algorithms in practice for the inclusion of finite automata. We give a generic construction of the quasi-order needed for antichain algorithms from a finite syntactic congruence. This yields the first antichain algorithm for OPLs, an algorithm that solves the ExpTime-hard language inclusion problem for OPLs in exponential time."}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Published Version","file":[{"date_created":"2023-07-24T15:11:05Z","date_updated":"2023-07-24T15:11:05Z","checksum":"5d4c8932ef3450615a53b9bb15d92eb2","success":1,"relation":"main_file","file_id":"13293","file_size":859379,"content_type":"application/pdf","creator":"esarac","file_name":"icalp23.pdf","access_level":"open_access"}],"_id":"13292","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 261","title":"Regular methods for operator precedence languages","ddc":["000"],"status":"public","has_accepted_license":"1","article_processing_charge":"Yes","day":"05","date_published":"2023-07-05T00:00:00Z","citation":{"ama":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. Regular methods for operator precedence languages. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023:129:1--129:20. doi:10.4230/LIPIcs.ICALP.2023.129","ista":"Henzinger TA, Kebis P, Mazzocchi NA, Sarac NE. 2023. Regular methods for operator precedence languages. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 129:1--129:20.","ieee":"T. A. Henzinger, P. Kebis, N. A. Mazzocchi, and N. E. Sarac, “Regular methods for operator precedence languages,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261, p. 129:1--129:20.","apa":"Henzinger, T. A., Kebis, P., Mazzocchi, N. A., & Sarac, N. E. (2023). Regular methods for operator precedence languages. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261, p. 129:1--129:20). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.129","mla":"Henzinger, Thomas A., et al. “Regular Methods for Operator Precedence Languages.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20, doi:10.4230/LIPIcs.ICALP.2023.129.","short":"T.A. Henzinger, P. Kebis, N.A. Mazzocchi, N.E. Sarac, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, p. 129:1--129:20.","chicago":"Henzinger, Thomas A, Pavol Kebis, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Regular Methods for Operator Precedence Languages.” In 50th International Colloquium on Automata, Languages, and Programming, 261:129:1--129:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.129."},"publication":"50th International Colloquium on Automata, Languages, and Programming","page":"129:1--129:20","ec_funded":1,"file_date_updated":"2023-07-24T15:11:05Z","author":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Kebis, Pavol","first_name":"Pavol","last_name":"Kebis"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","last_name":"Mazzocchi","first_name":"Nicolas Adrien","full_name":"Mazzocchi, Nicolas Adrien"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"volume":261,"date_updated":"2023-07-31T08:38:38Z","date_created":"2023-07-24T15:11:41Z","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093.\r\nWe thank Pierre Ganty for early discussions and the anonymous reviewers for their helpful comments.\r\n","year":"2023","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959772785"]},"month":"07","doi":"10.4230/LIPIcs.ICALP.2023.129","conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany","start_date":"2023-07-10","end_date":"2023-07-14"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2305.03447"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited."}],"type":"conference","oa_version":"Published Version","file":[{"file_name":"2023_SPAA_Fedorov.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2087937,"creator":"dernst","relation":"main_file","file_id":"13334","date_updated":"2023-07-31T10:53:08Z","date_created":"2023-07-31T10:53:08Z","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","success":1}],"status":"public","ddc":["000"],"title":"Provably-efficient and internally-deterministic parallel Union-Find","_id":"13262","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"17","scopus_import":"1","date_published":"2023-06-17T00:00:00Z","page":"261-271","citation":{"ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Orlando, FL, United States, 2023, pp. 261–271.","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., & Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3558481.3591082","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2023:261-271. doi:10.1145/3558481.3591082","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, 261–71. Association for Computing Machinery, 2023. https://doi.org/10.1145/3558481.3591082.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–71, doi:10.1145/3558481.3591082.","short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271."},"publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","file_date_updated":"2023-07-31T10:53:08Z","date_created":"2023-07-23T22:01:12Z","date_updated":"2023-07-31T10:54:32Z","author":[{"full_name":"Fedorov, Alexander","first_name":"Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"full_name":"Hashemi, Diba","first_name":"Diba","last_name":"Hashemi","id":"ed9595ea-2f8f-11ee-ba95-d2b546540783"},{"full_name":"Nadiradze, Giorgi","first_name":"Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publication_status":"published","year":"2023","publication_identifier":{"isbn":["9781450395458"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1145/3558481.3591082","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","location":"Orlando, FL, United States","start_date":"2023-06-17","end_date":"2023-06-19"},"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2304.09331"]}}]