[{"quality_controlled":"1","_id":"18703","article_processing_charge":"Yes","ddc":["000"],"APC_amount":"3143,76 EUR","external_id":{"isi":["001379596100014"],"pmid":["39642209"]},"OA_type":"hybrid","oa":1,"citation":{"short":"J. Svoboda, K. Chatterjee, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Svoboda J, Chatterjee K. 2024. Density amplifiers of cooperation for spatial games. Proceedings of the National Academy of Sciences of the United States of America. 121(50), e2405605121.","chicago":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2405605121\">https://doi.org/10.1073/pnas.2405605121</a>.","ama":"Svoboda J, Chatterjee K. Density amplifiers of cooperation for spatial games. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(50). doi:<a href=\"https://doi.org/10.1073/pnas.2405605121\">10.1073/pnas.2405605121</a>","ieee":"J. Svoboda and K. Chatterjee, “Density amplifiers of cooperation for spatial games,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 50. National Academy of Sciences, 2024.","mla":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 50, e2405605121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2405605121\">10.1073/pnas.2405605121</a>.","apa":"Svoboda, J., &#38; Chatterjee, K. (2024). Density amplifiers of cooperation for spatial games. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2405605121\">https://doi.org/10.1073/pnas.2405605121</a>"},"issue":"50","month":"12","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"date_created":"2024-12-22T23:01:47Z","status":"public","doi":"10.1073/pnas.2405605121","OA_place":"publisher","language":[{"iso":"eng"}],"volume":121,"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Density amplifiers of cooperation for spatial games","publisher":"National Academy of Sciences","abstract":[{"text":"Spatial games provide a simple and elegant mathematical model to study the evolution of cooperation in networks. In spatial games, individuals reside in vertices, adopt simple strategies, and interact with neighbors to receive a payoff. Depending on their own and neighbors’ payoffs, individuals can change their strategy. The payoff is determined by the Prisoners’ Dilemma, a classical matrix game, where players cooperate or defect. While cooperation is the desired behavior, defection provides a higher payoff for a selfish individual. There are many theoretical and empirical studies related to the role of the network in the evolution of cooperation. However, the fundamental question of whether there exist networks that for low initial cooperation rate ensure a high chance of fixation, i.e., cooperation spreads across the whole population, has remained elusive for spatial games with strong selection. In this work, we answer this fundamental question in the affirmative by presenting network structures that ensure high fixation probability for cooperators in the strong selection regime. Besides, our structures have many desirable properties: (a) they ensure the spread of cooperation even for a low initial density of cooperation and high temptation of defection, (b) they have constant degrees, and (c) the number of steps, until cooperation spreads, is at most quadratic in the size of the network.","lang":"eng"}],"pmid":1,"scopus_import":"1","ec_funded":1,"year":"2024","has_accepted_license":"1","date_published":"2024-12-10T00:00:00Z","type":"journal_article","isi":1,"department":[{"_id":"KrCh"}],"day":"10","file_date_updated":"2025-01-02T12:14:15Z","intvolume":"       121","file":[{"file_name":"2024_PNAS_Svoboda.pdf","file_size":2491151,"access_level":"open_access","checksum":"0115e9090b478e0644308c6dab58605b","creator":"dernst","file_id":"18721","content_type":"application/pdf","date_created":"2025-01-02T12:14:15Z","success":1,"date_updated":"2025-01-02T12:14:15Z","relation":"main_file"}],"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"author":[{"first_name":"Jakub","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"oa_version":"Published Version","article_type":"original","article_number":"e2405605121","publication":"Proceedings of the National Academy of Sciences of the United States of America","related_material":{"record":[{"status":"public","id":"20138","relation":"dissertation_contains"}]},"date_updated":"2026-07-27T12:52:03Z","acknowledgement":"J.S. and K.C. were supported by the European Research Council CoG 863818 (ForM-SMArt) and Austrian Science Fund 10.55776/COE12.","corr_author":"1"},{"corr_author":"1","date_updated":"2026-07-27T14:29:01Z","acknowledgement":"S.A.F. is indebted to ISTA for support. R.B.J. thanks the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 for funding. B.P. thanks Alistore ERI for providing a PhD scholarship.","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20607"}]},"publication":"Angewandte Chemie International Edition","article_number":"e202316476","article_type":"review","oa_version":"Published Version","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"author":[{"first_name":"Rajesh B","full_name":"Jethwa, Rajesh B","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","orcid":"0000-0002-0404-4356","last_name":"Jethwa"},{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","full_name":"Mondal, Soumyadip","first_name":"Soumyadip"},{"id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","last_name":"Pant","full_name":"Pant, Bhargavi","first_name":"Bhargavi"},{"orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","intvolume":"        63","file":[{"date_created":"2024-07-16T11:54:46Z","success":1,"relation":"main_file","date_updated":"2024-07-16T11:54:46Z","file_size":4766445,"access_level":"open_access","file_name":"2024_AngChemieInt_Jethwa.pdf","content_type":"application/pdf","file_id":"17261","checksum":"fe2c23454279eb9d76ed6ca9970c21c7","creator":"dernst"}],"day":"08","file_date_updated":"2024-07-16T11:54:46Z","type":"journal_article","isi":1,"department":[{"_id":"StFr"},{"_id":"GradSch"}],"date_published":"2024-07-08T00:00:00Z","scopus_import":"1","has_accepted_license":"1","ec_funded":1,"year":"2024","pmid":1,"keyword":["General Chemistry","Catalysis"],"abstract":[{"text":"The short history of research on Li-O2 batteries has seen a remarkable number of mechanistic U-turns over the years. From the initial use of carbonate electrolytes, that were then found to be entirely unsuitable, to the belief that (su)peroxide was solely responsible for degradation, before the more reactive singlet oxygen was found to form, to the hypothesis that capacity depends on a competing surface/solution mechanism before a practically exclusive solution mechanism was identified. Herein, we argue for an ever-fresh look at the reported data without bias towards supposedly established explanations. We explain how the latest findings on rate and capacity limits, as well as the origin of side reactions, are connected via the disproportionation (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the design of electrolytes and mediators on how to suppress side reactions and to enable high rate and high reversible capacity.","lang":"eng"}],"publisher":"Wiley","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries","language":[{"iso":"eng"}],"volume":63,"doi":"10.1002/anie.202316476","date_created":"2023-12-15T16:10:13Z","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413"}],"status":"public","citation":{"ama":"Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. 2024;63(28). doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>","mla":"Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 28, e202316476, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>.","ieee":"R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 28. Wiley, 2024.","apa":"Jethwa, R. B., Mondal, S., Pant, B., &#38; Freunberger, S. A. (2024). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>","short":"R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition 63 (2024).","ista":"Jethwa RB, Mondal S, Pant B, Freunberger SA. 2024. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. 63(28), e202316476.","chicago":"Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>."},"issue":"28","month":"07","oa":1,"external_id":{"isi":["001241932700001"],"pmid":["38095355"]},"ddc":["540"],"article_processing_charge":"Yes (via OA deal)","_id":"14687","quality_controlled":"1"},{"citation":{"short":"S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday Discussions 248 (2024) 175–189.","chicago":"Mondal, Soumyadip, Rajesh B Jethwa, Bhargavi Pant, Robert Hauschild, and Stefan Alexander Freunberger. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>. Royal Society of Chemistry, 2024. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>.","ista":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. 2024. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. 248, 175–189.","mla":"Mondal, Soumyadip, et al. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” <i>Faraday Discussions</i>, vol. 248, Royal Society of Chemistry, 2024, pp. 175–89, doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>.","ieee":"S. Mondal, R. B. Jethwa, B. Pant, R. Hauschild, and S. A. Freunberger, “Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes,” <i>Faraday Discussions</i>, vol. 248. Royal Society of Chemistry, pp. 175–189, 2024.","ama":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. 2024;248:175-189. doi:<a href=\"https://doi.org/10.1039/d3fd00088e\">10.1039/d3fd00088e</a>","apa":"Mondal, S., Jethwa, R. B., Pant, B., Hauschild, R., &#38; Freunberger, S. A. (2024). Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. <i>Faraday Discussions</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3fd00088e\">https://doi.org/10.1039/d3fd00088e</a>"},"month":"01","date_created":"2023-05-22T06:53:34Z","status":"public","doi":"10.1039/d3fd00088e","language":[{"iso":"eng"}],"volume":248,"_id":"13044","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","ddc":["540"],"external_id":{"isi":["001070423500001"],"pmid":["37750344"]},"oa":1,"pmid":1,"license":"https://creativecommons.org/licenses/by-nc/3.0/","scopus_import":"1","has_accepted_license":"1","year":"2024","tmp":{"name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"title":"Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes","publisher":"Royal Society of Chemistry","keyword":["Physical and Theoretical Chemistry"],"abstract":[{"lang":"eng","text":"Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation."}],"intvolume":"       248","file":[{"success":1,"date_created":"2024-07-16T07:46:39Z","relation":"main_file","date_updated":"2024-07-16T07:46:39Z","file_size":1303733,"access_level":"open_access","file_name":"2024_FaradayDiscussions_Mondal.pdf","creator":"dernst","checksum":"6515a227ed3e8942496fe6a1feeffd18","content_type":"application/pdf","file_id":"17249"}],"publication_status":"published","date_published":"2024-01-01T00:00:00Z","page":"175-189","type":"journal_article","isi":1,"department":[{"_id":"StFr"},{"_id":"Bio"}],"day":"01","file_date_updated":"2024-07-16T07:46:39Z","publication":"Faraday Discussions","related_material":{"record":[{"id":"20607","status":"public","relation":"dissertation_contains"}]},"date_updated":"2026-07-27T14:29:01Z","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Soumyadip","full_name":"Mondal, Soumyadip","last_name":"Mondal","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48"},{"full_name":"Jethwa, Rajesh B","first_name":"Rajesh B","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","orcid":"0000-0002-0404-4356","last_name":"Jethwa"},{"first_name":"Bhargavi","full_name":"Pant, Bhargavi","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","last_name":"Pant"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert"},{"orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander"}],"publication_identifier":{"eissn":["1364-5498"],"issn":["1359-6640"]},"oa_version":"Published Version","article_type":"original"},{"date_published":"2024-02-21T00:00:00Z","department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"type":"preprint","day":"21","publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Gallei","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","first_name":"Michelle C"},{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt","full_name":"Truckenbrodt, Sven M","first_name":"Sven M"},{"last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Kreuzinger, Caroline"},{"id":"F8660870-D756-11E9-98C5-34DFE5697425","last_name":"Inumella","orcid":"0009-0002-5890-120X","full_name":"Inumella, Syamala","first_name":"Syamala"},{"last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","first_name":"Vitali","full_name":"Vistunou, Vitali"},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie"},{"id":"937696FA-C996-11E9-8C7C-CF13E6697425","orcid":"0009-0000-7590-3501","last_name":"Vorlaufer","full_name":"Vorlaufer, Jakob","first_name":"Jakob"},{"first_name":"Wiebke","full_name":"Jahr, Wiebke","orcid":"0000-0003-0201-2315","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Randuch","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","full_name":"Randuch, Marek"},{"full_name":"Johnson, Alexander J","first_name":"Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","last_name":"Danzl"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.02.21.581330"}],"oa_version":"Preprint","publication":"bioRxiv","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"19003"},{"relation":"dissertation_contains","status":"public","id":"18681"}]},"acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742985, J.F.). It has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D., J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","date_updated":"2026-07-28T08:33:52Z","corr_author":"1","_id":"18689","article_processing_charge":"No","oa":1,"month":"02","citation":{"short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).","ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv, <a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>.","chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>.","mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>.","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>bioRxiv</i>. .","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>"},"status":"public","project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 679-2018","_id":"269B5B22-B435-11E9-9278-68D0E5697425","name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED"}],"date_created":"2024-12-19T12:28:00Z","OA_place":"repository","doi":"10.1101/2024.02.21.581330","language":[{"iso":"eng"}],"title":"Super-resolution expansion microscopy in plant roots","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"abstract":[{"text":"Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"year":"2024"},{"publication":"bioRxiv","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"ScienComp"}],"related_material":{"record":[{"id":"18879","status":"public","relation":"later_version"},{"relation":"dissertation_contains","id":"18681","status":"public"}]},"acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry, and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.).","ec_funded":1,"year":"2024","date_updated":"2026-07-28T08:33:51Z","corr_author":"1","title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Watson","first_name":"Jake F.","full_name":"Watson, Jake F."},{"first_name":"Victor","full_name":"Vargas-Barroso, Victor","last_name":"Vargas-Barroso"},{"first_name":"Rebecca J.","full_name":"Morse-Mora, Rebecca J.","last_name":"Morse-Mora"},{"first_name":"Andrea","full_name":"Navas-Olive, Andrea","last_name":"Navas-Olive"},{"full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli","orcid":"0000-0002-7667-6854"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G"},{"last_name":"Tomschik","first_name":"Matthias","full_name":"Tomschik, Matthias"},{"first_name":"Karl","full_name":"Rössler, Karl","last_name":"Rössler"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.05.02.592169"}],"oa_version":"Preprint","abstract":[{"text":"The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits.","lang":"eng"}],"month":"05","citation":{"apa":"Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>","ama":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>","mla":"Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","ieee":"J. F. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>bioRxiv</i>. .","chicago":"Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>.","ista":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv, <a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","short":"J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.)."},"status":"public","project":[{"name":"Synaptic computations of the hippocampal CA3 circuitry","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","grant_number":"101026635"},{"name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF"},{"name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137"}],"date_created":"2024-12-19T11:35:08Z","publication_status":"draft","doi":"10.1101/2024.05.02.592169","OA_place":"repository","language":[{"iso":"eng"}],"date_published":"2024-05-02T00:00:00Z","_id":"18688","article_processing_charge":"No","department":[{"_id":"JoDa"},{"_id":"PeJo"}],"type":"preprint","day":"02","oa":1},{"corr_author":"1","date_updated":"2026-07-28T08:33:52Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"11160","status":"public"},{"relation":"part_of_dissertation","id":"18688","status":"public"},{"id":"18677","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18689"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"oa_version":"Published Version","author":[{"full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","last_name":"Tavakoli","orcid":"0000-0002-7667-6854","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["978-3-99078-048-0"],"issn":["2663-337X"]},"doi_confirm":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","file":[{"relation":"source_file","date_updated":"2024-12-20T10:31:37Z","date_created":"2024-12-20T10:23:17Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18699","creator":"mtavakol","checksum":"b61651d417cafddd740a8528f46068c5","file_size":118593521,"access_level":"closed","file_name":"Thesis_Mojtaba Tavakoli_.docx"},{"embargo_to":"open_access","date_updated":"2026-07-28T08:33:51Z","relation":"main_file","date_created":"2024-12-20T10:25:12Z","file_id":"18700","content_type":"application/pdf","embargo":"2027-08-01","creator":"mtavakol","checksum":"c80bcfd1a34c23afc3538052325283e5","file_name":"Thesis_Mojtaba Tavakoli_.pdf","access_level":"closed","file_size":63885521}],"alternative_title":["ISTA Thesis"],"day":"20","file_date_updated":"2026-07-28T08:33:51Z","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"type":"dissertation","page":"230","date_published":"2024-12-20T00:00:00Z","year":"2024","has_accepted_license":"1","OA_embargo":"20","publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy","degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:18681","OA_place":"publisher","status":"public","das_tickbox":"1","project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24"}],"date_created":"2024-12-19T02:30:39Z","month":"12","citation":{"apa":"Tavakoli, M. (2024). <i>Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>","ama":"Tavakoli M. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>","ieee":"M. Tavakoli, “Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy,” Institute of Science and Technology Austria, 2024.","mla":"Tavakoli, Mojtaba. <i>Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>.","ista":"Tavakoli M. 2024. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria.","chicago":"Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>.","short":"M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology Austria, 2024."},"supervisor":[{"last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G"}],"ddc":["600","570"],"article_processing_charge":"No","_id":"18681"},{"publication_status":"draft","date_published":"2024-07-08T00:00:00Z","day":"08","department":[{"_id":"GaNo"},{"_id":"JoDa"}],"type":"preprint","related_material":{"record":[{"id":"18674","status":"public","relation":"dissertation_contains"},{"relation":"later_version","status":"public","id":"19704"},{"id":"18681","status":"public","relation":"dissertation_contains"}]},"publication":"bioRxiv","acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"}],"corr_author":"1","acknowledgement":"We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript. We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics, Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n","date_updated":"2026-07-28T08:33:51Z","author":[{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba"},{"last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia","first_name":"Julia"},{"first_name":"Michał","full_name":"Januszewski, Michał","last_name":"Januszewski"},{"full_name":"Vistunou, Vitali","first_name":"Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","last_name":"Vistunou"},{"last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie"},{"orcid":"0009-0000-7590-3501","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","first_name":"Jakob","full_name":"Vorlaufer, Jakob"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M","full_name":"Sommer, Christoph M"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kreuzinger","first_name":"Caroline","full_name":"Kreuzinger, Caroline"},{"full_name":"Oliveira, Bárbara","first_name":"Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira"},{"last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban","first_name":"Alban"},{"full_name":"Novarino, Gaia","first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jain","full_name":"Jain, Viren","first_name":"Viren"},{"full_name":"Danzl, Johann G","first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.03.01.582884"}],"status":"public","project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders","_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","grant_number":"101044865"},{"grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"date_created":"2024-12-18T14:48:24Z","month":"07","citation":{"ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy based dense connectomic reconstruction of mammalian brain tissue,” <i>bioRxiv</i>. .","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>","short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, BioRxiv (n.d.).","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>."},"language":[{"iso":"eng"}],"doi":"10.1101/2024.03.01.582884","OA_place":"repository","article_processing_charge":"No","_id":"18677","oa":1,"year":"2024","ec_funded":1,"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Light-microscopy based dense connectomic reconstruction of mammalian brain tissue","abstract":[{"text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner.","lang":"eng"}]},{"acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11420"},{"relation":"part_of_dissertation","status":"public","id":"14459"},{"status":"public","id":"9198","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"17469","status":"public"}]},"date_updated":"2026-06-18T17:55:53Z","corr_author":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr"}],"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"file":[{"relation":"main_file","date_updated":"2024-10-05T22:30:05Z","date_created":"2024-09-02T09:23:32Z","file_id":"17482","content_type":"application/pdf","embargo":"2024-10-04","creator":"ashevche","checksum":"da6dd3166078934577f6af93d27000e2","file_size":4468610,"access_level":"open_access","file_name":"thesis_a2b.pdf"},{"checksum":"76a39ef252239560923cdda4ce0a31a4","creator":"ashevche","content_type":"application/zip","file_id":"17483","access_level":"closed","file_size":15930999,"file_name":"Thesis Alex - ISTA.zip","relation":"source_file","date_updated":"2024-10-05T22:30:05Z","embargo_to":"open_access","date_created":"2024-09-02T09:23:46Z"}],"publication_status":"published","date_published":"2024-08-29T00:00:00Z","page":"232","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"file_date_updated":"2024-10-05T22:30:05Z","day":"29","year":"2024","has_accepted_license":"1","title":"High-dimensional limits in artificial neural networks","publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n"}],"citation":{"apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024.","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024."},"month":"08","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"}],"date_created":"2024-08-28T15:14:25Z","status":"public","OA_place":"repository","doi":"10.15479/at:ista:17465","language":[{"iso":"eng"}],"degree_awarded":"PhD","article_processing_charge":"No","_id":"17465","ddc":["519"],"supervisor":[{"full_name":"Mondelli, Marco","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","orcid":"0000-0002-3242-7020"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"oa":1},{"oa":1,"article_processing_charge":"No","_id":"17881","ddc":["539"],"supervisor":[{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","last_name":"Higginbotham","full_name":"Higginbotham, Andrew P","first_name":"Andrew P"}],"doi":"10.15479/at:ista:17881","OA_place":"publisher","language":[{"iso":"eng"}],"degree_awarded":"PhD","citation":{"apa":"Mukhopadhyay, S. (2024). <i>Thermal effects in one dimensional Josephson chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>","ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024.","mla":"Mukhopadhyay, Soham. <i>Thermal Effects in One Dimensional Josephson Chains</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>.","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria.","chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>.","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024."},"month":"09","date_created":"2024-09-08T10:23:25Z","project":[{"name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"}],"status":"public","abstract":[{"text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices.","lang":"eng"}],"title":"Thermal effects in one dimensional Josephson chains","publisher":"Institute of Science and Technology Austria","year":"2024","has_accepted_license":"1","type":"dissertation","page":"82","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"file_date_updated":"2025-03-13T23:30:04Z","day":"10","date_published":"2024-09-10T00:00:00Z","alternative_title":["ISTA Thesis"],"file":[{"checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","creator":"smukhopa","file_id":"18059","content_type":"application/pdf","embargo":"2025-03-13","access_level":"open_access","file_size":10297052,"file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","relation":"main_file","date_updated":"2025-03-13T23:30:04Z","date_created":"2024-09-12T10:46:04Z"},{"content_type":"application/zip","file_id":"18060","checksum":"e352667482701dd18a9a0e7418aef465","creator":"smukhopa","access_level":"closed","file_size":29178634,"file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","embargo_to":"open_access","relation":"source_file","date_updated":"2025-03-13T23:30:04Z","date_created":"2024-09-12T10:50:58Z"}],"publication_status":"published","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-043-5"]},"author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","orcid":"0000-0001-5263-5559","last_name":"Mukhopadhyay","first_name":"Soham","full_name":"Mukhopadhyay, Soham"}],"date_updated":"2026-06-03T07:16:04Z","corr_author":"1","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"related_material":{"record":[{"status":"public","id":"14032","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18057","status":"public"}]}},{"date_published":"2024-07-01T00:00:00Z","day":"01","department":[{"_id":"DaAl"},{"_id":"MaMo"}],"type":"conference","page":"24964-25015","publication_status":"published","intvolume":"       235","alternative_title":["PMLR"],"author":[{"full_name":"Kögler, Kevin","first_name":"Kevin","last_name":"Kögler","id":"94ec913c-dc85-11ea-9058-e5051ab2428b"},{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","last_name":"Shevchenko","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr"},{"first_name":"Hamed","full_name":"Hassani, Hamed","last_name":"Hassani"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","full_name":"Mondelli, Marco"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v235/kogler24a.html"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"17465","status":"public"}]},"publication":"Proceedings of the 41st International Conference on Machine Learning","corr_author":"1","acknowledgement":"Kevin Kogler, Alexander Shevchenko and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed\r\nHassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE).","date_updated":"2026-07-28T22:30:18Z","ddc":["000"],"_id":"17469","article_processing_charge":"No","quality_controlled":"1","oa":1,"conference":{"start_date":"2024-07-21","name":"ICML: International Conference on Machine Learning","end_date":"2024-07-27","location":"Vienna, Austria"},"external_id":{"arxiv":["2402.05013"]},"status":"public","date_created":"2024-08-29T11:47:57Z","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"month":"07","citation":{"apa":"Kögler, K., Shevchenko, A., Hassani, H., &#38; Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.","ama":"Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:24964-25015.","ieee":"K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 24964–25015.","mla":"Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 24964–5015.","chicago":"Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:24964–15. ML Research Press, 2024.","ista":"Kögler K, Shevchenko A, Hassani H, Mondelli M. 2024. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 24964–25015.","short":"K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 24964–25015."},"volume":235,"language":[{"iso":"eng"}],"publisher":"ML Research Press","title":"Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth","abstract":[{"text":"Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST.","lang":"eng"}],"year":"2024","scopus_import":"1"},{"status":"public","date_created":"2024-09-11T09:25:22Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Cavity electromechanics across a quantum phase transition","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","grant_number":"P33692"},{"_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2","name":"Protected states of quantum matter"}],"month":"08","citation":{"apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., &#38; Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, 2408.07829, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>.","ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” <i>arXiv</i>. .","ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>.","ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829.","short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.)."},"language":[{"iso":"eng"}],"OA_place":"repository","doi":"10.48550/arXiv.2408.07829","article_processing_charge":"No","_id":"18057","oa":1,"external_id":{"arxiv":["2408.07829"]},"year":"2024","ec_funded":1,"title":"Dual relaxation oscillations in a Josephson junction array","abstract":[{"lang":"eng","text":"We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions. The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions. The dual circuit quantitatively accounts for temporal\r\ndynamics of the array, including the dependence on biasing conditions.\r\nInjection locking the oscillations results in well-developed current plateaux.\r\nA thermal model explains the relaxation step of the oscillations."}],"publication_status":"draft","date_published":"2024-08-14T00:00:00Z","day":"14","department":[{"_id":"AnHi"},{"_id":"GradSch"}],"type":"preprint","related_material":{"record":[{"id":"20324","status":"public","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"17881"}]},"publication":"arXiv","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"corr_author":"1","acknowledgement":"We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n","date_updated":"2026-07-28T22:30:19Z","author":[{"orcid":"0000-0001-5263-5559","last_name":"Mukhopadhyay","id":"FDE60288-A89D-11E9-947F-1AF6E5697425","first_name":"Soham","full_name":"Mukhopadhyay, Soham"},{"first_name":"Diego A","full_name":"Lancheros Naranjo, Diego A","last_name":"Lancheros Naranjo","id":"6c55e976-15b2-11ec-abd3-d790e8937fde"},{"id":"5479D234-2D30-11EA-89CC-40953DDC885E","orcid":"0000-0002-0672-9295","last_name":"Senior","full_name":"Senior, Jorden L","first_name":"Jorden L"},{"orcid":"0000-0003-2607-2363","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"2408.07829","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2408.07829"}],"arxiv":1,"oa_version":"Preprint"},{"has_accepted_license":"1","year":"2024","scopus_import":"1","pmid":1,"abstract":[{"text":"Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group.","lang":"eng"}],"publisher":"Public Library of Science","title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"volume":20,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1011376","OA_place":"publisher","status":"public","date_created":"2024-09-08T22:01:11Z","project":[{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"},{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"month":"08","citation":{"apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>.","ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” <i>PLoS Genetics</i>, vol. 20, no. 8. Public Library of Science, 2024.","ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. 2024;20(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>.","ista":"Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8), e1011376.","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024)."},"issue":"8","oa":1,"OA_type":"gold","external_id":{"isi":["001304090200001"],"pmid":["39213449"]},"APC_amount":"3145,39 EUR","ddc":["570"],"_id":"17890","quality_controlled":"1","article_processing_charge":"Yes","corr_author":"1","acknowledgement":"We thank the Vicoso group for their valuable comments on the earlier draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support with the handling and sequencing of the samples, the scientific computing unit at ISTA for the computational resources, Brittney Wick for the help with hosting our data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the different stages of the project.\r\nThis research was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant ID FWF SFB F88-10) to BV. ","date_updated":"2026-07-28T22:30:30Z","related_material":{"record":[{"id":"17362","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"19386"}],"link":[{"url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project","relation":"software"}]},"publication":"PLoS Genetics","acknowledged_ssus":[{"_id":"ScienComp"}],"article_type":"original","article_number":"e1011376","oa_version":"Published Version","publication_identifier":{"eissn":["1553-7404"],"issn":["1553-7390"]},"author":[{"last_name":"Elkrewi","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","full_name":"Elkrewi, Marwan N"},{"first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","DOAJ_listed":"1","publication_status":"published","file":[{"relation":"main_file","date_updated":"2024-09-11T07:54:12Z","date_created":"2024-09-11T07:54:12Z","success":1,"content_type":"application/pdf","file_id":"18056","creator":"dernst","checksum":"f5d96b9af57126fc1063e951440477d6","file_size":8962687,"access_level":"open_access","file_name":"2024_PloSGenetics_Elkrewi.pdf"}],"intvolume":"        20","file_date_updated":"2024-09-11T07:54:12Z","day":"30","department":[{"_id":"BeVi"}],"type":"journal_article","isi":1,"date_published":"2024-08-30T00:00:00Z"},{"article_processing_charge":"No","_id":"17119","supervisor":[{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz"}],"ddc":["576"],"oa":1,"month":"06","citation":{"ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>"},"status":"public","date_created":"2024-06-07T16:14:13Z","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"doi":"10.15479/at:ista:17119","OA_place":"publisher","degree_awarded":"PhD","language":[{"iso":"eng"}],"title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","tmp":{"short":"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","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research."}],"keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"ec_funded":1,"has_accepted_license":"1","year":"2024","date_published":"2024-06-20T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"type":"dissertation","page":"105","file_date_updated":"2025-01-10T23:30:10Z","day":"20","file":[{"embargo_to":"open_access","relation":"source_file","date_updated":"2025-01-10T23:30:10Z","date_created":"2024-06-07T16:09:17Z","file_id":"17121","content_type":"application/zip","checksum":"fab59146e3b3dc2e5d214576984a2a63","creator":"rkelemen","file_size":180557931,"access_level":"closed","file_name":"thesis.zip"},{"file_name":"thesis_to_archive.pdf","file_size":19405484,"access_level":"open_access","checksum":"91cc4c25a792239e8a7688e8aec7c62a","creator":"rkelemen","file_id":"17213","embargo":"2025-01-10","content_type":"application/pdf","date_created":"2024-07-10T08:00:20Z","date_updated":"2025-01-10T23:30:10Z","relation":"main_file"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"orcid":"0000-0002-8489-9281","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","first_name":"Réka K","full_name":"Kelemen, Réka K"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"542","status":"public"},{"status":"public","id":"10767","relation":"part_of_dissertation"}]},"date_updated":"2026-04-07T13:21:37Z","corr_author":"1"},{"has_accepted_license":"1","year":"2024","abstract":[{"text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","title":"Biochemical and structural insights into ADAR1 RNA editing","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"degree_awarded":"PhD","language":[{"iso":"eng"}],"OA_place":"publisher","doi":"10.15479/at:ista:18477","status":"public","date_created":"2024-10-27T07:35:13Z","month":"10","citation":{"apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>.","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024."},"oa":1,"supervisor":[{"first_name":"Carrie A","full_name":"Bernecky, Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"}],"ddc":["572"],"article_processing_charge":"No","_id":"18477","corr_author":"1","date_updated":"2026-04-07T13:23:59Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"oa_version":"Published Version","author":[{"id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarek","first_name":"Beata M","full_name":"Kaczmarek, Beata M"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-045-9"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","file":[{"file_name":"20241029_PhD_thesis_BKaczmarek.docx","file_size":23136626,"access_level":"closed","checksum":"2053294ea4d770c495e4cc501e2a218b","creator":"bkaczmar","file_id":"18485","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-10-29T11:56:36Z","date_updated":"2025-10-29T23:30:02Z","relation":"source_file","embargo_to":"open_access"},{"creator":"bkaczmar","checksum":"8ce857a4cd44b776791eaf180ac9dbb3","file_id":"18486","embargo":"2025-10-29","content_type":"application/pdf","file_name":"20241029_PhD_thesis_BKaczmarek.pdf","file_size":11707360,"access_level":"open_access","date_updated":"2025-10-29T23:30:02Z","relation":"main_file","date_created":"2024-10-29T11:56:44Z"}],"alternative_title":["ISTA Thesis"],"day":"29","file_date_updated":"2025-10-29T23:30:02Z","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"page":"124","type":"dissertation","date_published":"2024-10-29T00:00:00Z"},{"has_accepted_license":"1","year":"2024","abstract":[{"lang":"eng","text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. "}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","doi":"10.15479/at:ista:15352","degree_awarded":"MS","language":[{"iso":"eng"}],"month":"05","citation":{"short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024.","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>.","ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>","apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>"},"status":"public","date_created":"2024-05-02T08:31:38Z","oa":1,"article_processing_charge":"No","_id":"15352","supervisor":[{"first_name":"Sandra","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","last_name":"Siegert"}],"ddc":["570"],"date_updated":"2026-04-07T13:05:00Z","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Murmann, Julie Stefanie","first_name":"Julie Stefanie","last_name":"Murmann","id":"1d390868-f128-11eb-9611-a0ca5f7833b5"}],"publication_identifier":{"issn":["2791-4585"]},"file":[{"date_created":"2024-05-02T12:26:13Z","date_updated":"2025-05-02T22:30:04Z","relation":"main_file","file_name":"Murmann_Thesis_final_2024_2.pdf","file_size":5936142,"access_level":"open_access","file_id":"15354","content_type":"application/pdf","embargo":"2025-05-02","checksum":"095817a6c944954ac3f277e547031a33","creator":"cchlebak"},{"relation":"source_file","date_updated":"2025-05-02T22:30:04Z","embargo_to":"open_access","date_created":"2024-05-02T12:37:56Z","checksum":"43b632255372973a437ac87739cfd4db","creator":"cchlebak","file_id":"15355","content_type":"application/x-zip-compressed","file_size":20645510,"access_level":"closed","file_name":"Murmann_Thesis_final_2024.zip"}],"alternative_title":["ISTA Master's Thesis"],"publication_status":"published","department":[{"_id":"SaSi"},{"_id":"GradSch"}],"type":"dissertation","page":"54","file_date_updated":"2025-05-02T22:30:04Z","day":"02","date_published":"2024-05-02T00:00:00Z"},{"abstract":[{"lang":"eng","text":"The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour."}],"title":"Adaptive hierarchical representations in the hippocampus","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","year":"2024","ec_funded":1,"oa":1,"_id":"14821","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L"}],"ddc":["570"],"OA_place":"publisher","doi":"10.15479/at:ista:14821","degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"01","citation":{"ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria."},"status":"public","date_created":"2024-01-16T14:25:21Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Heloisa","full_name":"Chiossi, Heloisa","orcid":"0009-0004-2973-278X","last_name":"Chiossi","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-07T13:21:56Z","corr_author":"1","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"page":"89","type":"dissertation","day":"19","file_date_updated":"2025-01-19T23:30:04Z","date_published":"2024-01-19T00:00:00Z","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"14838","creator":"hchiossi","checksum":"d3fa3de1abd5af5204c13e9d55375615","file_name":"PhD_Thesis_190124.docx","file_size":8656268,"access_level":"closed","embargo_to":"open_access","date_updated":"2025-01-19T23:30:04Z","relation":"source_file","date_created":"2024-01-19T11:04:05Z"},{"date_created":"2024-01-19T11:03:59Z","date_updated":"2025-01-19T23:30:04Z","relation":"main_file","file_name":"PhD_Thesis_190124.pdf","access_level":"open_access","file_size":6567275,"embargo":"2025-01-19","content_type":"application/pdf","file_id":"14839","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd","creator":"hchiossi"}],"alternative_title":["ISTA Thesis"],"publication_status":"published"},{"publication":"Neuron","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"15101","status":"public"}]},"acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","date_updated":"2026-07-28T22:30:33Z","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"JingJing","full_name":"Chen, JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kaufmann, Walter","first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chen","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","first_name":"Chong","full_name":"Chen, Chong"},{"id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Arai","first_name":"Itaru","full_name":"Arai, Itaru"},{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2344-1039","last_name":"Kim","first_name":"Olena","full_name":"Kim, Olena"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"oa_version":"Published Version","article_type":"original","file":[{"content_type":"application/pdf","file_id":"19614","checksum":"30098b4f0209556ddfb3540a23d07ca5","creator":"dernst","file_name":"2024_Neuron_Chen.pdf","access_level":"open_access","file_size":8192355,"date_updated":"2025-04-23T14:02:08Z","relation":"main_file","date_created":"2025-04-23T14:02:08Z","success":1}],"intvolume":"       112","publication_status":"published","date_published":"2024-03-06T00:00:00Z","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"isi":1,"type":"journal_article","page":"755-771.e9","file_date_updated":"2025-04-23T14:02:08Z","day":"06","PlanS_conform":"1","pmid":1,"year":"2024","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publisher":"Elsevier","abstract":[{"lang":"eng","text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission."}],"month":"03","citation":{"apa":"Chen, J., Kaufmann, W., Chen, C., Arai,  itaru, Kim, O., Shigemoto, R., &#38; Jonas, P. M. (2024). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. <i>Neuron</i>. 2024;112(5):755-771.e9. doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>","ieee":"J. Chen <i>et al.</i>, “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” <i>Neuron</i>, vol. 112, no. 5. Elsevier, p. 755–771.e9, 2024.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>, vol. 112, no. 5, Elsevier, 2024, p. 755–771.e9, doi:<a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">10.1016/j.neuron.2023.12.002</a>.","chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” <i>Neuron</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.neuron.2023.12.002\">https://doi.org/10.1016/j.neuron.2023.12.002</a>.","ista":"Chen J, Kaufmann W, Chen C, Arai  itaru, Kim O, Shigemoto R, Jonas PM. 2024. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. 112(5), 755–771.e9.","short":"J. Chen, W. Kaufmann, C. Chen,  itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron 112 (2024) 755–771.e9."},"issue":"5","status":"public","date_created":"2024-01-21T23:00:56Z","project":[{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits"},{"name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"OA_place":"publisher","doi":"10.1016/j.neuron.2023.12.002","volume":112,"language":[{"iso":"eng"}],"_id":"14843","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","ddc":["570"],"external_id":{"pmid":["38215739"],"isi":["001202925700001"]},"OA_type":"hybrid","oa":1},{"file":[{"file_name":"Thesis_Jingjing CHEN.docx","access_level":"closed","file_size":11271363,"file_id":"15104","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"jchen","checksum":"db4947474ffa271e66c254b6fe876a55","date_created":"2024-03-11T14:10:58Z","embargo_to":"open_access","date_updated":"2024-04-02T22:30:03Z","relation":"source_file"},{"file_name":"Thesis_Jingjing CHEN_merged.pdf","file_size":16627311,"access_level":"open_access","file_id":"15105","embargo":"2024-04-01","content_type":"application/pdf","creator":"jchen","checksum":"a5eeae8b5702cd540f5d03469bc33dde","date_created":"2024-03-11T14:11:06Z","date_updated":"2024-04-02T22:30:03Z","relation":"main_file"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"type":"dissertation","page":"84","day":"11","file_date_updated":"2024-04-02T22:30:03Z","date_published":"2024-03-11T00:00:00Z","date_updated":"2026-04-07T13:24:22Z","corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"related_material":{"record":[{"id":"14843","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"JingJing","full_name":"Chen, JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:15101","OA_place":"publisher","degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"03","citation":{"chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>","mla":"Chen, JingJing. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>"},"status":"public","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"date_created":"2024-03-11T10:09:54Z","oa":1,"article_processing_charge":"No","_id":"15101","supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M"}],"ddc":["570"],"ec_funded":1,"year":"2024","has_accepted_license":"1","abstract":[{"text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission.","lang":"eng"}],"title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publisher":"Institute of Science and Technology Austria"},{"oa":1,"supervisor":[{"last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G"}],"ddc":["570"],"article_processing_charge":"No","_id":"18471","degree_awarded":"PhD","language":[{"iso":"eng"}],"OA_place":"publisher","doi":"10.15479/at:ista:18471","status":"public","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"date_created":"2024-10-26T20:02:42Z","month":"10","citation":{"short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>.","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>","mla":"Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>.","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","apa":"Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape with tissue context</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>"},"abstract":[{"text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. ","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","title":"Visualizing the neuronal transcriptional landscape with tissue context","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","ec_funded":1,"year":"2024","file_date_updated":"2025-05-05T22:30:04Z","day":"28","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"page":"97","type":"dissertation","date_published":"2024-10-28T00:00:00Z","publication_status":"published","file":[{"date_created":"2024-10-26T22:29:06Z","embargo_to":"open_access","relation":"source_file","date_updated":"2025-05-05T22:30:04Z","access_level":"closed","file_size":183077763,"file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18475","checksum":"6d7c7725d040d8debc070dcb35ac965d","creator":"nagudelo"},{"embargo":"2025-05-05","file_id":"18476","content_type":"application/pdf","creator":"nagudelo","checksum":"52f9c0bf2bdafa3baf827b73814a53ff","file_size":47027710,"access_level":"open_access","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","relation":"main_file","date_updated":"2025-05-05T22:30:04Z","date_created":"2024-10-26T23:13:33Z"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","publication_identifier":{"isbn":["978-3-99078-044-2"],"issn":["2663-337X"]},"author":[{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","date_updated":"2026-04-14T08:34:37Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}]},{"department":[{"_id":"GradSch"},{"_id":"MaJö"}],"type":"dissertation","page":"86","file_date_updated":"2025-11-11T23:30:02Z","day":"22","date_published":"2024-11-22T00:00:00Z","file":[{"embargo_to":"open_access","relation":"source_file","date_updated":"2025-11-11T23:30:02Z","date_created":"2024-11-25T14:44:03Z","content_type":"application/zip","file_id":"18589","checksum":"ebb000d361c36b22ed6e639a931c6b7c","creator":"dgupta","file_size":75512262,"access_level":"closed","file_name":"PhD Thesis - Divyansh Gupta.zip"},{"file_size":6412619,"access_level":"open_access","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","checksum":"1282401eb71598bc311058b0fcefc6a1","creator":"dgupta","file_id":"18591","embargo":"2025-11-11","content_type":"application/pdf","date_created":"2024-11-26T11:43:19Z","relation":"main_file","date_updated":"2025-11-11T23:30:02Z"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-050-3"]},"author":[{"id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7400-6665","last_name":"Gupta","full_name":"Gupta, Divyansh","first_name":"Divyansh"}],"acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","date_updated":"2026-04-07T13:24:48Z","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"12349","status":"public"},{"id":"12370","status":"public","relation":"research_data"}]},"oa":1,"_id":"18574","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","full_name":"Jösch, Maximilian A"}],"ddc":["573"],"OA_place":"publisher","doi":"10.15479/at:ista:18574","degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"11","citation":{"mla":"Gupta, Divyansh. <i>Visual Adaptations to Natural Statistics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>.","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>","apa":"Gupta, D. (2024). <i>Visual adaptations to natural statistics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>","short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024.","chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>.","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria."},"status":"public","date_created":"2024-11-20T21:30:44Z","project":[{"name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","grant_number":"101086580","_id":"bdaf81a8-d553-11ed-ba76-c95961984540"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"756502","call_identifier":"H2020","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","name":"Circuits of Visual Attention"}],"abstract":[{"lang":"eng","text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n"}],"title":"Visual adaptations to natural statistics","tmp":{"short":"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","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","year":"2024","ec_funded":1,"OA_embargo":"12"}]