[{"citation":{"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. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>.","mla":"Elkrewi, Marwan N. <i>Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>","short":"M.N. Elkrewi, (2024).","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. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","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."},"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"related_material":{"record":[{"id":"15009","relation":"used_in_publication","status":"public"}]},"keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","contributor":[{"last_name":"Bett","first_name":"Vincent K","contributor_type":"researcher","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"first_name":"Ariana","contributor_type":"project_member","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","contributor_type":"supervisor","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"},{"last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","contributor_type":"researcher","first_name":"Marwan N"}],"project":[{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"doi":"10.15479/AT:ISTA:14705","_id":"14705","date_updated":"2026-05-18T12:46:40Z","publisher":"Institute of Science and Technology Austria","date_created":"2023-12-22T13:40:48Z","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"},"date_published":"2024-01-02T00:00:00Z","abstract":[{"lang":"eng","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."}],"ddc":["576"],"day":"02","title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","status":"public","has_accepted_license":"1","year":"2024","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"}],"month":"01","article_processing_charge":"No","retracted":"1"},{"has_accepted_license":"1","article_processing_charge":"No","author":[{"orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya"}],"month":"01","file":[{"file_name":"FinalSubmission_Thesis_OLUSANYA.zip","date_updated":"2024-01-03T18:30:13Z","file_size":16986244,"access_level":"closed","content_type":"application/zip","file_id":"14730","creator":"oolusany","checksum":"de179b1c6758f182ff0c70d8b38c1501","relation":"source_file","date_created":"2024-01-03T18:30:13Z"},{"success":1,"date_updated":"2024-01-03T18:31:34Z","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","access_level":"open_access","file_size":6460403,"file_id":"14731","content_type":"application/pdf","creator":"oolusany","checksum":"0e331585e3cd4823320aab4e69e64ccf","date_created":"2024-01-03T18:31:34Z","relation":"main_file"}],"date_published":"2024-01-19T00:00:00Z","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"}],"ddc":["576"],"status":"public","oa":1,"publisher":"Institute of Science and Technology Austria","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","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"related_material":{"record":[{"relation":"part_of_dissertation","id":"10658","status":"public"},{"status":"public","id":"10787","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14732"}]},"oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"doi":"10.15479/at:ista:14711","degree_awarded":"MS","page":"183","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"SSU"}],"publication_identifier":{"issn":["2663 - 337X"]},"type":"dissertation","year":"2024","supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani"}],"day":"19","title":"Local adaptation, genetic load and extinction in metapopulations","date_created":"2023-12-26T22:49:53Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"_id":"14711","date_updated":"2025-05-26T09:05:10Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896"},{"grant_number":"26380","name":"Polygenic Adaptation in a Metapopulation","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6"}],"file_date_updated":"2024-01-03T18:31:34Z"},{"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663 - 337X"]},"type":"dissertation","doi":"10.15479/at:ista:14821","page":"89","degree_awarded":"PhD","has_accepted_license":"1","author":[{"first_name":"Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","last_name":"Chiossi","full_name":"Chiossi, Heloisa"}],"month":"01","article_processing_charge":"No","date_published":"2024-01-19T00:00:00Z","ddc":["570"],"file":[{"access_level":"closed","file_size":8656268,"file_id":"14838","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhD_Thesis_190124.docx","date_updated":"2024-01-19T11:04:05Z","date_created":"2024-01-19T11:04:05Z","relation":"source_file","creator":"hchiossi","checksum":"d3fa3de1abd5af5204c13e9d55375615"},{"date_updated":"2024-01-19T11:03:59Z","file_name":"PhD_Thesis_190124.pdf","embargo_to":"open_access","file_size":6567275,"access_level":"closed","content_type":"application/pdf","file_id":"14839","creator":"hchiossi","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","embargo":"2025-01-19","relation":"main_file","date_created":"2024-01-19T11:03:59Z"}],"status":"public","date_created":"2024-01-16T14:25:21Z","publication_status":"published","alternative_title":["ISTA Thesis"],"citation":{"ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>.","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria."},"department":[{"_id":"GradSch"},{"_id":"JoCs"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file_date_updated":"2024-01-19T11:04:05Z","_id":"14821","date_updated":"2024-02-01T09:50:29Z","supervisor":[{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"}],"year":"2024","day":"19","title":"Adaptive hierarchical representations in the hippocampus"},{"ddc":["520"],"abstract":[{"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 &amp;lt; z &amp;lt; 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.","lang":"eng"}],"date_published":"2024-02-01T00:00:00Z","file":[{"relation":"main_file","date_created":"2024-01-23T12:30:45Z","checksum":"9d02df4035c4951cf63dee0db1e462e9","creator":"dernst","content_type":"application/pdf","file_id":"14879","file_size":4521738,"access_level":"open_access","file_name":"2024_MNAstronomSoc_Kramarenko.pdf","date_updated":"2024-01-23T12:30:45Z","success":1}],"quality_controlled":"1","status":"public","article_type":"original","has_accepted_license":"1","month":"02","author":[{"last_name":"Kramarenko","full_name":"Kramarenko, Ivan","first_name":"Ivan","id":"9a9394cb-3200-11ee-973b-f5ba2a8b16e4"},{"last_name":"Kerutt","full_name":"Kerutt, J","first_name":"J"},{"first_name":"A","full_name":"Verhamme, A","last_name":"Verhamme"},{"first_name":"P A","full_name":"Oesch, P A","last_name":"Oesch"},{"full_name":"Barrufet, L","last_name":"Barrufet","first_name":"L"},{"first_name":"Jorryt J","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","full_name":"Matthee, Jorryt J"},{"first_name":"H","full_name":"Kusakabe, H","last_name":"Kusakabe"},{"first_name":"I","full_name":"Goovaerts, I","last_name":"Goovaerts"},{"last_name":"Thai","full_name":"Thai, T T","first_name":"T T"}],"article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"arxiv":1,"publication":"Monthly Notices of the Royal Astronomical Society","oa_version":"Published Version","type":"journal_article","publication_identifier":{"eissn":["1365-2966"],"issn":["0035-8711"]},"keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"9853-9871","doi":"10.1093/mnras/stad3853","intvolume":"       527","publisher":"Oxford University Press","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"},"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).","volume":527,"title":"Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape","day":"01","external_id":{"arxiv":["2305.07044"]},"year":"2024","issue":"4","department":[{"_id":"GradSch"},{"_id":"JoMa"}],"citation":{"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 <i>z</i> ≳ 3 to Lyman Continuum Escape.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/mnras/stad3853\">https://doi.org/10.1093/mnras/stad3853</a>.","mla":"Kramarenko, Ivan, et al. “Linking UV Spectral Properties of MUSE Ly α Emitters at <i>z</i> ≳ 3 to Lyman Continuum Escape.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 527, no. 4, Oxford University Press, 2024, pp. 9853–71, doi:<a href=\"https://doi.org/10.1093/mnras/stad3853\">10.1093/mnras/stad3853</a>.","ama":"Kramarenko I, Kerutt J, Verhamme A, et al. Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape. <i>Monthly Notices of the Royal Astronomical Society</i>. 2024;527(4):9853-9871. doi:<a href=\"https://doi.org/10.1093/mnras/stad3853\">10.1093/mnras/stad3853</a>","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.","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 <i>z</i> ≳ 3 to Lyman continuum escape. Monthly Notices of the Royal Astronomical Society. 527(4), 9853–9871.","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 <i>z</i> ≳ 3 to Lyman continuum escape. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mnras/stad3853\">https://doi.org/10.1093/mnras/stad3853</a>","ieee":"I. Kramarenko <i>et al.</i>, “Linking UV spectral properties of MUSE Ly α emitters at <i>z</i> ≳ 3 to Lyman continuum escape,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 527, no. 4. Oxford University Press, pp. 9853–9871, 2024."},"file_date_updated":"2024-01-23T12:30:45Z","date_updated":"2024-01-23T12:33:50Z","_id":"14852","date_created":"2024-01-22T08:22:17Z","publication_status":"published"},{"status":"public","article_type":"original","quality_controlled":"1","file":[{"date_updated":"2024-02-05T10:06:35Z","file_name":"2023_IntJourCommons_Nomura.pdf","success":1,"content_type":"application/pdf","file_id":"14939","file_size":1305786,"access_level":"open_access","checksum":"b80ebc889033c365d8f8c05a0c655382","creator":"dernst","relation":"main_file","date_created":"2024-02-05T10:06:35Z"}],"abstract":[{"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.","lang":"eng"}],"ddc":["550"],"date_published":"2024-01-11T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","month":"01","author":[{"last_name":"Nomura","full_name":"Nomura, Keiko","first_name":"Keiko"},{"first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","last_name":"Rella","full_name":"Rella, Simon"},{"first_name":"Haily","full_name":"Merritt, Haily","last_name":"Merritt"},{"first_name":"Mathieu","last_name":"Baltussen","full_name":"Baltussen, Mathieu"},{"full_name":"Bird, Darcy","last_name":"Bird","first_name":"Darcy"},{"first_name":"Annika","last_name":"Tjuka","full_name":"Tjuka, Annika"},{"first_name":"Dan","full_name":"Falk, Dan","last_name":"Falk"}],"has_accepted_license":"1","doi":"10.5334/ijc.1275","type":"journal_article","publication_identifier":{"issn":["1875-0281"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Sociology and Political Science"],"language":[{"iso":"eng"}],"publication":"International Journal of the Commons","oa_version":"Published Version","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,"publisher":"Ubiquity Press","intvolume":"        18","title":"Tipping points of space debris in low earth orbit","day":"11","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.","volume":18,"year":"2024","issue":"1","date_updated":"2024-02-05T10:10:27Z","_id":"14901","file_date_updated":"2024-02-05T10:06:35Z","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"citation":{"short":"K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024).","apa":"Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., &#38; Falk, D. (2024). Tipping points of space debris in low earth orbit. <i>International Journal of the Commons</i>. Ubiquity Press. <a href=\"https://doi.org/10.5334/ijc.1275\">https://doi.org/10.5334/ijc.1275</a>","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. 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Ubiquity Press, 2024."},"publication_status":"published","date_created":"2024-01-30T11:58:02Z"},{"_id":"15020","date_updated":"2025-06-30T13:21:09Z","file_date_updated":"2024-02-23T14:20:16Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"},{"grant_number":"101055327","name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"citation":{"ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ista":"Hledik M. 2024. Genetic information and biological optimization. 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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"}],"article_processing_charge":"No","author":[{"first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","full_name":"Hledik, Michal"}],"month":"02","has_accepted_license":"1"},{"day":"01","title":"Panoramic visual statistics shape retina-wide organization of receptive fields","external_id":{"isi":["000955258300002"],"pmid":["36959418"]},"volume":26,"acknowledgement":"We thank Hiroki Asari for sharing the dataset of naturalistic images, Anton Sumser for sharing visual stimulus code, Yoav Ben Simon for initial explorative work with the generation of AAVs, and Tomas Vega-Zuñiga for help with immunostainings. We also thank Gasper Tkacik and members of the Neuroethology group for their comments on the manuscript. This research was supported by the Scientific Service Units of IST Austria through resources provided by Scientific Computing, the Preclinical Facility, the Lab Support Facility, and the Imaging and Optics Facility. This work was supported by European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 (DG), Austrian Science Fund (FWF) stand-alone grant P 34015 (WM), Human Frontiers Science Program LT000256/2018-L (AS), EMBO ALTF 1098-2017 (AS) and the European Research Council Starting Grant 756502 (MJ).","year":"2023","file_date_updated":"2023-10-04T11:40:51Z","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"grant_number":"756502","name":"Circuits of Visual Attention","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256"},{"grant_number":"ALTF 1098-2017","_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus"}],"_id":"12349","date_updated":"2023-10-04T11:41:05Z","citation":{"short":"D. Gupta, W.F. Mlynarski, A.L. Sumser, O. Symonova, J. Svaton, M.A. Jösch, Nature Neuroscience 26 (2023) 606–614.","ista":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. 2023. Panoramic visual statistics shape retina-wide organization of receptive fields. Nature Neuroscience. 26, 606–614.","apa":"Gupta, D., Mlynarski, W. F., Sumser, A. L., Symonova, O., Svaton, J., &#38; Jösch, M. A. (2023). Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>","chicago":"Gupta, Divyansh, Wiktor F Mlynarski, Anton L Sumser, Olga Symonova, Jan Svaton, and Maximilian A Jösch. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41593-023-01280-0\">https://doi.org/10.1038/s41593-023-01280-0</a>.","ama":"Gupta D, Mlynarski WF, Sumser AL, Symonova O, Svaton J, Jösch MA. Panoramic visual statistics shape retina-wide organization of receptive fields. <i>Nature Neuroscience</i>. 2023;26:606-614. doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>","mla":"Gupta, Divyansh, et al. “Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” <i>Nature Neuroscience</i>, vol. 26, Springer Nature, 2023, pp. 606–14, doi:<a href=\"https://doi.org/10.1038/s41593-023-01280-0\">10.1038/s41593-023-01280-0</a>.","ieee":"D. Gupta, W. F. Mlynarski, A. L. Sumser, O. Symonova, J. Svaton, and M. A. Jösch, “Panoramic visual statistics shape retina-wide organization of receptive fields,” <i>Nature Neuroscience</i>, vol. 26. Springer Nature, pp. 606–614, 2023."},"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publication_status":"published","pmid":1,"date_created":"2023-01-23T14:14:19Z","quality_controlled":"1","article_type":"original","status":"public","date_published":"2023-04-01T00:00:00Z","ddc":["570"],"abstract":[{"lang":"eng","text":"Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types."}],"file":[{"content_type":"application/pdf","file_id":"14395","file_size":6144866,"access_level":"open_access","date_updated":"2023-10-04T11:40:51Z","file_name":"2023_NatureNeuroscience_Gupta.pdf","success":1,"relation":"main_file","date_created":"2023-10-04T11:40:51Z","checksum":"a33d91e398e548f34003170e10988368","creator":"dernst"}],"author":[{"full_name":"Gupta, Divyansh","last_name":"Gupta","id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","first_name":"Divyansh"},{"first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F"},{"full_name":"Sumser, Anton L","last_name":"Sumser","orcid":"0000-0002-4792-1881","id":"3320A096-F248-11E8-B48F-1D18A9856A87","first_name":"Anton L"},{"last_name":"Symonova","full_name":"Symonova, 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of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. "}],"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","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"oa":1,"date_created":"2023-01-25T12:45:18Z","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:12370","_id":"12370","date_updated":"2023-10-04T11:41:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"file_date_updated":"2023-01-26T10:51:34Z","contributor":[{"last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Olga"},{"contributor_type":"researcher","id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","last_name":"Mlynarski"},{"first_name":"Jan","contributor_type":"researcher","id":"f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2","last_name":"Svaton"}],"type":"research_data","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism"},{"grant_number":"756502","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention"},{"name":"Neuronal networks of salience and spatial detection in the murine superior colliculus","_id":"266D407A-B435-11E9-9278-68D0E5697425","grant_number":"LT000256"},{"_id":"264FEA02-B435-11E9-9278-68D0E5697425","name":"Connecting sensory with motor processing in the superior colliculus","grant_number":"ALTF 1098-2017"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12349"}]},"citation":{"ista":"Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>.","apa":"Gupta, D., Sumser, A. L., &#38; Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">https://doi.org/10.15479/AT:ISTA:12370</a>","short":"D. Gupta, A.L. Sumser, M.A. Jösch, (2023).","mla":"Gupta, Divyansh, et al. <i>Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>.","ama":"Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12370\">10.15479/AT:ISTA:12370</a>","chicago":"Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12370\">https://doi.org/10.15479/AT:ISTA:12370</a>.","ieee":"D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023."},"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"ec_funded":1},{"acknowledgement":"This article is a version the author’s master thesis at the University of Bonn. The author would like to thank his advisor Valentin Blomer for introducing the problem, and giving generous feedback and encouragement along the way, especially during the global pandemic.\r\nThe author thanks Edgar Assing for his lectures on analytic number theory. Finally, the author is grateful to the anonymous referees for their valuable time and comments.\r\n","volume":207,"external_id":{"isi":["000912903000001"],"arxiv":["2103.08268"]},"title":"Density of the union of positive diagonal binary quadratic forms","day":"09","year":"2023","department":[{"_id":"GradSch"}],"citation":{"ieee":"Y. Diao, “Density of the union of positive diagonal binary quadratic forms,” <i>Acta Arithmetica</i>, vol. 207. Instytut Matematyczny, pp. 1–17, 2023.","mla":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” <i>Acta Arithmetica</i>, vol. 207, Instytut Matematyczny, 2023, pp. 1–17, doi:<a href=\"https://doi.org/10.4064/aa210830-24-11\">10.4064/aa210830-24-11</a>.","ama":"Diao Y. Density of the union of positive diagonal binary quadratic forms. <i>Acta Arithmetica</i>. 2023;207:1-17. doi:<a href=\"https://doi.org/10.4064/aa210830-24-11\">10.4064/aa210830-24-11</a>","chicago":"Diao, Yijie. “Density of the Union of Positive Diagonal Binary Quadratic Forms.” <i>Acta Arithmetica</i>. Instytut Matematyczny, 2023. <a href=\"https://doi.org/10.4064/aa210830-24-11\">https://doi.org/10.4064/aa210830-24-11</a>.","ista":"Diao Y. 2023. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 207, 1–17.","apa":"Diao, Y. (2023). Density of the union of positive diagonal binary quadratic forms. <i>Acta Arithmetica</i>. Instytut Matematyczny. <a href=\"https://doi.org/10.4064/aa210830-24-11\">https://doi.org/10.4064/aa210830-24-11</a>","short":"Y. Diao, Acta Arithmetica 207 (2023) 1–17."},"date_updated":"2023-10-17T09:15:17Z","_id":"12406","date_created":"2023-01-26T21:17:04Z","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.08268","open_access":"1"}],"abstract":[{"text":"Let X be a sufficiently large positive integer. We prove that one may choose a subset S of primes with cardinality O(logX) such that a positive proportion of integers less than X can be represented by x2+py2 for at least one p∈S.","lang":"eng"}],"date_published":"2023-01-09T00:00:00Z","status":"public","article_type":"original","quality_controlled":"1","article_processing_charge":"No","month":"01","author":[{"last_name":"Diao","full_name":"Diao, Yijie","first_name":"Yijie","id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b","orcid":"0000-0002-4989-5330"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","publication":"Acta Arithmetica","arxiv":1,"page":"1-17","doi":"10.4064/aa210830-24-11","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Algebra","Number Theory"],"publication_identifier":{"eissn":["1730-6264"],"issn":["0065-1036"]},"publisher":"Instytut Matematyczny","oa":1,"intvolume":"       207","isi":1},{"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"citation":{"mla":"Henzinger, Thomas A., et al. “Quantitative Safety and Liveness.” <i>26th International Conference Foundations of Software Science and Computation Structures</i>, vol. 13992, Springer Nature, 2023, pp. 349–70, doi:<a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">10.1007/978-3-031-30829-1_17</a>.","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Quantitative safety and liveness. In: <i>26th International Conference Foundations of Software Science and Computation Structures</i>. Vol 13992. Springer Nature; 2023:349-370. doi:<a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">10.1007/978-3-031-30829-1_17</a>","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Quantitative Safety and Liveness.” In <i>26th International Conference Foundations of Software Science and Computation Structures</i>, 13992:349–70. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">https://doi.org/10.1007/978-3-031-30829-1_17</a>.","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.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2023). Quantitative safety and liveness. In <i>26th International Conference Foundations of Software Science and Computation Structures</i> (Vol. 13992, pp. 349–370). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30829-1_17\">https://doi.org/10.1007/978-3-031-30829-1_17</a>","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 26th International Conference Foundations of Software Science and Computation Structures, Springer Nature, 2023, pp. 349–370.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Quantitative safety and liveness,” in <i>26th International Conference Foundations of Software Science and Computation Structures</i>, Paris, France, 2023, vol. 13992, pp. 349–370."},"project":[{"grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"file_date_updated":"2023-06-19T10:28:09Z","conference":{"end_date":"2023-04-27","name":"FOSSACS: Foundations of Software Science and Computation Structures","location":"Paris, France","start_date":"2023-04-22"},"date_updated":"2023-07-14T11:20:27Z","_id":"12467","date_created":"2023-01-31T07:23:56Z","publication_status":"published","alternative_title":["LNCS"],"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","volume":13992,"title":"Quantitative safety and liveness","day":"21","external_id":{"arxiv":["2301.11175"]},"year":"2023","ec_funded":1,"language":[{"iso":"eng"}],"publication":"26th International Conference Foundations of Software Science and Computation Structures","oa_version":"Published Version","arxiv":1,"type":"conference","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308284"],"issn":["0302-9743"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"349-370","doi":"10.1007/978-3-031-30829-1_17","intvolume":"     13992","publisher":"Springer Nature","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"},"ddc":["000"],"abstract":[{"text":"Safety and liveness are elementary concepts of computation, and the foundation of many verification paradigms. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In quantitative specification and verification, properties assign not truth values, but quantitative values to infinite traces (e.g., a cost, or the distance to a boolean property). We introduce quantitative safety and liveness, and we prove that our definitions induce conservative quantitative generalizations of both (1)~the safety-progress hierarchy of boolean properties and (2)~the safety-liveness decomposition of boolean properties. In particular, we show that every quantitative property can be written as the pointwise minimum of a quantitative safety property and a quantitative liveness property. Consequently, like boolean properties, also quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. Moreover, quantitative properties can be approximated naturally. We prove that every quantitative property that has both safe and co-safe approximations can be monitored arbitrarily precisely by a monitor that uses only a finite number of states.","lang":"eng"}],"date_published":"2023-04-21T00:00:00Z","file":[{"success":1,"date_updated":"2023-01-31T07:22:21Z","file_name":"qsl.pdf","file_size":449027,"access_level":"open_access","content_type":"application/pdf","file_id":"12468","creator":"esarac","checksum":"981025aed580b6b27c426cb8856cf63e","relation":"main_file","date_created":"2023-01-31T07:22:21Z"},{"date_created":"2023-06-19T10:28:09Z","relation":"main_file","creator":"dernst","checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","access_level":"open_access","file_size":1048171,"file_id":"13153","content_type":"application/pdf","success":1,"file_name":"2023_LNCS_HenzingerT.pdf","date_updated":"2023-06-19T10:28:09Z"}],"quality_controlled":"1","status":"public","has_accepted_license":"1","month":"04","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi"},{"full_name":"Sarac, Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E"}],"article_processing_charge":"No","scopus_import":"1"},{"_id":"12470","date_updated":"2023-08-31T12:26:58Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"file_date_updated":"2023-07-27T22:30:54Z","citation":{"ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","apa":"Michalska, J. M. (2023). <i>A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12470\">https://doi.org/10.15479/at:ista:12470</a>.","ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>","mla":"Michalska, Julia M. <i>A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12470\">10.15479/at:ista:12470</a>."},"department":[{"_id":"GradSch"},{"_id":"JoDa"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-01-31T15:10:53Z","day":"09","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","year":"2023","supervisor":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl","full_name":"Danzl, Johann G"}],"page":"201","degree_awarded":"PhD","doi":"10.15479/at:ista:12470","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]},"type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","id":"11943","status":"public"},{"id":"11950","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","ec_funded":1,"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"},"oa":1,"publisher":"Institute of Science and Technology Austria","status":"public","file":[{"embargo":"2023-07-09","date_created":"2023-01-31T15:11:42Z","relation":"main_file","creator":"cchlebak","checksum":"1a2306e5f59f52df598e7ecfadf921ac","access_level":"open_access","file_size":41771714,"file_id":"12471","content_type":"application/pdf","file_name":"20230109_PhD_thesis_JM_final.pdf","date_updated":"2023-07-27T22:30:54Z"},{"file_id":"12472","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":66983464,"embargo_to":"open_access","file_name":"20230109_PhD_thesis_JM_final.docx","date_updated":"2023-07-10T22:30:04Z","date_created":"2023-01-31T15:11:51Z","relation":"source_file","checksum":"0bebbdee0773443959e1f6ab8caf281f","creator":"cchlebak"}],"date_published":"2023-01-09T00:00:00Z","ddc":["610"],"abstract":[{"lang":"eng","text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy."}],"article_processing_charge":"No","author":[{"last_name":"Michalska","full_name":"Michalska, Julia M","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235"}],"month":"01","has_accepted_license":"1"},{"citation":{"ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","apa":"Zens, B. (2023). <i>Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","mla":"Zens, Bettina. <i>Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12491\">10.15479/at:ista:12491</a>","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12491\">https://doi.org/10.15479/at:ista:12491</a>."},"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"file_date_updated":"2024-02-08T23:30:04Z","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"_id":"12491","date_updated":"2024-02-08T23:30:05Z","date_created":"2023-02-02T14:50:20Z","publication_status":"published","alternative_title":["ISTA Thesis"],"day":"02","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","supervisor":[{"last_name":"Schur","full_name":"Schur, Florian KM","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"year":"2023","oa_version":"Published Version","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"8586","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-027-5"]},"keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"type":"dissertation","degree_awarded":"PhD","doi":"10.15479/at:ista:12491","page":"187","oa":1,"publisher":"Institute of Science and Technology Austria","date_published":"2023-02-02T00:00:00Z","ddc":["570"],"abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"file":[{"file_size":23082464,"access_level":"open_access","content_type":"application/pdf","file_id":"12527","date_updated":"2024-02-08T23:30:04Z","file_name":"PhDThesis_BettinaZens_2023_final.pdf","embargo":"2024-02-07","relation":"main_file","date_created":"2023-02-07T13:07:38Z","creator":"bzens","checksum":"069d87f025e0799bf9e3c375664264f2"},{"file_size":106169509,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12528","date_updated":"2024-02-08T23:30:04Z","file_name":"PhDThesis_BettinaZens_2023_final.docx","embargo_to":"open_access","relation":"source_file","date_created":"2023-02-07T13:09:05Z","creator":"bzens","checksum":"8c66ed203495d6e078ed1002a866520c"}],"status":"public","has_accepted_license":"1","author":[{"last_name":"Zens","full_name":"Zens, Bettina","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87"}],"month":"02","article_processing_charge":"No"},{"related_material":{"record":[{"relation":"used_in_publication","id":"12675","status":"public"}]},"department":[{"_id":"GradSch"},{"_id":"PaSc"}],"oa_version":"Published Version","citation":{"short":"L.M. Becker, P. Schanda, (2023).","apa":"Becker, L. M., &#38; Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12497\">https://doi.org/10.15479/AT:ISTA:12497</a>","ista":"Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12497\">10.15479/AT:ISTA:12497</a>.","chicago":"Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12497\">https://doi.org/10.15479/AT:ISTA:12497</a>.","mla":"Becker, Lea Marie, and Paul Schanda. <i>Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12497\">10.15479/AT:ISTA:12497</a>.","ama":"Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12497\">10.15479/AT:ISTA:12497</a>","ieee":"L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023."},"date_updated":"2024-02-21T12:14:06Z","doi":"10.15479/AT:ISTA:12497","_id":"12497","file_date_updated":"2023-03-24T09:42:03Z","type":"research_data","contributor":[{"last_name":"Berbon","first_name":"Mélanie","contributor_type":"researcher"},{"first_name":"Alicia","contributor_type":"researcher","last_name":"Vallet"},{"last_name":"Grelard","contributor_type":"researcher","first_name":"Axelle"},{"first_name":"Estelle","contributor_type":"researcher","last_name":"Morvan"},{"contributor_type":"researcher","first_name":"Benjamin","last_name":"Bardiaux"},{"last_name":"Lichtenecker","first_name":"Roman","contributor_type":"researcher"},{"last_name":"Ernst","first_name":"Matthias","contributor_type":"researcher"},{"first_name":"Antoine","contributor_type":"researcher","last_name":"Loquet"},{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","contributor_type":"contact_person"},{"last_name":"Becker","first_name":"Lea Marie","contributor_type":"researcher","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2023-02-03T08:08:02Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"file":[{"relation":"main_file","date_created":"2023-03-23T10:03:16Z","checksum":"fd9a28620a81a82991fb70f4fd6591d9","creator":"lbecker","content_type":"application/zip","file_id":"12743","file_size":87018103,"access_level":"open_access","file_name":"Research_Data.zip","date_updated":"2023-03-24T09:34:20Z"},{"relation":"main_file","date_created":"2023-03-24T07:13:55Z","creator":"dernst","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","file_size":747,"access_level":"open_access","content_type":"text/plain","file_id":"12755","date_updated":"2023-03-24T09:42:03Z","file_name":"README.txt"}],"ddc":["572"],"abstract":[{"lang":"eng","text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and  HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture."}],"date_published":"2023-03-23T00:00:00Z","status":"public","title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","day":"23","year":"2023","has_accepted_license":"1","article_processing_charge":"No","month":"03","author":[{"first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","last_name":"Becker","full_name":"Becker, Lea Marie"},{"last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}]},{"acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","volume":7,"external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","day":"01","year":"2023","issue":"1","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"citation":{"ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” <i>Evolution Letters</i>, vol. 7, no. 1. Oxford University Press, 2023.","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>.","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>.","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. 2023;7(1). doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., &#38; Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004."},"date_updated":"2023-08-16T11:44:32Z","_id":"12521","project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"file_date_updated":"2023-08-16T11:43:33Z","date_created":"2023-02-06T13:59:12Z","pmid":1,"publication_status":"published","file":[{"file_size":2592189,"access_level":"open_access","content_type":"application/pdf","file_id":"14068","success":1,"file_name":"2023_EvLetters_Mrnjavac.pdf","date_updated":"2023-08-16T11:43:33Z","relation":"main_file","date_created":"2023-08-16T11:43:33Z","creator":"dernst","checksum":"a240a041cb9b9b7c8ba93a4706674a3f"}],"ddc":["570"],"abstract":[{"text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.","lang":"eng"}],"date_published":"2023-02-01T00:00:00Z","status":"public","article_type":"original","quality_controlled":"1","has_accepted_license":"1","article_number":"qrac004","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","month":"02","author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","first_name":"Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Evolution Letters","doi":"10.1093/evlett/qrac004","type":"journal_article","publication_identifier":{"issn":["2056-3744"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"oa":1,"publisher":"Oxford University Press","intvolume":"         7","isi":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"}},{"ddc":["570"],"abstract":[{"lang":"eng","text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics."}],"date_published":"2023-02-08T00:00:00Z","file":[{"access_level":"open_access","file_size":8369317,"file_id":"12532","content_type":"application/pdf","date_updated":"2024-02-09T23:30:03Z","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","embargo":"2024-02-08","date_created":"2023-02-09T08:03:32Z","relation":"main_file","creator":"cchlebak","checksum":"57d8da3a6c749eb1556b7435fe266a5f"},{"relation":"source_file","date_created":"2023-02-10T09:32:06Z","creator":"cchlebak","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","file_size":11204408,"access_level":"closed","content_type":"application/x-zip-compressed","file_id":"12535","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","date_updated":"2024-02-09T23:30:03Z","embargo_to":"open_access"}],"status":"public","has_accepted_license":"1","month":"02","author":[{"first_name":"Kseniia","id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","last_name":"Kirillova","full_name":"Kirillova, Kseniia"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Published Version","type":"dissertation","publication_identifier":{"issn":["2791-4585"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"46","doi":"10.15479/at:ista:12531","degree_awarded":"MS","publisher":"Institute of Science and Technology Austria","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","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"title":"Panoramic functional gradients across the mouse retina","day":"08","supervisor":[{"orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","last_name":"Jösch"}],"year":"2023","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"citation":{"short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","apa":"Kirillova, K. (2023). <i>Panoramic functional gradients across the mouse retina</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12531\">https://doi.org/10.15479/at:ista:12531</a>.","ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>","mla":"Kirillova, Kseniia. <i>Panoramic Functional Gradients across the Mouse Retina</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12531\">10.15479/at:ista:12531</a>.","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023."},"file_date_updated":"2024-02-09T23:30:03Z","date_updated":"2024-02-09T23:30:04Z","_id":"12531","date_created":"2023-02-09T07:45:05Z","publication_status":"published","alternative_title":["ISTA Master's Thesis"]},{"article_type":"original","status":"public","quality_controlled":"1","date_published":"2023-01-24T00:00:00Z","abstract":[{"lang":"eng","text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front."}],"scopus_import":"1","article_processing_charge":"No","author":[{"last_name":"Rojas Vega","full_name":"Rojas Vega, Mauricio Nicolas","first_name":"Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d"},{"first_name":"Pablo","full_name":"De Castro, Pablo","last_name":"De Castro"},{"first_name":"Rodrigo","last_name":"Soto","full_name":"Soto, Rodrigo"}],"month":"01","article_number":"014608","doi":"10.1103/PhysRevE.107.014608","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","arxiv":1,"oa_version":"Preprint","publication":"Physical Review E","language":[{"iso":"eng"}],"oa":1,"publisher":"American Physical Society","isi":1,"intvolume":"       107","external_id":{"isi":["000963909800006"],"arxiv":["2301.01856"]},"day":"24","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","volume":107,"acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","issue":"1","year":"2023","_id":"12545","date_updated":"2023-08-01T13:09:45Z","citation":{"ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608.","apa":"Rojas Vega, M. N., De Castro, P., &#38; Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">https://doi.org/10.1103/PhysRevE.107.014608</a>","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” <i>Physical Review E</i>, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">10.1103/PhysRevE.107.014608</a>.","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. <i>Physical Review E</i>. 2023;107(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">10.1103/PhysRevE.107.014608</a>","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.107.014608\">https://doi.org/10.1103/PhysRevE.107.014608</a>.","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” <i>Physical Review E</i>, vol. 107, no. 1. American Physical Society, 2023."},"department":[{"_id":"GradSch"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01856","open_access":"1"}],"publication_status":"published","date_created":"2023-02-12T23:00:59Z"},{"publication_status":"published","pmid":1,"date_created":"2023-02-24T10:45:01Z","file_date_updated":"2023-08-16T12:33:31Z","date_updated":"2024-02-21T12:14:06Z","_id":"12675","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"citation":{"apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202219314\">https://doi.org/10.1002/anie.202219314</a>","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 62(19), e202219314.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International Edition 62 (2023).","mla":"Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19, e202219314, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/anie.202219314\">10.1002/anie.202219314</a>.","ama":"Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. <i>Angewandte Chemie International Edition</i>. 2023;62(19). doi:<a href=\"https://doi.org/10.1002/anie.202219314\">10.1002/anie.202219314</a>","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” <i>Angewandte Chemie International Edition</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/anie.202219314\">https://doi.org/10.1002/anie.202219314</a>.","ieee":"L. M. Becker <i>et al.</i>, “The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” <i>Angewandte Chemie International Edition</i>, vol. 62, no. 19. Wiley, 2023."},"year":"2023","issue":"19","title":"The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues","day":"01","external_id":{"pmid":["36738230"],"isi":["000956919900001"]},"acknowledgement":"We thank AlbertA. Smith (Leipzig)for insightful discussions. This work was supported by funding from the European Research Council (StG-2012-311318 to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518 CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS) at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University.","volume":62,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"intvolume":"        62","isi":1,"oa":1,"publisher":"Wiley","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["General Chemistry","Catalysis"],"publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"doi":"10.1002/anie.202219314","language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Angewandte Chemie International Edition","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/dancing-styles-of-atoms/"}],"record":[{"relation":"other","id":"14861","status":"public"},{"status":"public","id":"12497","relation":"research_data"}]},"month":"05","author":[{"last_name":"Becker","full_name":"Becker, Lea Marie","first_name":"Lea Marie","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"first_name":"Mélanie","last_name":"Berbon","full_name":"Berbon, Mélanie"},{"first_name":"Alicia","last_name":"Vallet","full_name":"Vallet, Alicia"},{"full_name":"Grelard, Axelle","last_name":"Grelard","first_name":"Axelle"},{"last_name":"Morvan","full_name":"Morvan, Estelle","first_name":"Estelle"},{"first_name":"Benjamin","full_name":"Bardiaux, Benjamin","last_name":"Bardiaux"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"first_name":"Matthias","full_name":"Ernst, Matthias","last_name":"Ernst"},{"first_name":"Antoine","last_name":"Loquet","full_name":"Loquet, Antoine"},{"last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_number":"e202219314","quality_controlled":"1","status":"public","article_type":"original","abstract":[{"lang":"eng","text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein--protein interactions. By studying a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have characterized the dynamic behavior of Phe and Tyr aromatic rings to show that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips, on a variety of time scales from ns to µs. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from a NMR structural ensemble of such amyloid cross-β architecture."}],"ddc":["540"],"date_published":"2023-05-01T00:00:00Z","file":[{"file_id":"14072","content_type":"application/pdf","access_level":"open_access","file_size":1422445,"file_name":"2023_AngewChemInt_Becker.pdf","date_updated":"2023-08-16T12:33:31Z","success":1,"date_created":"2023-08-16T12:33:31Z","relation":"main_file","checksum":"7dd083ed8850faa55c34e411ed390de9","creator":"dernst"}]},{"year":"2023","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","day":"01","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","date_created":"2023-02-24T12:20:47Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611977554.ch173"}],"citation":{"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.","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., &#38; Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">https://doi.org/10.1137/1.9781611977554.ch173</a>","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.” <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">10.1137/1.9781611977554.ch173</a>.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:<a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">10.1137/1.9781611977554.ch173</a>","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 4590–4605. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/1.9781611977554.ch173\">https://doi.org/10.1137/1.9781611977554.ch173</a>.","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in <i>Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Florence, Italy, 2023, pp. 4590–4605."},"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"_id":"12676","date_updated":"2025-07-14T09:09:50Z","conference":{"start_date":"2023-01-22","location":"Florence, Italy","name":"SODA: Symposium on Discrete Algorithms","end_date":"2023-01-25"},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"article_processing_charge":"No","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","first_name":"Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X"},{"orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","full_name":"Svoboda, Jakub","last_name":"Svoboda"}],"month":"02","date_published":"2023-02-01T00:00:00Z","abstract":[{"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.","lang":"eng"}],"status":"public","quality_controlled":"1","oa":1,"publisher":"Society for Industrial and Applied Mathematics","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"page":"4590-4605","doi":"10.1137/1.9781611977554.ch173","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["9781611977554"]},"type":"conference"},{"issue":"6","year":"2023","day":"01","title":"Erdős-Ko-Rado and Hilton-Milner theorems for two-forms","external_id":{"arxiv":["2201.10892"]},"volume":346,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2201.10892"}],"publication_status":"published","date_created":"2023-02-26T23:01:00Z","_id":"12680","date_updated":"2023-10-04T11:54:57Z","citation":{"chicago":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” <i>Discrete Mathematics</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.disc.2023.113363\">https://doi.org/10.1016/j.disc.2023.113363</a>.","mla":"Ivanov, Grigory, and Seyda Köse. “Erdős-Ko-Rado and Hilton-Milner Theorems for Two-Forms.” <i>Discrete Mathematics</i>, vol. 346, no. 6, 113363, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.disc.2023.113363\">10.1016/j.disc.2023.113363</a>.","ama":"Ivanov G, Köse S. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. <i>Discrete Mathematics</i>. 2023;346(6). doi:<a href=\"https://doi.org/10.1016/j.disc.2023.113363\">10.1016/j.disc.2023.113363</a>","short":"G. Ivanov, S. Köse, Discrete Mathematics 346 (2023).","ista":"Ivanov G, Köse S. 2023. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. 346(6), 113363.","apa":"Ivanov, G., &#38; Köse, S. (2023). Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. <i>Discrete Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.disc.2023.113363\">https://doi.org/10.1016/j.disc.2023.113363</a>","ieee":"G. Ivanov and S. Köse, “Erdős-Ko-Rado and Hilton-Milner theorems for two-forms,” <i>Discrete Mathematics</i>, vol. 346, no. 6. Elsevier, 2023."},"department":[{"_id":"UlWa"},{"_id":"GradSch"}],"author":[{"first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","last_name":"Ivanov","full_name":"Ivanov, Grigory"},{"id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","first_name":"Seyda","full_name":"Köse, Seyda","last_name":"Köse"}],"month":"06","scopus_import":"1","article_processing_charge":"No","article_number":"113363","quality_controlled":"1","article_type":"letter_note","status":"public","date_published":"2023-06-01T00:00:00Z","abstract":[{"text":"The celebrated Erdős–Ko–Rado theorem about the maximal size of an intersecting family of r-element subsets of  was extended to the setting of exterior algebra in [5, Theorem 2.3] and in [6, Theorem 1.4]. However, the equality case has not been settled yet. In this short note, we show that the extension of the Erdős–Ko–Rado theorem and the characterization of the equality case therein, as well as those of the Hilton–Milner theorem to the setting of exterior algebra in the simplest non-trivial case of two-forms follow from a folklore puzzle about possible arrangements of an intersecting family of lines.","lang":"eng"}],"intvolume":"       346","publisher":"Elsevier","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0012-365X"]},"type":"journal_article","doi":"10.1016/j.disc.2023.113363","arxiv":1,"oa_version":"Preprint","publication":"Discrete Mathematics","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"13331","status":"public"}]}},{"year":"2023","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","last_name":"Jösch"}],"day":"10","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","alternative_title":["ISTA Thesis"],"publication_status":"published","date_created":"2023-03-08T15:19:45Z","_id":"12716","date_updated":"2023-04-05T10:59:04Z","project":[{"name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","grant_number":"756502"}],"file_date_updated":"2023-03-08T15:08:46Z","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.","mla":"Burnett, Laura. <i>To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>.","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:<a href=\"https://doi.org/10.15479/at:ista:12716\">10.15479/at:ista:12716</a>","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. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>.","apa":"Burnett, L. (2023). <i>To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12716\">https://doi.org/10.15479/at:ista:12716</a>","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.","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."},"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"article_processing_charge":"No","author":[{"orcid":"0000-0002-8937-410X","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","full_name":"Burnett, Laura","last_name":"Burnett"}],"month":"03","has_accepted_license":"1","status":"public","file":[{"access_level":"closed","file_size":23029260,"file_id":"12717","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-03-08T15:08:46Z","file_name":"Burnett_Thesis_2023.docx","date_created":"2023-03-08T15:08:46Z","relation":"source_file","creator":"lburnett","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332"},{"relation":"main_file","date_created":"2023-03-08T15:08:46Z","checksum":"cebc77705288bf4382db9b3541483cd0","creator":"lburnett","content_type":"application/pdf","file_id":"12718","file_size":11959869,"access_level":"open_access","file_name":"Burnett_Thesis_2023_pdfA.pdf","date_updated":"2023-03-08T15:08:46Z","success":1}],"date_published":"2023-03-10T00:00:00Z","ddc":["599","573"],"abstract":[{"text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","oa":1,"page":"178","degree_awarded":"PhD","doi":"10.15479/at:ista:12716","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"publication_identifier":{"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1}]