[{"day":"14","month":"02","article_processing_charge":"No","has_accepted_license":"1","date_published":"2024-02-14T00:00:00Z","doi":"10.21942/UVA.24829896","citation":{"ista":"Giubertoni G, Woutersen S. 2024. Dataset Collagen Self Assembly in H2O and D2O, Figshare, 10.21942/UVA.24829896.","ieee":"G. Giubertoni and S. Woutersen, “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024.","apa":"Giubertoni, G., & Woutersen, S. (2024). Dataset Collagen Self Assembly in H2O and D2O. Figshare. https://doi.org/10.21942/UVA.24829896","ama":"Giubertoni G, Woutersen S. Dataset Collagen Self Assembly in H2O and D2O. 2024. doi:10.21942/UVA.24829896","chicago":"Giubertoni, G., and S. Woutersen. “Dataset Collagen Self Assembly in H2O and D2O.” Figshare, 2024. https://doi.org/10.21942/UVA.24829896.","mla":"Giubertoni, G., and S. Woutersen. Dataset Collagen Self Assembly in H2O and D2O. Figshare, 2024, doi:10.21942/UVA.24829896.","short":"G. Giubertoni, S. Woutersen, (2024)."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.21942/UVA.24829896"}],"oa":1,"abstract":[{"lang":"eng","text":"This zip file contains data, and analysis for the paper \"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration\"."}],"extern":"1","type":"research_data_reference","author":[{"full_name":"Giubertoni, G.","first_name":"G.","last_name":"Giubertoni"},{"first_name":"S.","last_name":"Woutersen","full_name":"Woutersen, S."}],"related_material":{"record":[{"id":"15116","status":"public","relation":"used_in_publication"}]},"date_created":"2024-03-19T10:47:16Z","date_updated":"2024-03-19T11:41:33Z","oa_version":"Published Version","_id":"15126","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","status":"public","title":"Dataset Collagen Self Assembly in H2O and D2O","ddc":["550"],"publisher":"Figshare"},{"acknowledgement":"We thank previous students, postdocs, and collaborators, particularly J. Geiger, and (in alphabetical order) H. Alle, J. Bischofberger, C. Borges-Merjane, D. Engel, M. Frotscher, S. Hallermann, M. Heckmann, S. Jamrichova, O. Kim, L. Li, K. Lichter, P. Lin, J. Lübke, Y. Okamoto, C. Pawlu, C. Schmidt-Hieber, N. Spruston, and N. Vyleta for their outstanding experimental contributions. We also thank P. Castillo, J. Geiger, T. Sakaba, S. Siegert, T. Vogels, and J. Watson for critically reading the manuscript, E. Kralli-Beller for text editing, and J. Malikovic and L. Slomianka for useful discussions. We apologize that, due to space constraints, not all relevant papers could be cited.\r\nThis project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, AdG “GIANTSYN”) and the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein Award; P 36232-B, stand-alone grant), both to P.J.","year":"2024","pmid":1,"publication_status":"published","publisher":"AAAS","department":[{"_id":"PeJo"}],"author":[{"full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676","first_name":"David H","last_name":"Vandael"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"date_updated":"2024-03-20T07:42:52Z","date_created":"2024-03-17T23:00:57Z","volume":383,"ec_funded":1,"external_id":{"pmid":["38452088"]},"quality_controlled":"1","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"}],"doi":"10.1126/science.adg6757","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1095-9203"]},"_id":"15117","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Structure, biophysics, and circuit function of a \"giant\" cortical presynaptic terminal","status":"public","intvolume":" 383","oa_version":"None","type":"journal_article","abstract":[{"text":"The hippocampal mossy fiber synapse, formed between axons of dentate gyrus granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the trisynaptic circuitry of the hippocampus. Because of its comparatively large size, this synapse is accessible to direct presynaptic recording, allowing a rigorous investigation of the biophysical mechanisms of synaptic transmission and plasticity. Furthermore, because of its placement in the very center of the hippocampal memory circuit, this synapse seems to be critically involved in several higher network functions, such as learning, memory, pattern separation, and pattern completion. Recent work based on new technologies in both nanoanatomy and nanophysiology, including presynaptic patch-clamp recording, paired recording, super-resolution light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy, has provided new insights into the structure, biophysics, and network function of this intriguing synapse. This brings us one step closer to answering a fundamental question in neuroscience: how basic synaptic properties shape higher network computations.","lang":"eng"}],"issue":"6687","publication":"Science","citation":{"chicago":"Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science. AAAS, 2024. https://doi.org/10.1126/science.adg6757.","short":"D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757.","mla":"Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science, vol. 383, no. 6687, AAAS, 2024, p. eadg6757, doi:10.1126/science.adg6757.","apa":"Vandael, D. H., & Jonas, P. M. (2024). Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. AAAS. https://doi.org/10.1126/science.adg6757","ieee":"D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal,” Science, vol. 383, no. 6687. AAAS, p. eadg6757, 2024.","ista":"Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757.","ama":"Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. 2024;383(6687):eadg6757. doi:10.1126/science.adg6757"},"article_type":"review","page":"eadg6757","date_published":"2024-03-08T00:00:00Z","scopus_import":"1","day":"08","article_processing_charge":"No"},{"date_published":"2024-03-08T00:00:00Z","page":"108","citation":{"chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","ama":"Cultrera di Montesano S. 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This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"doi":"10.15479/at:ista:15094","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"I4887","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","name":"Discretization in Geometry and Dynamics"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"publication_identifier":{"issn":["2663 - 337X"]},"month":"03","date_created":"2024-03-08T15:28:10Z","date_updated":"2024-03-20T09:36:57Z","related_material":{"record":[{"id":"11660","relation":"part_of_dissertation","status":"public"},{"id":"11658","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"13182"},{"relation":"part_of_dissertation","status":"public","id":"15090"},{"relation":"part_of_dissertation","status":"public","id":"15091"},{"status":"public","relation":"part_of_dissertation","id":"15093"}]},"author":[{"last_name":"Cultrera di Montesano","first_name":"Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano"}],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2024","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file_date_updated":"2024-03-14T14:14:35Z"},{"status":"public","title":"Dynamically maintaining the persistent homology of time series","_id":"15093","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right."}],"page":"243 - 295","publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)","citation":{"ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11","ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorigthms, 243–295.","ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.","short":"S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11."},"date_published":"2024-01-04T00:00:00Z","day":"04","article_processing_charge":"No","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","editor":[{"full_name":"Woodruff, David P.","first_name":"David P.","last_name":"Woodruff"}],"department":[{"_id":"HeEd"},{"_id":"MoHe"}],"year":"2024","acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","date_created":"2024-03-08T10:27:39Z","date_updated":"2024-03-20T09:36:56Z","author":[{"orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano","first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano"},{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Lara","last_name":"Ost","full_name":"Ost, Lara"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15094"}]},"ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Wittgenstein Award - Monika Henzinger","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 "}],"external_id":{"arxiv":["2311.01115"]},"main_file_link":[{"url":"https://arxiv.org/abs/2311.01115","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SODA: Symposium on Discrete Algorigthms","location":"Alexandria, VA, USA","start_date":"2024-01-07","end_date":"2024-01-10"},"doi":"10.1137/1.9781611977912.11","month":"01","publication_identifier":{"eisbn":["9781611977912"]}},{"abstract":[{"lang":"eng","text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided."}],"type":"preprint","article_number":"2212.03128","oa_version":"Preprint","date_updated":"2024-03-20T09:36:56Z","date_created":"2024-03-08T10:13:59Z","related_material":{"record":[{"id":"15094","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Cultrera di Montesano","first_name":"Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano"},{"first_name":"Ondrej","last_name":"Draganov","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","full_name":"Draganov, Ondrej"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"first_name":"Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza"}],"department":[{"_id":"HeEd"}],"status":"public","title":"Chromatic alpha complexes","publication_status":"submitted","year":"2024","_id":"15091","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","day":"07","month":"02","language":[{"iso":"eng"}],"date_published":"2024-02-07T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03128"}],"external_id":{"arxiv":["2212.03128"]},"citation":{"ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv.","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv.","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128."},"publication":"arXiv"}]