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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. ","lang":"eng"}],"day":"26","doi":"10.15479/AT:ISTA:12370","type":"research_data","date_published":"2023-01-26T00:00:00Z","year":"2023","citation":{"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>","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>","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.","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>.","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>.","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>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"date_updated":"2023-10-04T11:41:04Z"},{"date_published":"2023-01-09T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0065-1036"],"eissn":["1730-6264"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2103.08268","open_access":"1"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Acta Arithmetica","oa_version":"Preprint","month":"01","language":[{"iso":"eng"}],"keyword":["Algebra","Number Theory"],"date_updated":"2023-10-17T09:15:17Z","year":"2023","citation":{"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>","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>","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.","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>.","short":"Y. Diao, Acta Arithmetica 207 (2023) 1–17.","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>.","ista":"Diao Y. 2023. Density of the union of positive diagonal binary quadratic forms. Acta Arithmetica. 207, 1–17."},"isi":1,"external_id":{"arxiv":["2103.08268"],"isi":["000912903000001"]},"arxiv":1,"doi":"10.4064/aa210830-24-11","day":"09","abstract":[{"lang":"eng","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."}],"volume":207,"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","_id":"12406","author":[{"last_name":"Diao","first_name":"Yijie","full_name":"Diao, Yijie","orcid":"0000-0002-4989-5330","id":"7b7eb4ca-eb2c-11ec-b98b-accec0b20c3b"}],"publication_status":"published","date_created":"2023-01-26T21:17:04Z","department":[{"_id":"GradSch"}],"article_processing_charge":"No","title":"Density of the union of positive diagonal binary quadratic forms","intvolume":"       207","page":"1-17","quality_controlled":"1","publisher":"Instytut Matematyczny","article_type":"original"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","file":[{"success":1,"relation":"main_file","access_level":"open_access","creator":"esarac","file_id":"12468","file_size":449027,"checksum":"981025aed580b6b27c426cb8856cf63e","date_created":"2023-01-31T07:22:21Z","file_name":"qsl.pdf","content_type":"application/pdf","date_updated":"2023-01-31T07:22:21Z"},{"file_name":"2023_LNCS_HenzingerT.pdf","content_type":"application/pdf","date_updated":"2023-06-19T10:28:09Z","file_size":1048171,"checksum":"f16e2af1e0eb243158ab0f0fe74e7d5a","date_created":"2023-06-19T10:28:09Z","creator":"dernst","file_id":"13153","success":1,"relation":"main_file","access_level":"open_access"}],"type":"conference","date_published":"2023-04-21T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"isbn":["9783031308284"],"issn":["0302-9743"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"conference":{"location":"Paris, France","end_date":"2023-04-27","name":"FOSSACS: Foundations of Software Science and Computation Structures","start_date":"2023-04-22"},"has_accepted_license":"1","publication":"26th International Conference Foundations of Software Science and Computation Structures","month":"04","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020"}],"oa_version":"Published Version","ddc":["000"],"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","volume":13992,"external_id":{"arxiv":["2301.11175"]},"year":"2023","citation":{"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.","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>.","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>","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>","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.","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>.","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."},"date_updated":"2023-07-14T11:20:27Z","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"}],"day":"21","doi":"10.1007/978-3-031-30829-1_17","arxiv":1,"file_date_updated":"2023-06-19T10:28:09Z","ec_funded":1,"quality_controlled":"1","page":"349-370","publisher":"Springer Nature","author":[{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mazzocchi, Nicolas Adrien","last_name":"Mazzocchi","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"full_name":"Sarac, Naci E","first_name":"Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"scopus_import":"1","_id":"12467","intvolume":"     13992","title":"Quantitative safety and liveness","alternative_title":["LNCS"],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"article_processing_charge":"No","date_created":"2023-01-31T07:23:56Z","publication_status":"published"},{"author":[{"last_name":"Michalska","first_name":"Julia M","full_name":"Michalska, Julia M","orcid":"0000-0003-3862-1235","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"}],"_id":"12470","title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"article_processing_charge":"No","date_created":"2023-01-31T15:10:53Z","file_date_updated":"2023-07-27T22:30:54Z","page":"201","ec_funded":1,"publisher":"Institute of Science and Technology Austria","date_updated":"2023-08-31T12:26:58Z","citation":{"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>.","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.","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>","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>","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","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.","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>."},"year":"2023","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."}],"doi":"10.15479/at:ista:12470","degree_awarded":"PhD","day":"09","ddc":["610"],"has_accepted_license":"1","month":"01","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"oa_version":"Published Version","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"date_published":"2023-01-09T00:00:00Z","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"supervisor":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]},"related_material":{"record":[{"id":"11943","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"11950","relation":"part_of_dissertation"}]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"date_updated":"2023-07-27T22:30:54Z","content_type":"application/pdf","file_name":"20230109_PhD_thesis_JM_final.pdf","date_created":"2023-01-31T15:11:42Z","embargo":"2023-07-09","checksum":"1a2306e5f59f52df598e7ecfadf921ac","file_size":41771714,"file_id":"12471","creator":"cchlebak","access_level":"open_access","relation":"main_file"},{"creator":"cchlebak","file_id":"12472","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"20230109_PhD_thesis_JM_final.docx","date_updated":"2023-07-10T22:30:04Z","checksum":"0bebbdee0773443959e1f6ab8caf281f","file_size":66983464,"embargo_to":"open_access","date_created":"2023-01-31T15:11:51Z"}]},{"publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-02-08T23:30:04Z","page":"187","alternative_title":["ISTA Thesis"],"title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","article_processing_charge":"No","date_created":"2023-02-02T14:50:20Z","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"publication_status":"published","author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","last_name":"Zens","full_name":"Zens, Bettina"}],"_id":"12491","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"}],"day":"02","doi":"10.15479/at:ista:12491","degree_awarded":"PhD","citation":{"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>.","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","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>","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>","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","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>.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023."},"year":"2023","date_updated":"2024-02-08T23:30:05Z","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"],"language":[{"iso":"eng"}],"month":"02","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"_id":"059B463C-7A3F-11EA-A408-12923DDC885E","name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Published Version","has_accepted_license":"1","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"8586","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_id":"12527","creator":"bzens","access_level":"open_access","relation":"main_file","date_updated":"2024-02-08T23:30:04Z","file_name":"PhDThesis_BettinaZens_2023_final.pdf","content_type":"application/pdf","date_created":"2023-02-07T13:07:38Z","embargo":"2024-02-07","file_size":23082464,"checksum":"069d87f025e0799bf9e3c375664264f2"},{"creator":"bzens","file_id":"12528","access_level":"closed","relation":"source_file","file_name":"PhDThesis_BettinaZens_2023_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-02-08T23:30:04Z","embargo_to":"open_access","file_size":106169509,"checksum":"8c66ed203495d6e078ed1002a866520c","date_created":"2023-02-07T13:09:05Z"}],"oa":1,"supervisor":[{"last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"type":"dissertation","date_published":"2023-02-02T00:00:00Z"},{"has_accepted_license":"1","_id":"12497","author":[{"first_name":"Lea Marie","last_name":"Becker","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"date_created":"2023-02-03T08:08:02Z","oa_version":"Published Version","title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","month":"03","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"file_date_updated":"2023-03-24T09:42:03Z","contributor":[{"first_name":"Mélanie","last_name":"Berbon","contributor_type":"researcher"},{"last_name":"Vallet","contributor_type":"researcher","first_name":"Alicia"},{"last_name":"Grelard","contributor_type":"researcher","first_name":"Axelle"},{"first_name":"Estelle","last_name":"Morvan","contributor_type":"researcher"},{"first_name":"Benjamin","contributor_type":"researcher","last_name":"Bardiaux"},{"last_name":"Lichtenecker","contributor_type":"researcher","first_name":"Roman"},{"first_name":"Matthias","last_name":"Ernst","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Loquet","first_name":"Antoine"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","contributor_type":"contact_person","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Lea Marie","contributor_type":"researcher","last_name":"Becker","orcid":"0000-0002-6401-5151","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"}],"publisher":"Institute of Science and Technology Austria","citation":{"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>.","short":"L.M. Becker, P. Schanda, (2023).","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>.","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>.","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.","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>","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>"},"year":"2023","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"date_updated":"2024-02-21T12:14:06Z","type":"research_data","date_published":"2023-03-23T00:00:00Z","day":"23","doi":"10.15479/AT:ISTA:12497","oa":1,"abstract":[{"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.","lang":"eng"}],"file":[{"file_id":"12743","creator":"lbecker","access_level":"open_access","relation":"main_file","date_updated":"2023-03-24T09:34:20Z","content_type":"application/zip","file_name":"Research_Data.zip","date_created":"2023-03-23T10:03:16Z","file_size":87018103,"checksum":"fd9a28620a81a82991fb70f4fd6591d9"},{"file_id":"12755","creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2023-03-24T09:42:03Z","content_type":"text/plain","file_name":"README.txt","date_created":"2023-03-24T07:13:55Z","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","file_size":747}],"related_material":{"record":[{"id":"12675","relation":"used_in_publication","status":"public"}]},"ddc":["572"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"},{"publication":"Evolution Letters","has_accepted_license":"1","oa_version":"Published Version","project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"month":"02","article_number":"qrac004","language":[{"iso":"eng"}],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-02-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["2056-3744"]},"oa":1,"file":[{"checksum":"a240a041cb9b9b7c8ba93a4706674a3f","file_size":2592189,"date_created":"2023-08-16T11:43:33Z","content_type":"application/pdf","file_name":"2023_EvLetters_Mrnjavac.pdf","date_updated":"2023-08-16T11:43:33Z","relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","file_id":"14068"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12521","pmid":1,"scopus_import":"1","author":[{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","first_name":"Andrea","full_name":"Mrnjavac, Andrea"},{"id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"}],"issue":"1","publication_status":"published","article_processing_charge":"Yes (via OA deal)","date_created":"2023-02-06T13:59:12Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","intvolume":"         7","quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-08-16T11:43:33Z","publisher":"Oxford University Press","article_type":"original","date_updated":"2023-08-16T11:44:32Z","year":"2023","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>.","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>","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.","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>.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023)."},"isi":1,"external_id":{"isi":["001021692200001"],"pmid":["37065438"]},"doi":"10.1093/evlett/qrac004","day":"01","abstract":[{"lang":"eng","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."}],"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,"ddc":["570"]},{"ddc":["570"],"date_updated":"2024-02-09T23:30:04Z","citation":{"ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","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>.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","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>.","ieee":"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>","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>"},"year":"2023","degree_awarded":"MS","doi":"10.15479/at:ista:12531","day":"08","abstract":[{"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.","lang":"eng"}],"page":"46","file_date_updated":"2024-02-09T23:30:03Z","publisher":"Institute of Science and Technology Austria","_id":"12531","author":[{"id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","full_name":"Kirillova, Kseniia","last_name":"Kirillova","first_name":"Kseniia"}],"publication_status":"published","date_created":"2023-02-09T07:45:05Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"alternative_title":["ISTA Master's Thesis"],"title":"Panoramic functional gradients across the mouse retina","file":[{"file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","content_type":"application/pdf","date_updated":"2024-02-09T23:30:03Z","file_size":8369317,"checksum":"57d8da3a6c749eb1556b7435fe266a5f","date_created":"2023-02-09T08:03:32Z","embargo":"2024-02-08","creator":"cchlebak","file_id":"12532","access_level":"open_access","relation":"main_file"},{"date_updated":"2024-02-09T23:30:03Z","content_type":"application/x-zip-compressed","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","date_created":"2023-02-10T09:32:06Z","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","file_size":11204408,"embargo_to":"open_access","file_id":"12535","creator":"cchlebak","access_level":"closed","relation":"source_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"date_published":"2023-02-08T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2791-4585"]},"supervisor":[{"first_name":"Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","month":"02"},{"quality_controlled":"1","publisher":"American Physical Society","article_type":"original","_id":"12545","scopus_import":"1","author":[{"id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","last_name":"Rojas Vega","first_name":"Mauricio Nicolas","full_name":"Rojas Vega, Mauricio Nicolas"},{"full_name":"De Castro, Pablo","first_name":"Pablo","last_name":"De Castro"},{"first_name":"Rodrigo","last_name":"Soto","full_name":"Soto, Rodrigo"}],"issue":"1","publication_status":"published","date_created":"2023-02-12T23:00:59Z","department":[{"_id":"GradSch"}],"article_processing_charge":"No","title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","intvolume":"       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.","volume":107,"date_updated":"2023-08-01T13:09:45Z","citation":{"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.","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>","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>","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.","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>."},"year":"2023","isi":1,"external_id":{"arxiv":["2301.01856"],"isi":["000963909800006"]},"arxiv":1,"doi":"10.1103/PhysRevE.107.014608","day":"24","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"publication":"Physical Review E","oa_version":"Preprint","month":"01","article_number":"014608","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01856"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2023-01-24T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"oa":1},{"file_date_updated":"2023-08-16T12:33:31Z","quality_controlled":"1","article_type":"original","publisher":"Wiley","issue":"19","author":[{"first_name":"Lea Marie","last_name":"Becker","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"full_name":"Berbon, Mélanie","first_name":"Mélanie","last_name":"Berbon"},{"first_name":"Alicia","last_name":"Vallet","full_name":"Vallet, Alicia"},{"full_name":"Grelard, Axelle","first_name":"Axelle","last_name":"Grelard"},{"full_name":"Morvan, Estelle","last_name":"Morvan","first_name":"Estelle"},{"first_name":"Benjamin","last_name":"Bardiaux","full_name":"Bardiaux, Benjamin"},{"full_name":"Lichtenecker, Roman","first_name":"Roman","last_name":"Lichtenecker"},{"full_name":"Ernst, Matthias","last_name":"Ernst","first_name":"Matthias"},{"full_name":"Loquet, Antoine","first_name":"Antoine","last_name":"Loquet"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"_id":"12675","pmid":1,"intvolume":"        62","title":"The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"article_processing_charge":"Yes (via OA deal)","date_created":"2023-02-24T10:45:01Z","publication_status":"published","ddc":["540"],"volume":62,"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.","external_id":{"isi":["000956919900001"],"pmid":["36738230"]},"isi":1,"citation":{"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>.","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).","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.","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>","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","date_updated":"2024-02-21T12:14:06Z","abstract":[{"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.","lang":"eng"}],"day":"01","doi":"10.1002/anie.202219314","keyword":["General Chemistry","Catalysis"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Angewandte Chemie International Edition","article_number":"e202219314","month":"05","oa_version":"Published Version","related_material":{"record":[{"relation":"other","id":"14861","status":"public"},{"status":"public","id":"12497","relation":"research_data"}],"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/dancing-styles-of-atoms/"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"content_type":"application/pdf","file_name":"2023_AngewChemInt_Becker.pdf","date_updated":"2023-08-16T12:33:31Z","file_size":1422445,"checksum":"7dd083ed8850faa55c34e411ed390de9","date_created":"2023-08-16T12:33:31Z","creator":"dernst","file_id":"14072","success":1,"relation":"main_file","access_level":"open_access"}],"type":"journal_article","date_published":"2023-05-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"oa":1,"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"url":"https://doi.org/10.1137/1.9781611977554.ch173","open_access":"1"}],"oa":1,"publication_identifier":{"isbn":["9781611977554"]},"type":"conference","date_published":"2023-02-01T00:00:00Z","conference":{"end_date":"2023-01-25","location":"Florence, Italy","name":"SODA: Symposium on Discrete Algorithms","start_date":"2023-01-22"},"language":[{"iso":"eng"}],"month":"02","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"oa_version":"Published Version","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}],"day":"01","doi":"10.1137/1.9781611977554.ch173","year":"2023","citation":{"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>.","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.","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>","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."},"date_updated":"2025-07-14T09:09:50Z","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","ec_funded":1,"page":"4590-4605","title":"Faster algorithm for turn-based stochastic games with bounded treewidth","article_processing_charge":"No","date_created":"2023-02-24T12:20:47Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication_status":"published","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","first_name":"Tobias","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165"},{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","first_name":"Raimundo J","last_name":"Saona Urmeneta","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","last_name":"Svoboda","orcid":"0000-0002-1419-3267","full_name":"Svoboda, Jakub"}],"_id":"12676"},{"publication":"Discrete Mathematics","oa_version":"Preprint","article_number":"113363","month":"06","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2023-06-01T00:00:00Z","publication_identifier":{"issn":["0012-365X"]},"oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2201.10892","open_access":"1"}],"related_material":{"record":[{"id":"13331","relation":"dissertation_contains","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","scopus_import":"1","_id":"12680","issue":"6","author":[{"first_name":"Grigory","last_name":"Ivanov","full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb","first_name":"Seyda","last_name":"Köse","full_name":"Köse, Seyda"}],"department":[{"_id":"UlWa"},{"_id":"GradSch"}],"date_created":"2023-02-26T23:01:00Z","article_processing_charge":"No","publication_status":"published","intvolume":"       346","title":"Erdős-Ko-Rado and Hilton-Milner theorems for two-forms","quality_controlled":"1","publisher":"Elsevier","article_type":"letter_note","year":"2023","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>.","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.","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>","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>","ista":"Ivanov G, Köse S. 2023. Erdős-Ko-Rado and Hilton-Milner theorems for two-forms. Discrete Mathematics. 346(6), 113363.","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>.","short":"G. Ivanov, S. Köse, Discrete Mathematics 346 (2023)."},"date_updated":"2023-10-04T11:54:57Z","external_id":{"arxiv":["2201.10892"]},"day":"01","doi":"10.1016/j.disc.2023.113363","arxiv":1,"abstract":[{"lang":"eng","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."}],"volume":346},{"ddc":["599","573"],"citation":{"ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","mla":"Burnett, Laura. <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>.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. <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>","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>"},"year":"2023","date_updated":"2023-04-05T10:59:04Z","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"}],"day":"10","doi":"10.15479/at:ista:12716","degree_awarded":"PhD","file_date_updated":"2023-03-08T15:08:46Z","ec_funded":1,"page":"178","publisher":"Institute of Science and Technology Austria","author":[{"id":"3B717F68-F248-11E8-B48F-1D18A9856A87","first_name":"Laura","last_name":"Burnett","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura"}],"_id":"12716","alternative_title":["ISTA Thesis"],"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","article_processing_charge":"No","date_created":"2023-03-08T15:19:45Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","file":[{"creator":"lburnett","file_id":"12717","relation":"source_file","access_level":"closed","file_name":"Burnett_Thesis_2023.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-03-08T15:08:46Z","file_size":23029260,"checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332","date_created":"2023-03-08T15:08:46Z"},{"file_size":11959869,"checksum":"cebc77705288bf4382db9b3541483cd0","date_created":"2023-03-08T15:08:46Z","content_type":"application/pdf","file_name":"Burnett_Thesis_2023_pdfA.pdf","date_updated":"2023-03-08T15:08:46Z","access_level":"open_access","success":1,"relation":"main_file","creator":"lburnett","file_id":"12718"}],"type":"dissertation","date_published":"2023-03-10T00:00:00Z","oa":1,"supervisor":[{"last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"03","project":[{"grant_number":"756502","name":"Circuits of Visual Attention","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}]},{"language":[{"iso":"eng"}],"keyword":["General Physics and Astronomy"],"month":"03","article_number":"106901","oa_version":"Preprint","publication":"Physical Review Letters","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.09443","open_access":"1"}],"oa":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"date_published":"2023-03-10T00:00:00Z","type":"journal_article","article_type":"original","publisher":"American Physical Society","quality_controlled":"1","title":"Spin-electric coupling in lead halide perovskites","intvolume":"       130","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"article_processing_charge":"No","date_created":"2023-03-14T13:11:59Z","author":[{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"},{"id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","full_name":"Shiva Kumar, Abhishek","last_name":"Shiva Kumar","first_name":"Abhishek"},{"last_name":"Lorenc","first_name":"Dusan","full_name":"Lorenc, Dusan","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87"},{"id":"e32c111f-f6e0-11ea-865d-eb955baea334","full_name":"Ashourishokri, Younes","first_name":"Younes","last_name":"Ashourishokri"},{"full_name":"Zhumekenov, Ayan A.","first_name":"Ayan A.","last_name":"Zhumekenov"},{"full_name":"Bakr, Osman M.","first_name":"Osman M.","last_name":"Bakr"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek"}],"issue":"10","_id":"12723","scopus_import":"1","volume":130,"abstract":[{"lang":"eng","text":"Lead halide perovskites enjoy a number of remarkable optoelectronic properties. To explain their origin, it is necessary to study how electromagnetic fields interact with these systems. We address this problem here by studying two classical quantities: Faraday rotation and the complex refractive index in a paradigmatic perovskite CH3NH3PbBr3 in a broad wavelength range. We find that the minimal coupling of electromagnetic fields to the k⋅p Hamiltonian is insufficient to describe the observed data even on the qualitative level. To amend this, we demonstrate that there exists a relevant atomic-level coupling between electromagnetic fields and the spin degree of freedom. This spin-electric coupling allows for quantitative description of a number of previous as well as present experimental data. In particular, we use it here to show that the Faraday effect in lead halide perovskites is dominated by the Zeeman splitting of the energy levels and has a substantial beyond-Becquerel contribution. Finally, we present general symmetry-based phenomenological arguments that in the low-energy limit our effective model includes all basis coupling terms to the electromagnetic field in the linear order."}],"arxiv":1,"doi":"10.1103/physrevlett.130.106901","day":"10","isi":1,"external_id":{"isi":["000982435900002"],"arxiv":["2203.09443"]},"date_updated":"2023-08-01T13:39:04Z","citation":{"ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Spin-electric coupling in lead halide perovskites. <i>Physical Review Letters</i>. 2023;130(10). doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106901\">10.1103/physrevlett.130.106901</a>","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A. A., Bakr, O. M., … Alpichshev, Z. (2023). Spin-electric coupling in lead halide perovskites. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.130.106901\">https://doi.org/10.1103/physrevlett.130.106901</a>","ieee":"A. Volosniev <i>et al.</i>, “Spin-electric coupling in lead halide perovskites,” <i>Physical Review Letters</i>, vol. 130, no. 10. American Physical Society, 2023.","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Spin-Electric Coupling in Lead Halide Perovskites.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevlett.130.106901\">https://doi.org/10.1103/physrevlett.130.106901</a>.","mla":"Volosniev, Artem, et al. “Spin-Electric Coupling in Lead Halide Perovskites.” <i>Physical Review Letters</i>, vol. 130, no. 10, 106901, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevlett.130.106901\">10.1103/physrevlett.130.106901</a>.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review Letters 130 (2023).","ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Spin-electric coupling in lead halide perovskites. Physical Review Letters. 130(10), 106901."},"year":"2023"},{"publication":"Physical Review B","oa_version":"Preprint","article_number":"125201","month":"03","language":[{"iso":"eng"}],"type":"journal_article","date_published":"2023-03-15T00:00:00Z","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.04022","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","scopus_import":"1","_id":"12724","issue":"12","author":[{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"},{"id":"5e9a6931-eb97-11eb-a6c2-e96f7058d77a","first_name":"Abhishek","last_name":"Shiva Kumar","full_name":"Shiva Kumar, Abhishek"},{"id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","full_name":"Lorenc, Dusan","last_name":"Lorenc","first_name":"Dusan"},{"id":"e32c111f-f6e0-11ea-865d-eb955baea334","full_name":"Ashourishokri, Younes","last_name":"Ashourishokri","first_name":"Younes"},{"full_name":"Zhumekenov, Ayan","first_name":"Ayan","last_name":"Zhumekenov"},{"full_name":"Bakr, Osman M.","last_name":"Bakr","first_name":"Osman M."},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","first_name":"Zhanybek","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek"}],"date_created":"2023-03-14T13:13:05Z","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"ZhAl"},{"_id":"MiLe"}],"publication_status":"published","intvolume":"       107","title":"Effective model for studying optical properties of lead halide perovskites","quality_controlled":"1","publisher":"American Physical Society","article_type":"original","citation":{"ista":"Volosniev A, Shiva Kumar A, Lorenc D, Ashourishokri Y, Zhumekenov A, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Effective model for studying optical properties of lead halide perovskites. Physical Review B. 107(12), 125201.","mla":"Volosniev, Artem, et al. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” <i>Physical Review B</i>, vol. 107, no. 12, 125201, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.107.125201\">10.1103/physrevb.107.125201</a>.","short":"A. Volosniev, A. Shiva Kumar, D. Lorenc, Y. Ashourishokri, A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, Physical Review B 107 (2023).","chicago":"Volosniev, Artem, Abhishek Shiva Kumar, Dusan Lorenc, Younes Ashourishokri, Ayan Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Effective Model for Studying Optical Properties of Lead Halide Perovskites.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.107.125201\">https://doi.org/10.1103/physrevb.107.125201</a>.","ieee":"A. Volosniev <i>et al.</i>, “Effective model for studying optical properties of lead halide perovskites,” <i>Physical Review B</i>, vol. 107, no. 12. American Physical Society, 2023.","apa":"Volosniev, A., Shiva Kumar, A., Lorenc, D., Ashourishokri, Y., Zhumekenov, A., Bakr, O. M., … Alpichshev, Z. (2023). Effective model for studying optical properties of lead halide perovskites. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.107.125201\">https://doi.org/10.1103/physrevb.107.125201</a>","ama":"Volosniev A, Shiva Kumar A, Lorenc D, et al. Effective model for studying optical properties of lead halide perovskites. <i>Physical Review B</i>. 2023;107(12). doi:<a href=\"https://doi.org/10.1103/physrevb.107.125201\">10.1103/physrevb.107.125201</a>"},"year":"2023","date_updated":"2023-08-01T13:39:47Z","external_id":{"arxiv":["2204.04022"],"isi":["000972602200006"]},"isi":1,"day":"15","arxiv":1,"doi":"10.1103/physrevb.107.125201","abstract":[{"lang":"eng","text":"We use general symmetry-based arguments to construct an effective model suitable for studying optical properties of lead halide perovskites. To build the model, we identify an atomic-level interaction between electromagnetic fields and the spin degree of freedom that should be added to a minimally coupled k⋅p Hamiltonian. As a first application, we study two basic optical characteristics of the material: the Verdet constant and the refractive index. Beyond these linear characteristics of the material, the model is suitable for calculating nonlinear effects such as the third-order optical susceptibility. Analysis of this quantity shows that the geometrical properties of the spin-electric term imply isotropic optical response of the system, and that optical anisotropy of lead halide perovskites is a manifestation of hopping of charge carriers. To illustrate this, we discuss third-harmonic generation."}],"volume":107},{"language":[{"iso":"eng"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"oa_version":"None","month":"03","file":[{"creator":"cchlebak","file_id":"12745","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","access_level":"closed","relation":"main_file","content_type":"application/pdf","file_name":"Thesis_Riedl_2023.pdf","date_updated":"2023-11-24T11:57:46Z","file_size":63734746,"checksum":"eba0e19fe57a8c15e7aeab55a845efb7","date_created":"2023-03-23T12:49:23Z"},{"date_created":"2023-03-23T12:54:34Z","file_size":339473651,"checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","embargo_to":"open_access","date_updated":"2023-09-24T22:30:03Z","content_type":"application/octet-stream","file_name":"Thesis_Riedl_2023_source.rar","access_level":"closed","relation":"source_file","file_id":"12746","creator":"cchlebak"}],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","id":"10703","relation":"part_of_dissertation"},{"id":"10791","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7932"},{"status":"public","relation":"part_of_dissertation","id":"461"},{"id":"14530","relation":"new_edition","status":"public"}]},"type":"dissertation","date_published":"2023-03-23T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof"}],"page":"260","file_date_updated":"2023-11-24T11:57:46Z","publisher":"Institute of Science and Technology Austria","_id":"12726","author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Riedl","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"date_created":"2023-03-15T13:22:13Z","publication_status":"published","title":"Synchronization in collectively moving active matter","alternative_title":["ISTA Thesis"],"ddc":["530"],"year":"2023","citation":{"ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>","apa":"Riedl, M. (2023). <i>Synchronization in collectively moving active matter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12726\">https://doi.org/10.15479/at:ista:12726</a>.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","mla":"Riedl, Michael. <i>Synchronization in Collectively Moving Active Matter</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12726\">10.15479/at:ista:12726</a>.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria."},"date_updated":"2023-11-30T10:55:13Z","day":"23","degree_awarded":"PhD","doi":"10.15479/at:ista:12726","abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex."}]},{"publication_status":"published","article_processing_charge":"No","date_created":"2023-03-17T13:30:48Z","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"alternative_title":["ISTA Thesis"],"title":"Ergodicity breaking in disordered and kinetically constrained quantum many-body systems","_id":"12732","author":[{"id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","first_name":"Pietro","last_name":"Brighi"}],"publisher":"Institute of Science and Technology Austria","page":"158","ec_funded":1,"file_date_updated":"2023-03-23T16:43:14Z","doi":"10.15479/at:ista:12732","degree_awarded":"PhD","day":"21","abstract":[{"text":"Nonergodic systems, whose out-of-equilibrium dynamics fail to thermalize, provide a fascinating research direction both for fundamental reasons and for application in state of the art quantum devices.\r\nGoing beyond the description of statistical mechanics, ergodicity breaking yields a new paradigm in quantum many-body physics, introducing novel phases of matter with no counterpart at equilibrium.\r\nIn this Thesis, we address different open questions in the field, focusing on disorder-induced many-body localization (MBL) and on weak ergodicity breaking in kinetically constrained models.\r\nIn particular, we contribute to the debate about transport in kinetically constrained models, studying the effect of $U(1)$ conservation and inversion-symmetry breaking in a family of quantum East models.\r\nUsing tensor network techniques, we analyze the dynamics of large MBL systems beyond the limit of exact numerical methods.\r\nIn this setting, we approach the debated topic of the coexistence of localized and thermal eigenstates separated by energy thresholds known as many-body mobility edges.\r\nInspired by recent experiments, our work further investigates the localization of a small bath induced by the coupling to a large localized chain, the so-called MBL proximity effect.\r\n\r\nIn the first Chapter, we introduce a family of particle-conserving kinetically constrained models, inspired by the quantum East model.\r\nThe system we study features strong inversion-symmetry breaking, due to the nature of the correlated hopping.\r\nWe show that these models host so-called quantum Hilbert space fragmentation, consisting of disconnected subsectors in an entangled basis, and further provide an analytical description of this phenomenon.\r\nWe further probe its effect on dynamics of simple product states, showing revivals in fidelity and local observalbes.\r\nThe study of dynamics within the largest subsector reveals an anomalous transient superdiffusive behavior crossing over to slow logarithmic dynamics at later times.\r\nThis work suggests that particle conserving constrained models with inversion-symmetry breaking realize new universality classes of dynamics and invite their further theoretical and experimental studies.\r\n\r\nNext, we use kinetic constraints and disorder to design a model with many-body mobility edges in particle density.\r\nThis feature allows to study the dynamics of localized and thermal states in large systems beyond the limitations of previous studies.\r\nThe time-evolution shows typical signatures of localization at small densities, replaced by thermal behavior at larger densities.\r\nOur results provide evidence in favor of the stability of many-body mobility edges, which was recently challenged by a theoretical argument.\r\nTo support our findings, we probe the mechanism proposed as a cause of delocalization in many-body localized systems with mobility edges suggesting its ineffectiveness in the model studied.\r\n\r\nIn the last Chapter of this Thesis, we address the topic of many-body localization proximity effect.\r\nWe study a model inspired by recent experiments, featuring Anderson localized coupled to a small bath of free hard-core bosons.\r\nThe interaction among the two particle species results in non-trivial dynamics, which we probe using tensor network techniques.\r\nOur simulations show convincing evidence of many-body localization proximity effect when the bath is composed by a single free particle and interactions are strong.\r\nWe furthter observe an anomalous entanglement dynamics, which we explain through a phenomenological theory.\r\nFinally, we extract highly excited eigenstates of large systems, providing supplementary evidence in favor of our findings.","lang":"eng"}],"date_updated":"2023-09-20T10:44:12Z","year":"2023","citation":{"mla":"Brighi, Pietro. <i>Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>.","short":"P. Brighi, Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems, Institute of Science and Technology Austria, 2023.","ista":"Brighi P. 2023. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. Institute of Science and Technology Austria.","apa":"Brighi, P. (2023). <i>Ergodicity breaking in disordered and kinetically constrained quantum many-body systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>","ama":"Brighi P. Ergodicity breaking in disordered and kinetically constrained quantum many-body systems. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12732\">10.15479/at:ista:12732</a>","ieee":"P. Brighi, “Ergodicity breaking in disordered and kinetically constrained quantum many-body systems,” Institute of Science and Technology Austria, 2023.","chicago":"Brighi, Pietro. “Ergodicity Breaking in Disordered and Kinetically Constrained Quantum Many-Body Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12732\">https://doi.org/10.15479/at:ista:12732</a>."},"ddc":["530"],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"None","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"month":"03","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"date_published":"2023-03-21T00:00:00Z","type":"dissertation","file":[{"access_level":"closed","relation":"source_file","file_id":"12753","creator":"pbrighi","date_created":"2023-03-23T16:42:56Z","file_size":42167561,"checksum":"5d2de651ef9449c1b8dc27148ca74777","date_updated":"2023-03-23T16:42:56Z","file_name":"Thesis_sub_PBrighi.zip","content_type":"application/zip"},{"access_level":"open_access","success":1,"relation":"main_file","creator":"pbrighi","file_id":"12754","file_size":13977000,"checksum":"7caa153d4a5b0873a79358787d2dfe1e","date_created":"2023-03-23T16:43:14Z","content_type":"application/pdf","file_name":"Thesis_PBrighi.pdf","date_updated":"2023-03-23T16:43:14Z"}],"related_material":{"record":[{"status":"public","id":"11470","relation":"part_of_dissertation"},{"id":"8308","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"11469"},{"relation":"part_of_dissertation","id":"12750","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public"},{"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1145/3572848.3577512","open_access":"1"}],"acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","type":"conference_poster","date_published":"2023-02-25T00:00:00Z","citation":{"chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. <i>Unexpected Scaling in Path Copying Trees</i>. <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3572848.3577512\">https://doi.org/10.1145/3572848.3577512</a>.","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, <i>Unexpected scaling in path copying trees</i>. Association for Computing Machinery, 2023, pp. 438–440.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., &#38; Kokorin, I. (2023). <i>Unexpected scaling in path copying trees</i>. <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i> (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3572848.3577512\">https://doi.org/10.1145/3572848.3577512</a>","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. <i>Unexpected Scaling in Path Copying Trees</i>. Association for Computing Machinery; 2023:438-440. doi:<a href=\"https://doi.org/10.1145/3572848.3577512\">10.1145/3572848.3577512</a>","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” <i>Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming</i>, Association for Computing Machinery, 2023, pp. 438–40, doi:<a href=\"https://doi.org/10.1145/3572848.3577512\">10.1145/3572848.3577512</a>.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023."},"year":"2023","date_updated":"2023-03-20T07:57:27Z","oa":1,"abstract":[{"text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al.","lang":"eng"}],"publication_identifier":{"isbn":["9798400700156"]},"day":"25","doi":"10.1145/3572848.3577512","language":[{"iso":"eng"}],"quality_controlled":"1","page":"438-440","conference":{"location":"Montreal, QB, Canada","end_date":"2023-03-01","start_date":"2023-02-25","name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming"},"publisher":"Association for Computing Machinery","author":[{"last_name":"Aksenov","first_name":"Vitaly","full_name":"Aksenov, Vitaly"},{"full_name":"Brown, Trevor A","first_name":"Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","full_name":"Fedorov, Alexander","first_name":"Alexander","last_name":"Fedorov"},{"full_name":"Kokorin, Ilya","first_name":"Ilya","last_name":"Kokorin"}],"_id":"12736","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","title":"Unexpected scaling in path copying trees","month":"02","article_processing_charge":"No","date_created":"2023-03-19T23:00:58Z","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publication_status":"published","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"month":"03","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"Nature Computational Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"date_created":"2023-08-16T12:39:57Z","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","file_size":4474284,"date_updated":"2023-08-16T12:39:57Z","file_name":"2023_NatureCompScience_Lombardi.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14073","creator":"dernst"}],"oa":1,"publication_identifier":{"eissn":["2662-8457"]},"type":"journal_article","date_published":"2023-03-20T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","publisher":"Springer Nature","file_date_updated":"2023-08-16T12:39:57Z","ec_funded":1,"quality_controlled":"1","page":"254-263","intvolume":"         3","title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","article_processing_charge":"No","date_created":"2023-03-26T22:01:08Z","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"publication_status":"published","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"full_name":"Pepic, Selver","first_name":"Selver","last_name":"Pepic","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425"},{"last_name":"Shriki","first_name":"Oren","full_name":"Shriki, Oren"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","first_name":"Daniele"}],"scopus_import":"1","_id":"12762","ddc":["570"],"acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.).","volume":3,"abstract":[{"lang":"eng","text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations."}],"day":"20","doi":"10.1038/s43588-023-00410-9","arxiv":1,"external_id":{"arxiv":["2108.06686"]},"citation":{"ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” <i>Nature Computational Science</i>, vol. 3, Springer Nature, 2023, pp. 254–63, doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>.","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” <i>Nature Computational Science</i>, vol. 3. Springer Nature, pp. 254–263, 2023.","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” <i>Nature Computational Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., &#38; De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. 2023;3:254-263. doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>"},"year":"2023","date_updated":"2023-08-16T12:41:53Z"},{"file_date_updated":"2023-04-20T07:02:59Z","page":"127","ec_funded":1,"publisher":"Institute of Science and Technology Austria","author":[{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk","first_name":"Vladyslav","full_name":"Kravchuk, Vladyslav"}],"_id":"12781","alternative_title":["ISTA Thesis"],"title":"Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"date_created":"2023-03-31T12:24:42Z","article_processing_charge":"No","ddc":["570","572"],"date_updated":"2023-08-04T08:54:51Z","year":"2023","citation":{"ieee":"V. Kravchuk, “Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog,” Institute of Science and Technology Austria, 2023.","chicago":"Kravchuk, Vladyslav. “Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>.","ama":"Kravchuk V. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>","apa":"Kravchuk, V. (2023). <i>Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12781\">https://doi.org/10.15479/at:ista:12781</a>","ista":"Kravchuk V. 2023. Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog. Institute of Science and Technology Austria.","mla":"Kravchuk, Vladyslav. <i>Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12781\">10.15479/at:ista:12781</a>.","short":"V. Kravchuk, Structural and Mechanistic Study of Bacterial Complex I and Its Cyanobacterial Ortholog, Institute of Science and Technology Austria, 2023."},"abstract":[{"lang":"eng","text":"Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. \r\n\r\nComplex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. \r\n\r\nCyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.\r\n\r\nIn summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.\r\n"}],"doi":"10.15479/at:ista:12781","degree_awarded":"PhD","day":"23","language":[{"iso":"eng"}],"has_accepted_license":"1","month":"03","acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Published Version","project":[{"_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E","grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model"},{"grant_number":"101020697","name":"Structure and mechanism of respiratory chain molecular machines","call_identifier":"H2020","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12138"}]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"date_created":"2023-04-19T14:33:41Z","embargo":"2024-04-20","embargo_to":"local","file_size":6071553,"checksum":"5ebb6345cb4119f93460c81310265a6d","date_updated":"2023-04-19T14:33:41Z","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final_1.pdf","content_type":"application/pdf","access_level":"closed","relation":"main_file","file_id":"12852","creator":"vkravchu"},{"relation":"source_file","access_level":"closed","creator":"vkravchu","file_id":"12853","embargo_to":"local","checksum":"c12055c48411d030d2afa51de2166221","file_size":19468766,"date_created":"2023-04-19T14:33:52Z","embargo":"2024-04-20","file_name":"VladyslavKravchuk_PhD_Thesis_PostSub_Final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-04-20T07:02:59Z"}],"date_published":"2023-03-23T00:00:00Z","type":"dissertation","supervisor":[{"first_name":"Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["978-3-99078-029-9"],"issn":["2663-337X"]}}]