[{"scopus_import":"1","day":"15","issue":"7927","quality_controlled":"1","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"name":"RNA-directed DNA methylation in plant development","call_identifier":"FWF","grant_number":"P29988","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"oa":1,"abstract":[{"lang":"eng","text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization."}],"date_created":"2023-01-16T10:04:48Z","fulldoi":"https://doi.org/10.1038/s41586-022-05187-x","acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","type":"journal_article","volume":609,"publication_status":"published","file_date_updated":"2023-11-02T17:12:37Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"pmid":1,"language":[{"iso":"eng"}],"citation":{"apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581."},"isi":1,"article_type":"original","publication":"Nature","status":"public","author":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"},{"first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zuzana","last_name":"Gelová","full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","last_name":"Johnson","first_name":"Alexander J"},{"full_name":"Mazur, Ewa","last_name":"Mazur","first_name":"Ewa"},{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237","first_name":"Lesia","last_name":"Rodriguez Solovey"},{"full_name":"Roosjen, Mark","first_name":"Mark","last_name":"Roosjen"},{"last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Branka D.","last_name":"Živanović","full_name":"Živanović, Branka D."},{"last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9","full_name":"Zou, Minxia"},{"last_name":"Fiedler","first_name":"Lukas","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"first_name":"Caterina","last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","full_name":"Giannini, Caterina"},{"first_name":"Peter","last_name":"Grones","full_name":"Grones, Peter"},{"full_name":"Hrtyan, Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","last_name":"Hrtyan","first_name":"Mónika"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann"},{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"last_name":"Narasimhan","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek","last_name":"Randuch"},{"full_name":"Rýdza, Nikola","last_name":"Rýdza","first_name":"Nikola"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"last_name":"Tan","first_name":"Shutang","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anastasiia","last_name":"Teplova","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"}],"page":"575-581","date_updated":"2026-08-14T09:33:45Z","publisher":"Springer Nature","ec_funded":1,"has_accepted_license":"1","date_published":"2022-09-15T00:00:00Z","ddc":["580"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"oa_version":"Submitted Version","file":[{"date_created":"2023-11-02T17:12:37Z","content_type":"application/pdf","file_id":"14483","success":1,"access_level":"open_access","creator":"amally","checksum":"a6055c606aefb900bf62ae3e7d15f921","date_updated":"2023-11-02T17:12:37Z","relation":"main_file","file_size":79774945,"file_name":"Friml Nature 2022_merged.pdf"}],"external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"_id":"12291","month":"09","doi":"10.1038/s41586-022-05187-x","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"article_processing_charge":"No","corr_author":"1","intvolume":"       609","year":"2022","title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","related_material":{"record":[{"status":"public","id":"20364","relation":"dissertation_contains"},{"id":"19395","relation":"dissertation_contains","status":"public"}]}},{"file":[{"relation":"source_file","file_name":"src.zip","file_size":13210143,"creator":"mlechner","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","date_updated":"2022-05-13T12:49:00Z","access_level":"closed","date_created":"2022-05-13T12:33:26Z","file_id":"11378","content_type":"application/zip"},{"file_size":2732536,"file_name":"thesis_main-a2.pdf","relation":"main_file","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","creator":"mlechner","date_updated":"2022-05-17T15:19:39Z","access_level":"open_access","file_id":"11382","content_type":"application/pdf","date_created":"2022-05-16T08:02:28Z"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["004"],"date_published":"2022-05-12T00:00:00Z","keyword":["neural networks","verification","machine learning"],"has_accepted_license":"1","ec_funded":1,"publisher":"Institute of Science and Technology Austria","date_updated":"2026-08-19T09:28:05Z","page":"124","author":[{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","first_name":"Mathias","last_name":"Lechner"}],"status":"public","supervisor":[{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"citation":{"apa":"Lechner, M. (2022). <i>Learning verifiable representations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","mla":"Lechner, Mathias. <i>Learning Verifiable Representations</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>.","chicago":"Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11362\">https://doi.org/10.15479/at:ista:11362</a>.","ama":"Lechner M. Learning verifiable representations. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11362\">10.15479/at:ista:11362</a>","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria."},"related_material":{"record":[{"id":"11366","relation":"part_of_dissertation","status":"public"},{"id":"7808","relation":"part_of_dissertation","status":"public"},{"id":"10666","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"10667","status":"public"},{"relation":"part_of_dissertation","id":"10665","status":"public"}]},"title":"Learning verifiable representations","year":"2022","corr_author":"1","article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-017-6"]},"doi":"10.15479/at:ista:11362","month":"05","_id":"11362","tmp":{"short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"degree_awarded":"PhD","date_created":"2022-05-12T07:14:01Z","fulldoi":"https://doi.org/10.15479/at:ista:11362","abstract":[{"text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks.","lang":"eng"}],"oa":1,"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"},{"grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"day":"12","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher","file_date_updated":"2022-05-17T15:19:39Z","publication_status":"published","type":"dissertation"},{"citation":{"apa":"Alwen, J., Auerbach, B., Cueto Noval, M., Klein, K., Pascual Perez, G., Pietrzak, K. Z., &#38; Walter, M. (2022). CoCoA: Concurrent continuous group key agreement. In <i>Advances in Cryptology – EUROCRYPT 2022</i> (Vol. 13276, pp. 815–844). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">https://doi.org/10.1007/978-3-031-07085-3_28</a>","ieee":"J. Alwen <i>et al.</i>, “CoCoA: Concurrent continuous group key agreement,” in <i>Advances in Cryptology – EUROCRYPT 2022</i>, Trondheim, Norway, 2022, vol. 13276, pp. 815–844.","short":"J. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2022, Springer Nature, Cham, 2022, pp. 815–844.","mla":"Alwen, Joël, et al. “CoCoA: Concurrent Continuous Group Key Agreement.” <i>Advances in Cryptology – EUROCRYPT 2022</i>, vol. 13276, Springer Nature, 2022, pp. 815–844, doi:<a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">10.1007/978-3-031-07085-3_28</a>.","chicago":"Alwen, Joël, Benedikt Auerbach, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “CoCoA: Concurrent Continuous Group Key Agreement.” In <i>Advances in Cryptology – EUROCRYPT 2022</i>, 13276:815–844. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">https://doi.org/10.1007/978-3-031-07085-3_28</a>.","ista":"Alwen J, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2022. CoCoA: Concurrent continuous group key agreement. Advances in Cryptology – EUROCRYPT 2022. EUROCRYPT: Theory and Applications of Cryptology and Information Security, LNCS, vol. 13276, 815–844.","ama":"Alwen J, Auerbach B, Cueto Noval M, et al. CoCoA: Concurrent continuous group key agreement. In: <i>Advances in Cryptology – EUROCRYPT 2022</i>. Vol 13276. Cham: Springer Nature; 2022:815–844. doi:<a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">10.1007/978-3-031-07085-3_28</a>"},"isi":1,"publication":"Advances in Cryptology – EUROCRYPT 2022","status":"public","page":"815–844","date_updated":"2026-09-07T14:12:36Z","author":[{"full_name":"Alwen, Joël","first_name":"Joël","last_name":"Alwen"},{"orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","first_name":"Benedikt","last_name":"Auerbach"},{"full_name":"Cueto Noval, Miguel","orcid":"0000-0002-2505-4246","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","first_name":"Miguel","last_name":"Cueto Noval"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein"},{"id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","full_name":"Pascual Perez, Guillermo","orcid":"0000-0001-8630-415X","last_name":"Pascual Perez","first_name":"Guillermo"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"first_name":"Michael","last_name":"Walter","full_name":"Walter, Michael"}],"publisher":"Springer Nature","ec_funded":1,"date_published":"2022-05-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"oa_version":"Preprint","_id":"11476","external_id":{"isi":["000832305300028"]},"doi":"10.1007/978-3-031-07085-3_28","month":"05","place":"Cham","publication_identifier":{"eisbn":["9783031070853"],"isbn":["9783031070846"],"eissn":["1611-3349"],"issn":["0302-9743"]},"article_processing_charge":"No","corr_author":"1","intvolume":"     13276","year":"2022","title":"CoCoA: Concurrent continuous group key agreement","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18088"}]},"scopus_import":"1","day":"25","quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"oa":1,"abstract":[{"text":"Messaging platforms like Signal are widely deployed and provide strong security in an asynchronous setting. It is a challenging problem to construct a protocol with similar security guarantees that can efficiently scale to large groups. A major bottleneck are the frequent key rotations users need to perform to achieve post compromise forward security.\r\n\r\nIn current proposals – most notably in TreeKEM (which is part of the IETF’s Messaging Layer Security (MLS) protocol draft) – for users in a group of size n to rotate their keys, they must each craft a message of size log(n) to be broadcast to the group using an (untrusted) delivery server.\r\n\r\nIn larger groups, having users sequentially rotate their keys requires too much bandwidth (or takes too long), so variants allowing any T≤n users to simultaneously rotate their keys in just 2 communication rounds have been suggested (e.g. “Propose and Commit” by MLS). Unfortunately, 2-round concurrent updates are either damaging or expensive (or both); i.e. they either result in future operations being more costly (e.g. via “blanking” or “tainting”) or are costly themselves requiring Ω(T) communication for each user [Bienstock et al., TCC’20].\r\n\r\nIn this paper we propose CoCoA; a new scheme that allows for T concurrent updates that are neither damaging nor costly. That is, they add no cost to future operations yet they only require Ω(log2(n)) communication per user. To circumvent the [Bienstock et al.] lower bound, CoCoA increases the number of rounds needed to complete all updates from 2 up to (at most) log(n); though typically fewer rounds are needed.\r\n\r\nThe key insight of our protocol is the following: in the (non-concurrent version of) TreeKEM, a delivery server which gets T concurrent update requests will approve one and reject the remaining T−1. In contrast, our server attempts to apply all of them. If more than one user requests to rotate the same key during a round, the server arbitrarily picks a winner. Surprisingly, we prove that regardless of how the server chooses the winners, all previously compromised users will recover after at most log(n) such update rounds.\r\n\r\nTo keep the communication complexity low, CoCoA is a server-aided CGKA. That is, the delivery server no longer blindly forwards packets, but instead actively computes individualized packets tailored to each user. As the server is untrusted, this change requires us to develop new mechanisms ensuring robustness of the protocol.","lang":"eng"}],"date_created":"2022-06-30T16:48:00Z","fulldoi":"https://doi.org/10.1007/978-3-031-07085-3_28","acknowledgement":"We thank Marta Mularczyk and Yiannis Tselekounis for their very helpful feedback on an earlier draft of this paper.","conference":{"end_date":"2022-06-03","name":"EUROCRYPT: Theory and Applications of Cryptology and Information Security","location":"Trondheim, Norway","start_date":"2022-05-30"},"type":"conference","publication_status":"published","volume":13276,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/251"}],"alternative_title":["LNCS"],"language":[{"iso":"eng"}]},{"status":"public","date_updated":"2026-06-18T10:49:27Z","page":"132","author":[{"first_name":"Olena","last_name":"Kim","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2344-1039","full_name":"Kim, Olena"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"citation":{"chicago":"Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>.","ama":"Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>","ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria.","mla":"Kim, Olena. <i>Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11196\">10.15479/at:ista:11196</a>.","apa":"Kim, O. (2022). <i>Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11196\">https://doi.org/10.15479/at:ista:11196</a>","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022."},"supervisor":[{"last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","file":[{"embargo":"2023-04-19","file_size":21273537,"file_name":"Olena_KIM_thesis_final.pdf","relation":"main_file","date_updated":"2023-04-20T22:30:03Z","checksum":"1616a8bf6f13a57c892dac873dcd0936","creator":"okim","access_level":"open_access","content_type":"application/pdf","file_id":"11220","date_created":"2022-04-20T14:21:56Z"},{"embargo_to":"open_access","relation":"source_file","file_size":59248569,"file_name":"KIM_thesis_final.zip","date_updated":"2023-04-20T22:30:03Z","creator":"okim","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","access_level":"closed","date_created":"2022-04-20T14:22:56Z","file_id":"11221","content_type":"application/x-zip-compressed"}],"has_accepted_license":"1","date_published":"2022-04-20T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["570"],"department":[{"_id":"PeJo"},{"_id":"GradSch"}],"month":"04","doi":"10.15479/at:ista:11196","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","_id":"11196","title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","related_material":{"record":[{"relation":"part_of_dissertation","id":"7473","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"11222"}]},"corr_author":"1","year":"2022","project":[{"call_identifier":"H2020","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","grant_number":"708497","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","grant_number":"Z00312"}],"day":"20","fulldoi":"https://doi.org/10.15479/at:ista:11196","date_created":"2022-04-20T09:47:12Z","degree_awarded":"PhD","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa":1,"abstract":[{"lang":"eng","text":"One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n"}],"file_date_updated":"2023-04-20T22:30:03Z","type":"dissertation","publication_status":"published","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"]},{"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"file_date_updated":"2023-09-09T22:30:03Z","publication_status":"published","type":"dissertation","degree_awarded":"PhD","acknowledgement":"I would like to acknowledge ISTA and all the people from the Scientific Service Units and at ISTA, in particular Dorota Jaworska for excellent technical and scientific support as well as ÖAW for funding my research for over 3 years (DOC ÖAW Fellowship PR1022OEAW02).","fulldoi":"https://doi.org/10.15479/at:ista:11879","date_created":"2022-08-17T07:58:53Z","abstract":[{"lang":"eng","text":"As the overall global mean surface temperature is increasing due to climate change, plant\r\nadaptation to those stressful conditions is of utmost importance for their survival. Plants are\r\nsessile organisms, thus to compensate for their lack of mobility, they evolved a variety of\r\nmechanisms enabling them to flexibly adjust their physiological, growth and developmental\r\nprocesses to fluctuating temperatures and to survive in harsh environments. While these unique\r\nadaptation abilities provide an important evolutionary advantage, overall modulation of plant\r\ngrowth and developmental program due to non-optimal temperature negatively affects biomass\r\nproduction, crop productivity or sensitivity to pathogens. Thus, understanding molecular\r\nprocesses underlying plant adaptation to increased temperature can provide important\r\nresources for breeding strategies to ensure sufficient agricultural food production.\r\nAn increase in ambient temperature by a few degrees leads to profound changes in organ growth\r\nincluding enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and\r\ncotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin,\r\none of the best-studied growth hormones, plays an essential role in this process by direct\r\nactivation of transcriptional and non-transcriptional processes resulting in elongation growth\r\n(Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature\r\n(hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key\r\ncomponents of the polar auxin transport (PAT) machinery, which controls the amount and\r\ndirection of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence,\r\nPIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT\r\nthrough either chemical or genetic means dramatically affecting the adaptive responses to hAT.\r\nIntriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether\r\nand how PINs at the level of expression adapt to fluctuation in temperature is scarcely\r\nunderstood.\r\nWith genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN\r\nauxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via\r\nadjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we\r\nidentified three Zinc-Finger (ZF) transcription factors as novel molecular components of the\r\nthermo-regulatory network, which through negative regulation of PIN transcription adjust the\r\ntransport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the\r\nnegative feedback loop attenuating the activity of the thermo-sensing pathway to restrain\r\nexaggerated growth and developmental responses to hAT."}],"oa":1,"project":[{"name":"Hormonal regulation of plant adaptive responses to environmental signals","_id":"2685A872-B435-11E9-9278-68D0E5697425"}],"day":"17","title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","year":"2022","corr_author":"1","publication_identifier":{"isbn":["978-3-99078-022-0"],"issn":["2663-337X"]},"article_processing_charge":"No","doi":"10.15479/at:ista:11879","month":"08","_id":"11879","oa_version":"Published Version","file":[{"file_id":"11907","content_type":"application/pdf","date_created":"2022-08-17T12:08:49Z","access_level":"open_access","checksum":"a2c2fdc28002538840490bfa6a08b2cb","creator":"cartner","date_updated":"2023-09-09T22:30:03Z","file_size":11113608,"file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","relation":"main_file","embargo":"2023-09-08"},{"access_level":"closed","date_created":"2022-08-17T12:08:59Z","content_type":"application/octet-stream","file_id":"11908","relation":"source_file","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","file_size":19097730,"embargo_to":"open_access","creator":"cartner","checksum":"66b461c074b815fbe63481b3f46a9f43","date_updated":"2023-09-09T22:30:03Z"}],"ddc":["580"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"has_accepted_license":"1","keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"date_published":"2022-08-17T00:00:00Z","page":"128","date_updated":"2026-04-07T14:30:39Z","author":[{"first_name":"Christina","last_name":"Artner","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","status":"public","supervisor":[{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Artner C. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","chicago":"Artner, Christina. “Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>.","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","apa":"Artner, C. (2022). <i>Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>","mla":"Artner, Christina. <i>Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11879\">10.15479/at:ista:11879</a>."}},{"status":"public","ec_funded":1,"publisher":"Institute of Science and Technology Austria","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096","last_name":"Dotter","first_name":"Christoph"}],"page":"152","date_updated":"2026-04-07T14:30:57Z","citation":{"ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022.","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","apa":"Dotter, C. (2022). <i>Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>","mla":"Dotter, Christoph. <i>Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>.","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","ama":"Dotter C. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12094\">10.15479/at:ista:12094</a>","chicago":"Dotter, Christoph. “Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12094\">https://doi.org/10.15479/at:ista:12094</a>."},"supervisor":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"file":[{"date_created":"2023-01-24T13:15:45Z","file_id":"12365","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","date_updated":"2023-09-20T22:30:03Z","relation":"main_file","file_name":"220923_Thesis_CDotter_Final.pdf","file_size":20457465,"embargo":"2023-09-19"},{"relation":"source_file","file_name":"latex_source_CDotter_Thesis_2022.zip","file_size":22433512,"embargo_to":"open_access","creator":"cchlebak","checksum":"ad01bb20da163be6893b7af832e58419","date_updated":"2023-09-20T22:30:03Z","access_level":"closed","date_created":"2023-02-02T09:15:35Z","content_type":"application/x-zip-compressed","file_id":"12482"}],"oa_version":"Published Version","date_published":"2022-09-19T00:00:00Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"ddc":["570"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"09","doi":"10.15479/at:ista:12094","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"_id":"12364","related_material":{"record":[{"relation":"part_of_dissertation","id":"11160","status":"public"},{"status":"public","id":"3","relation":"part_of_dissertation"}]},"title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","corr_author":"1","year":"2022","project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers","grant_number":"707964","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","call_identifier":"FWF","grant_number":"I04205","_id":"2690FEAC-B435-11E9-9278-68D0E5697425"}],"day":"19","fulldoi":"https://doi.org/10.15479/at:ista:12094","date_created":"2023-01-24T13:09:57Z","degree_awarded":"PhD","oa":1,"abstract":[{"text":"Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders character\u0002ized by behavioral symptoms such as problems in social communication and interaction, as\r\nwell as repetitive, restricted behaviors and interests. These disorders show a high degree\r\nof heritability and hundreds of risk genes have been identifed using high throughput\r\nsequencing technologies. This genetic heterogeneity has hampered eforts in understanding\r\nthe pathogenesis of ASD but at the same time given rise to the concept of convergent\r\nmechanisms. Previous studies have identifed that risk genes for ASD broadly converge\r\nonto specifc functional categories with transcriptional regulation being one of the biggest\r\ngroups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory\r\nconsequences of some of them in the context of neurodevelopment.\r\nFirst, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead\r\nto perturbations of gene regulatory programs in early cell fate specifcation. In addition,\r\nadult animals display abnormal learning behavior which is mirrored at the transcriptional\r\nlevel by altered activity dependent regulation of postsynaptic gene expression. Lastly,\r\nwe link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR\r\ncomplex.\r\nSecond, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral\r\norganoids we demonstrate profound changes in the developmental trajectories of both\r\ninhibitory and excitatory neurons using single cell RNA-sequencing. While the former\r\nwere generated earlier in CHD8+/- organoids, the generation of the latter was shifted to\r\nlater times in favor of a prolonged progenitor expansion phase and ultimately increased\r\norganoid size.\r\nFinally, by modeling heterozygous mutations for four ASD associated chromatin modifers,\r\nASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of\r\nregulatory convergence across three of those genes. We observe a shift from dorsal cortical\r\nexcitatory neuron fates towards partially ventralized cell types resembling cells from the\r\nlateral ganglionic eminence. As this project is still ongoing at the time of writing, future\r\nexperiments will aim at elucidating the regulatory mechanisms underlying this shift with\r\nthe aim of linking these three ASD risk genes through biological convergence.","lang":"eng"}],"file_date_updated":"2023-09-20T22:30:03Z","type":"dissertation","publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher"},{"author":[{"last_name":"Jevtic","first_name":"Marijo","full_name":"Jevtic, Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-07T14:31:19Z","page":"108","publisher":"Institute of Science and Technology Austria","status":"public","supervisor":[{"first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ista":"Jevtic M. 2022. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. Institute of Science and Technology Austria.","ama":"Jevtic M. Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>","chicago":"Jevtic, Marijo. “Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>.","mla":"Jevtic, Marijo. <i>Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11393\">10.15479/at:ista:11393</a>.","ieee":"M. Jevtic, “Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus,” Institute of Science and Technology Austria, 2022.","short":"M. Jevtic, Contextual Fear Learning Induced Changes in AMPA Receptor Subtypes along the Proximodistal Axis in Dorsal Hippocampus, Institute of Science and Technology Austria, 2022.","apa":"Jevtic, M. (2022). <i>Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11393\">https://doi.org/10.15479/at:ista:11393</a>"},"oa_version":"Published Version","file":[{"file_id":"11395","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2022-05-17T09:08:06Z","access_level":"closed","checksum":"8fc695d88020d70d231dad0e9f10b138","creator":"cchlebak","date_updated":"2023-05-17T22:30:03Z","file_name":"MJ thesis.docx","file_size":56427603,"relation":"source_file","embargo_to":"open_access"},{"access_level":"open_access","content_type":"application/pdf","file_id":"11397","date_created":"2022-05-17T12:09:25Z","file_size":4351981,"file_name":"MJ_thesis_PDFA.pdf","relation":"main_file","embargo":"2023-05-16","checksum":"c1dd20a1aece521b3500607b00e463d6","creator":"cchlebak","date_updated":"2023-05-17T22:30:03Z"}],"ddc":["570"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"RySh"}],"has_accepted_license":"1","date_published":"2022-05-16T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","doi":"10.15479/at:ista:11393","month":"05","_id":"11393","title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","related_material":{"record":[{"status":"public","id":"7391","relation":"part_of_dissertation"}]},"year":"2022","corr_author":"1","day":"16","degree_awarded":"PhD","date_created":"2022-05-17T08:57:41Z","fulldoi":"https://doi.org/10.15479/at:ista:11393","oa":1,"abstract":[{"text":"AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is\r\nimplicated in complex processes such as learning and memory and various neurological\r\ndiseases. These receptors are composed of different subunits and the subunit composition can\r\naffect channel properties, receptor trafficking and interaction with other associated proteins.\r\nUsing the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for\r\nelectron microscopy I investigated the number, density, and localization of AMPAR subunits,\r\nGluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse\r\nhippocampus. I have found that the immunogold labeling for all of these subunits in the\r\npostsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual\r\nincrease from the pyramidal cell soma towards the distal part of stratum radiatum. The densities\r\nof extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities,\r\nwhile the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those\r\nfor other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their\r\ndensities were higher in the periphery than center of synapses. In contrast, the GluA3-\r\ncontaining receptors were more centrally localized compared to the GluA1- and GluA2-\r\ncontaining receptors.\r\nThe hippocampus plays a central role in learning and memory. Contextual learning has been\r\nshown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus.\r\nHowever, proximodistal heterogeneity of this plasticity and particular contribution of different\r\nAMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a\r\nhippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an\r\nincrease in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area.\r\nThe intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred\r\npattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but\r\nnot stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings\r\nfurther contribute to our understanding of how specific hippocampal subregions and AMPA\r\nreceptor subunits are involved in physiological learning.\r\nAlthough the immunolabeling results above shed light on subunit-specific plasticity in\r\nAMPAR distribution, no tools to visualize and study the subunit composition at the single\r\nchannel level in situ have been available. Electron microscopy with conventional immunogold\r\nlabeling approaches has limitations in the single channel analysis because of the large size of\r\nantibodies and steric hindrance hampering multiple subunit labeling of single channels. I\r\nmanaged to develop a new chemical labeling system using a short peptide tag and small\r\nsynthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to\r\nproteins of interest (reactive tag system). I additionally made substantial progress into adapting\r\nthis system for AMPA receptor subunits.","lang":"eng"}],"file_date_updated":"2023-05-17T22:30:03Z","publication_status":"published","type":"dissertation","language":[{"iso":"eng"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"EM-Fac"}]},{"corr_author":"1","year":"2022","title":"Controllable states of superconducting Qubit ensembles","_id":"12366","month":"09","doi":"10.15479/at:ista:12132","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-024-4"]},"article_processing_charge":"No","has_accepted_license":"1","date_published":"2022-09-26T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["530"],"department":[{"_id":"GradSch"},{"_id":"JoFi"}],"oa_version":"Published Version","file":[{"date_created":"2023-01-25T09:41:49Z","file_id":"12367","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","checksum":"39eabb1e006b41335f17f3b29af09648","date_updated":"2023-01-26T23:30:44Z","relation":"main_file","file_size":56076868,"file_name":"Final_Thesis_ES_Redchenko.pdf","embargo":"2022-12-28"}],"citation":{"mla":"Redchenko, Elena. <i>Controllable States of Superconducting Qubit Ensembles</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>.","short":"E. Redchenko, Controllable States of Superconducting Qubit Ensembles, Institute of Science and Technology Austria, 2022.","ieee":"E. Redchenko, “Controllable states of superconducting Qubit ensembles,” Institute of Science and Technology Austria, 2022.","apa":"Redchenko, E. (2022). <i>Controllable states of superconducting Qubit ensembles</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>","ama":"Redchenko E. Controllable states of superconducting Qubit ensembles. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12132\">10.15479/at:ista:12132</a>","ista":"Redchenko E. 2022. Controllable states of superconducting Qubit ensembles. Institute of Science and Technology Austria.","chicago":"Redchenko, Elena. “Controllable States of Superconducting Qubit Ensembles.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12132\">https://doi.org/10.15479/at:ista:12132</a>."},"supervisor":[{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink"}],"status":"public","page":"168","author":[{"full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","last_name":"Redchenko","first_name":"Elena"}],"date_updated":"2026-04-07T14:22:39Z","publisher":"Institute of Science and Technology Austria","ec_funded":1,"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"},{"_id":"EM-Fac"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher","language":[{"iso":"eng"}],"type":"dissertation","publication_status":"published","file_date_updated":"2023-01-26T23:30:44Z","oa":1,"abstract":[{"lang":"eng","text":"Recent substantial advances in the feld of superconducting circuits have shown its\r\npotential as a leading platform for future quantum computing. In contrast to classical\r\ncomputers based on bits that are represented by a single binary value, 0 or 1, quantum\r\nbits (or qubits) can be in a superposition of both. Thus, quantum computers can store\r\nand handle more information at the same time and a quantum advantage has already\r\nbeen demonstrated for two types of computational tasks. Rapid progress in academic\r\nand industry labs accelerates the development of superconducting processors which may\r\nsoon fnd applications in complex computations, chemical simulations, cryptography, and\r\noptimization. Now that these machines are scaled up to tackle such problems the questions\r\nof qubit interconnects and networks becomes very relevant. How to route signals on-chip\r\nbetween diferent processor components? What is the most efcient way to entangle\r\nqubits? And how to then send and process entangled signals between distant cryostats\r\nhosting superconducting processors?\r\nIn this thesis, we are looking for solutions to these problems by studying the collective\r\nbehavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable\r\ndirectional scattering of microwave photons from a pair of qubits in a waveguide. Such a\r\ndevice can route microwave photons on-chip with a high diode efciency. Then we focus\r\non studying ultra-strong coupling regimes between light (microwave photons) and matter\r\n(superconducting qubits), a regime that could be promising for extremely fast multi-qubit\r\nentanglement generation. Finally, we show coherent pulse storage and periodic revivals\r\nin a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage\r\ndevice could be used as part of a quantum repeater that is needed for longer-distance\r\nquantum communication.\r\nThe achieved high degree of control over multi-qubit ensembles highlights not only the\r\nbeautiful physics of circuit quantum electrodynamics, it also represents the frst step\r\ntoward new quantum simulation and communication methods, and certain techniques\r\nmay also fnd applications in future superconducting quantum computing hardware.\r\n"}],"date_created":"2023-01-25T09:17:02Z","fulldoi":"https://doi.org/10.15479/at:ista:12132","degree_awarded":"PhD","day":"26","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","grant_number":"862644","name":"Quantum readout techniques and technologies","call_identifier":"H2020"}]},{"article_processing_charge":"No","doi":"10.15479/AT:ISTA:10934","month":"04","_id":"10934","title":"In vitro reconstitution of Escherichia coli divisome activation","related_material":{"record":[{"status":"public","id":"11373","relation":"used_in_publication"},{"status":"public","relation":"used_in_publication","id":"14280"}],"link":[{"url":"https://doi.org/10.5281/zenodo.6400639","description":"A custom written code (FRAPdiff) to quantify the Off binding rate and Diffusion coefficient of membrane bound proteins. Written by Christoph Sommer.","relation":"software"}]},"year":"2022","corr_author":"1","date_updated":"2026-09-14T22:30:11Z","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":" 0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","first_name":"Philipp"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"status":"public","citation":{"mla":"Radler, Philipp. <i>In Vitro Reconstitution of Escherichia Coli Divisome Activation</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>.","short":"P. Radler, (2022).","ieee":"P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022.","apa":"Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">https://doi.org/10.15479/AT:ISTA:10934</a>","ama":"Radler P. In vitro reconstitution of Escherichia coli divisome activation. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>","ista":"Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>.","chicago":"Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">https://doi.org/10.15479/AT:ISTA:10934</a>."},"oa_version":"Submitted Version","file":[{"creator":"pradler","checksum":"52d50202e04e9daa618a58e686d8ab58","date_updated":"2022-04-22T10:15:19Z","relation":"main_file","file_size":13469,"file_name":"Inventory for Data repository.docx","date_created":"2022-04-22T10:15:19Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"11328","success":1,"access_level":"open_access"},{"date_updated":"2022-03-31T12:57:36Z","checksum":"3e1518dd9fe9266b9bcc67695cb5015c","creator":"pradler","file_name":"Raw Data 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(4.0)"},"date_created":"2022-03-31T11:32:32Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:10934","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","oa":1,"abstract":[{"text":"FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments.  Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. ","lang":"eng"}]},{"project":[{"_id":"26199CA4-B435-11E9-9278-68D0E5697425","name":"Implications of a TGFβ/Dpp-activated subpopulation for Drosophila macrophage migration","grant_number":"24800"}],"day":"20","fulldoi":"https://doi.org/10.15479/at:ista:11193","date_created":"2022-04-20T08:59:07Z","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","oa":1,"abstract":[{"lang":"eng","text":"The infiltration of immune cells into tissues underlies the establishment of tissue-resident\r\nmacrophages and responses to infections and tumors. However, the mechanisms immune\r\ncells utilize to collectively migrate through tissue barriers in vivo are not yet well understood.\r\nIn this thesis, I describe two mechanisms that Drosophila immune cells (hemocytes) use to\r\novercome the tissue barrier of the germband in the embryo. One strategy is the strengthening\r\nof the actin cortex through developmentally controlled transcriptional regulation induced by\r\nthe Drosophila proto-oncogene family member Dfos, which I show in Chapter 2. Dfos induces\r\nexpression of the tetraspanin TM4SF and the filamin Cher leading to higher levels of the\r\nactivated formin Dia at the cortex and increased cortical F-actin. This enhanced cortical\r\nstrength allows hemocytes to overcome the physical resistance of the surrounding tissue and\r\ntranslocate their nucleus to move forward. This mechanism affects the speed of migration\r\nwhen hemocytes face a confined environment in vivo.\r\nAnother aspect of the invasion process is the initial step of the leading hemocytes entering\r\nthe tissue, which potentially guides the follower cells. In Chapter 3, I describe a novel\r\nsubpopulation of hemocytes activated by BMP signaling prior to tissue invasion that leads\r\npenetration into the germband. Hemocytes that are deficient in BMP signaling activation\r\nshow impaired persistence at the tissue entry, while their migration speed remains\r\nunaffected.\r\nThis suggests that there might be different mechanisms controlling immune cell migration\r\nwithin the confined environment in vivo, one of these being the general ability to overcome\r\nthe resistance of the surrounding tissue and another affecting the order of hemocytes that\r\ncollectively invade the tissue in a stream of individual cells.\r\nTogether, my findings provide deeper insights into transcriptional changes in immune\r\ncells that enable efficient tissue invasion and pave the way for future studies investigating the\r\nearly colonization of tissues by macrophages in higher organisms. Moreover, they extend the\r\ncurrent view of Drosophila immune cell heterogeneity and point toward a potentially\r\nconserved role for canonical BMP signaling in specifying immune cells that lead the migration\r\nof tissue resident macrophages during embryogenesis."}],"file_date_updated":"2023-04-21T22:30:03Z","type":"dissertation","publication_status":"published","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher","status":"public","date_updated":"2026-04-07T14:24:19Z","page":"170","author":[{"last_name":"Wachner","first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","full_name":"Wachner, Stephanie"}],"publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Wachner, Stephanie. “Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>.","ama":"Wachner S. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>","ista":"Wachner S. 2022. Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells. Institute of Science and Technology Austria.","mla":"Wachner, Stephanie. <i>Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11193\">10.15479/at:ista:11193</a>.","apa":"Wachner, S. (2022). <i>Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11193\">https://doi.org/10.15479/at:ista:11193</a>","short":"S. Wachner, Transcriptional Regulation by Dfos and BMP-Signaling Support Tissue Invasion of Drosophila Immune Cells, Institute of Science and Technology Austria, 2022.","ieee":"S. Wachner, “Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells,” Institute of Science and Technology Austria, 2022."},"supervisor":[{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E"}],"oa_version":"Published Version","file":[{"checksum":"999ab16884c4522486136ebc5ae8dbff","creator":"cchlebak","date_updated":"2023-04-21T22:30:03Z","file_size":8820951,"file_name":"Thesis_Stephanie_Wachner_20200414_formatted.pdf","relation":"main_file","embargo":"2023-04-20","content_type":"application/pdf","file_id":"11195","date_created":"2022-04-20T09:03:57Z","access_level":"open_access"},{"creator":"cchlebak","checksum":"fd92b1e38d53bdf8b458213882d41383","date_updated":"2023-04-21T22:30:03Z","relation":"source_file","file_name":"Thesis_Stephanie_Wachner_20200414.zip","file_size":65864612,"embargo_to":"open_access","date_created":"2022-04-22T12:41:00Z","file_id":"11329","content_type":"application/x-zip-compressed","access_level":"closed"}],"has_accepted_license":"1","date_published":"2022-04-20T00:00:00Z","ddc":["570"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"DaSi"}],"month":"04","doi":"10.15479/at:ista:11193","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","_id":"11193","title":"Transcriptional regulation by Dfos and BMP-signaling support tissue invasion of Drosophila immune cells","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10614"},{"status":"public","relation":"part_of_dissertation","id":"544"}]},"corr_author":"1","year":"2022"},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"file_date_updated":"2023-04-12T22:30:03Z","type":"dissertation","publication_status":"published","date_created":"2023-01-25T14:27:43Z","fulldoi":"https://doi.org/10.15479/at:ista:12378","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","oa":1,"abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\u0002automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\u0002like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia."}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"day":"11","related_material":{"record":[{"status":"public","id":"12244","relation":"part_of_dissertation"}]},"title":"MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes","corr_author":"1","year":"2022","doi":"10.15479/at:ista:12378","month":"11","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"_id":"12378","file":[{"creator":"cchlebak","checksum":"8cd3ddfe9b53381dcf086023d8d8893a","date_updated":"2023-04-12T22:30:03Z","relation":"source_file","file_name":"Gloria_Colombo_Thesis.docx","file_size":23890382,"embargo_to":"open_access","date_created":"2023-01-25T14:31:32Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12379","access_level":"closed"},{"date_updated":"2023-04-12T22:30:03Z","creator":"cchlebak","checksum":"8af4319c18b516e8758e9a6cb02b103b","embargo":"2023-04-11","relation":"main_file","file_name":"Gloria_Colombo_Thesis.pdf","file_size":13802421,"date_created":"2023-01-25T14:31:36Z","content_type":"application/pdf","file_id":"12380","access_level":"open_access"}],"oa_version":"Published Version","date_published":"2022-11-11T00:00:00Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"SaSi"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["570"],"status":"public","publisher":"Institute of Science and Technology Austria","ec_funded":1,"author":[{"orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria","last_name":"Colombo"}],"date_updated":"2026-04-07T14:29:41Z","page":"142","citation":{"chicago":"Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>.","ama":"Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>","ista":"Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria.","mla":"Colombo, Gloria. <i>MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12378\">10.15479/at:ista:12378</a>.","apa":"Colombo, G. (2022). <i>MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12378\">https://doi.org/10.15479/at:ista:12378</a>","short":"G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022.","ieee":"G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022."},"supervisor":[{"orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","first_name":"Sandra"}]},{"abstract":[{"text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work.","lang":"eng"}],"oa":1,"fulldoi":"https://doi.org/10.15479/at:ista:11388","date_created":"2022-05-16T16:49:18Z","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","day":"18","alternative_title":["ISTA Thesis"],"OA_place":"publisher","language":[{"iso":"eng"}],"type":"dissertation","publication_status":"published","file_date_updated":"2023-05-20T22:30:03Z","date_published":"2022-05-18T00:00:00Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"ddc":["576"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file":[{"access_level":"open_access","file_id":"11398","content_type":"application/pdf","date_created":"2022-05-19T13:03:13Z","file_size":8247240,"file_name":"thesis_sb_final_pdfa.pdf","relation":"main_file","embargo":"2023-05-19","checksum":"4d75e6a619df7e8a9d6e840aee182380","creator":"sbelohla","date_updated":"2023-05-20T22:30:03Z"},{"date_created":"2022-05-19T13:07:47Z","content_type":"application/x-zip-compressed","file_id":"11399","access_level":"closed","creator":"sbelohla","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","date_updated":"2023-05-20T22:30:03Z","relation":"source_file","file_size":7094,"file_name":"thesis_sb_final.zip","embargo_to":"open_access"}],"oa_version":"Published Version","citation":{"chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","mla":"Belohlavy, Stefanie. <i>The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11388\">10.15479/at:ista:11388</a>.","apa":"Belohlavy, S. (2022). <i>The genetic basis of complex traits studied via analysis of evolve and resequence experiments</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11388\">https://doi.org/10.15479/at:ista:11388</a>","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022."},"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"}],"status":"public","publisher":"Institute of Science and Technology Austria","author":[{"id":"43FE426A-F248-11E8-B48F-1D18A9856A87","full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","first_name":"Stefanie","last_name":"Belohlavy"}],"page":"98","date_updated":"2026-04-07T14:29:57Z","corr_author":"1","year":"2022","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6713"}]},"title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","_id":"11388","month":"05","doi":"10.15479/at:ista:11388","article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-018-3"]}},{"oa":1,"abstract":[{"text":"Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening.","lang":"eng"}],"fulldoi":"https://doi.org/10.15479/at:ista:12401","date_created":"2023-01-26T11:55:16Z","degree_awarded":"PhD","day":"22","alternative_title":["ISTA Thesis"],"OA_place":"publisher","language":[{"iso":"eng"}],"type":"dissertation","publication_status":"published","file_date_updated":"2023-12-21T23:30:03Z","date_published":"2022-12-22T00:00:00Z","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["610"],"file":[{"access_level":"open_access","date_created":"2023-01-26T11:58:14Z","content_type":"application/pdf","file_id":"12402","relation":"main_file","file_size":42059787,"file_name":"PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf","embargo":"2023-12-20","creator":"cchlebak","checksum":"cc4a2b4a7e3c4ee8ef7f2dbf909b12bd","date_updated":"2023-12-21T23:30:03Z"},{"relation":"source_file","file_name":"Source Files - Saren Tasciyan - PhD Thesis.zip","file_size":261256696,"embargo_to":"open_access","creator":"cchlebak","checksum":"f1b4ca98b8ab0cb043b1830971e9bd9c","date_updated":"2023-12-21T23:30:03Z","access_level":"closed","date_created":"2023-01-26T12:00:10Z","content_type":"application/x-zip-compressed","file_id":"12403"}],"oa_version":"Published Version","citation":{"ista":"Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria.","ama":"Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>","chicago":"Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>.","mla":"Tasciyan, Saren. <i>Role of Microenvironment Heterogeneity in Cancer Cell Invasion</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12401\">10.15479/at:ista:12401</a>.","ieee":"S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022.","short":"S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022.","apa":"Tasciyan, S. (2022). <i>Role of microenvironment heterogeneity in cancer cell invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12401\">https://doi.org/10.15479/at:ista:12401</a>"},"supervisor":[{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-14T09:07:14Z","author":[{"last_name":"Tasciyan","first_name":"Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X"}],"page":"105","corr_author":"1","year":"2022","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7885"},{"id":"10703","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"679","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9429","status":"public"}]},"title":"Role of microenvironment heterogeneity in cancer cell invasion","_id":"12401","month":"12","doi":"10.15479/at:ista:12401","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]}},{"corr_author":"1","year":"2022","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","related_material":{"record":[{"id":"12248","relation":"used_in_publication","status":"public"}]},"type":"research_data","_id":"11653","doi":"10.15479/AT:ISTA:11653","month":"08","file_date_updated":"2022-08-08T22:30:04Z","contributor":[{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","last_name":"Mrnjavac"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"first_name":"Luca","last_name":"Sax"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"last_name":"Hontoria ","first_name":"Francisco"},{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"has_accepted_license":"1","oa":1,"date_published":"2022-08-05T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"date_created":"2022-07-26T11:01:47Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:11653","oa_version":"Published Version","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)"},"file":[{"access_level":"open_access","date_created":"2022-07-26T12:37:52Z","content_type":"application/x-zip-compressed","title":"Supplementary Datasets","file_id":"11655","relation":"main_file","file_name":"Data.zip","file_size":2209382998,"embargo":"2022-08-07","creator":"melkrewi","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","date_updated":"2022-08-08T22:30:04Z"}],"citation":{"apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","short":"M.N. Elkrewi, (2022).","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>.","ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>."},"day":"05","status":"public","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi"}],"date_updated":"2025-04-15T08:34:17Z","publisher":"Institute of Science and Technology Austria"},{"degree_awarded":"PhD","date_created":"2022-08-19T08:52:30Z","fulldoi":"https://doi.org/10.15479/at:ista:11932","acknowledgement":"I acknowledge the support from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","oa":1,"abstract":[{"lang":"eng","text":"The ability to form and retrieve memories is central to survival. In mammals, the hippocampus\r\nis a brain region essential to the acquisition and consolidation of new memories. It is also\r\ninvolved in keeping track of one’s position in space and aids navigation. Although this\r\nspace-memory has been a source of contradiction, evidence supports the view that the role of\r\nthe hippocampus in navigation is memory, thanks to the formation of cognitive maps. First\r\nintroduced by Tolman in 1948, cognitive maps are generally used to organize experiences in\r\nmemory; however, the detailed mechanisms by which these maps are formed and stored are not\r\nyet agreed upon. Some influential theories describe this process as involving three fundamental\r\nsteps: initial encoding by the hippocampus, interactions between the hippocampus and other\r\ncortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how\r\nthe investigation of cognitive maps of space helped to shed light on each of these three memory\r\nprocesses.\r\nThe first study included in this thesis deals with the initial encoding of spatial memories in\r\nthe hippocampus. Much is known about encoding at the level of single cells, but less about\r\ntheir co-activity or joint contribution to the encoding of novel spatial information. I will\r\ndescribe the structure of an interaction network that allows for efficient encoding of noisy\r\nspatial information during the first exploration of a novel environment.\r\nThe second study describes the interactions between the hippocampus and the prefrontal\r\ncortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert\r\nwith the hippocampus, is involved in various processes, including memory storage and spatial\r\nnavigation. Nonetheless, the detailed mechanisms by which PFC receives information from the\r\nhippocampus are not clear. I will show how a transient improvement in theta phase locking of\r\nPFC cells enables interactions of cell pairs across the two regions.\r\nThe third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around\r\ngoal locations, a correlate of learning, can shed light on the transition from short- to long-term\r\nspatial memories and the speed of consolidation in different brain areas.\r\nThe studies included in this thesis represent the main scientific contributions of my Ph.D. They\r\ninvolve statistical analyses and models of neural responses of cells in different brain areas of\r\nrats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings\r\non principles of memory formation and retention, including the mechanisms, the speed, and\r\nthe duration of these processes."}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"day":"19","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher","file_date_updated":"2023-06-20T22:30:04Z","publication_status":"published","type":"dissertation","file":[{"checksum":"2dbb70c74aaa3b64c1f463e943baf09c","creator":"mnardin","date_updated":"2023-06-20T22:30:04Z","file_name":"Michele Nardin, Ph.D. Thesis - ISTA (1).zip","file_size":13515457,"relation":"source_file","embargo_to":"open_access","content_type":"application/zip","file_id":"11935","date_created":"2022-08-19T16:31:34Z","access_level":"closed"},{"access_level":"open_access","file_id":"11941","content_type":"application/pdf","date_created":"2022-08-22T09:43:50Z","embargo":"2023-06-19","file_name":"Michele_Nardin_Phd_Thesis_PDFA.pdf","file_size":9906458,"relation":"main_file","date_updated":"2023-06-20T22:30:04Z","checksum":"0ec94035ea35a47a9f589ed168e60b48","creator":"mnardin"}],"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["573"],"date_published":"2022-08-19T00:00:00Z","has_accepted_license":"1","ec_funded":1,"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"}],"page":"136","date_updated":"2026-07-06T12:47:25Z","status":"public","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"citation":{"ama":"Nardin M. On the encoding, transfer, and consolidation of spatial memories. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>","ista":"Nardin M. 2022. On the encoding, transfer, and consolidation of spatial memories. Institute of Science and Technology Austria.","chicago":"Nardin, Michele. “On the Encoding, Transfer, and Consolidation of Spatial Memories.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>.","mla":"Nardin, Michele. <i>On the Encoding, Transfer, and Consolidation of Spatial Memories</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11932\">10.15479/at:ista:11932</a>.","short":"M. Nardin, On the Encoding, Transfer, and Consolidation of Spatial Memories, Institute of Science and Technology Austria, 2022.","ieee":"M. Nardin, “On the encoding, transfer, and consolidation of spatial memories,” Institute of Science and Technology Austria, 2022.","apa":"Nardin, M. (2022). <i>On the encoding, transfer, and consolidation of spatial memories</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11932\">https://doi.org/10.15479/at:ista:11932</a>"},"related_material":{"record":[{"status":"public","id":"6194","relation":"part_of_dissertation"},{"id":"10077","relation":"part_of_dissertation","status":"public"}]},"title":"On the encoding, transfer, and consolidation of spatial memories","year":"2022","corr_author":"1","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"month":"08","doi":"10.15479/at:ista:11932","_id":"11932"},{"title":"Pathogen-mediated sexual selection and immunization in ant colonies","year":"2022","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","doi":"10.15479/AT:ISTA:10727","month":"02","_id":"10727","oa_version":"Published Version","file":[{"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"10728","date_created":"2022-02-04T15:36:12Z","embargo_to":"open_access","file_size":6757886,"file_name":"Thesis_Sina_Metzler.docx","relation":"source_file","date_updated":"2023-02-03T23:30:03Z","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","creator":"smetzler"},{"access_level":"open_access","date_created":"2022-02-04T15:36:43Z","content_type":"application/pdf","file_id":"10730","relation":"main_file","file_size":6314921,"file_name":"Thesis_Sina_Metzler_A2.pdf","embargo":"2023-02-02","creator":"smetzler","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","date_updated":"2023-02-03T23:30:03Z"},{"access_level":"open_access","date_created":"2022-02-07T10:35:02Z","file_id":"10742","content_type":"application/pdf","embargo":"2023-02-02","relation":"main_file","file_name":"Thesis_Sina_Metzler_print.pdf","file_size":6882557,"date_updated":"2023-02-04T23:30:03Z","creator":"smetzler","checksum":"dedd14b7be7a75d63018dbfc68dd8113"}],"ddc":["570"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"has_accepted_license":"1","date_published":"2022-02-07T00:00:00Z","date_updated":"2026-04-07T14:30:18Z","author":[{"id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494","full_name":"Metzler, Sina","first_name":"Sina","last_name":"Metzler"}],"ec_funded":1,"publisher":"Institute of Science and Technology Austria","status":"public","supervisor":[{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer"}],"citation":{"mla":"Metzler, Sina. <i>Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>.","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","ieee":"S. Metzler, “Pathogen-mediated sexual selection and immunization in ant colonies,” Institute of Science and Technology Austria, 2022.","apa":"Metzler, S. (2022). <i>Pathogen-mediated sexual selection and immunization in ant colonies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>","ama":"Metzler S. Pathogen-mediated sexual selection and immunization in ant colonies. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10727\">10.15479/AT:ISTA:10727</a>","ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","chicago":"Metzler, Sina. “Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10727\">https://doi.org/10.15479/AT:ISTA:10727</a>."},"language":[{"iso":"eng"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"LifeSc"}],"file_date_updated":"2023-02-04T23:30:03Z","publication_status":"published","type":"dissertation","degree_awarded":"PhD","fulldoi":"https://doi.org/10.15479/AT:ISTA:10727","date_created":"2022-02-04T15:45:12Z","abstract":[{"text":"Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization).\r\nIn the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression.\r\nIn the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners.\r\nFirst, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care.\r\nIn the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history.","lang":"eng"}],"oa":1,"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402"}],"day":"07"},{"related_material":{"record":[{"relation":"dissertation_contains","id":"13074","status":"public"}]},"title":"AC/DC: Alternating Compressed/DeCompressed training of deep neural networks","year":"2021","arxiv":1,"intvolume":"        34","corr_author":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"month":"12","_id":"11458","external_id":{"arxiv":["2106.12379"]},"oa_version":"Published Version","department":[{"_id":"GradSch"},{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_published":"2021-12-06T00:00:00Z","publisher":"Neural Information Processing Systems Foundation","ec_funded":1,"author":[{"id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra","first_name":"Elena-Alexandra","last_name":"Peste"},{"full_name":"Iofinova, Eugenia B","orcid":"0000-0002-7778-3221","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","last_name":"Iofinova","first_name":"Eugenia B"},{"last_name":"Vladu","first_name":"Adrian","full_name":"Vladu, Adrian"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian"}],"page":"8557-8570","date_updated":"2026-06-18T17:18:20Z","status":"public","publication":"35th Conference on Neural Information Processing Systems","citation":{"mla":"Krumes, Alexandra, et al. “AC/DC: Alternating Compressed/DeCompressed Training of Deep Neural Networks.” <i>35th Conference on Neural Information Processing Systems</i>, vol. 34, Neural Information Processing Systems Foundation, 2021, pp. 8557–70.","apa":"Krumes, A., Iofinova, E. B., Vladu, A., &#38; Alistarh, D.-A. (2021). AC/DC: Alternating Compressed/DeCompressed training of deep neural networks. In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 34, pp. 8557–8570). Virtual, Online: Neural Information Processing Systems Foundation.","short":"A. Krumes, E.B. Iofinova, A. Vladu, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 8557–8570.","ieee":"A. Krumes, E. B. Iofinova, A. Vladu, and D.-A. Alistarh, “AC/DC: Alternating Compressed/DeCompressed training of deep neural networks,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, Online, 2021, vol. 34, pp. 8557–8570.","chicago":"Krumes, Alexandra, Eugenia B Iofinova, Adrian Vladu, and Dan-Adrian Alistarh. “AC/DC: Alternating Compressed/DeCompressed Training of Deep Neural Networks.” In <i>35th Conference on Neural Information Processing Systems</i>, 34:8557–70. Neural Information Processing Systems Foundation, 2021.","ista":"Krumes A, Iofinova EB, Vladu A, Alistarh D-A. 2021. AC/DC: Alternating Compressed/DeCompressed training of deep neural networks. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 34, 8557–8570.","ama":"Krumes A, Iofinova EB, Vladu A, Alistarh D-A. AC/DC: Alternating Compressed/DeCompressed training of deep neural networks. In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 34. Neural Information Processing Systems Foundation; 2021:8557-8570."},"language":[{"iso":"eng"}],"alternative_title":["Advances in Neural Information Processing Systems"],"acknowledged_ssus":[{"_id":"ScienComp"}],"main_file_link":[{"open_access":"1","url":"https://proceedings.neurips.cc/paper/2021/file/48000647b315f6f00f913caa757a70b3-Paper.pdf"}],"publication_status":"published","volume":34,"type":"conference","conference":{"location":"Virtual, Online","start_date":"2021-12-06","end_date":"2021-12-14","name":"NeurIPS: Neural Information Processing Systems"},"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML), and a CNRS PEPS grant. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp). We would also like to thank Christoph Lampert for his feedback on an earlier version of this work, as well as for providing hardware for the Transformer-XL experiments.","date_created":"2022-06-20T12:11:53Z","oa":1,"abstract":[{"lang":"eng","text":"The increasing computational requirements of deep neural networks (DNNs) have led to significant interest in obtaining DNN models that are sparse, yet accurate. Recent work has investigated the even harder case of sparse training, where the DNN weights are, for as much as possible, already sparse to reduce computational costs during training. Existing sparse training methods are often empirical and can have lower accuracy relative to the dense baseline. In this paper, we present a general approach called Alternating Compressed/DeCompressed (AC/DC) training of DNNs, demonstrate convergence for a variant of the algorithm, and show that AC/DC outperforms existing sparse training methods in accuracy at similar computational budgets; at high sparsity levels, AC/DC even outperforms existing methods that rely on accurate pre-trained dense models. An important property of AC/DC is that it allows co-training of dense and sparse models, yielding accurate sparse–dense model pairs at the end of the training process. This is useful in practice, where compressed variants may be desirable for deployment in resource-constrained settings without re-doing the entire training flow, and also provides us with insights into the accuracy gap between dense and compressed models. The code is available at: https://github.com/IST-DASLab/ACDC."}],"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"quality_controlled":"1","day":"06","scopus_import":"1"},{"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher","file_date_updated":"2021-09-15T14:37:30Z","publication_status":"published","type":"dissertation","degree_awarded":"PhD","date_created":"2021-09-13T11:12:34Z","fulldoi":"https://doi.org/10.15479/at:ista:10007","oa":1,"abstract":[{"lang":"eng","text":"The present thesis is concerned with the derivation of weak-strong uniqueness principles for curvature driven interface evolution problems not satisfying a comparison principle. The specific examples being treated are two-phase Navier-Stokes flow with surface tension, modeling the evolution of two incompressible, viscous and immiscible fluids separated by a sharp interface, and multiphase mean curvature flow, which serves as an idealized model for the motion of grain boundaries in an annealing polycrystalline material. Our main results - obtained in joint works with Julian Fischer, Tim Laux and Theresa M. Simon - state that prior to the formation of geometric singularities due to topology changes, the weak solution concept of Abels (Interfaces Free Bound. 9, 2007) to two-phase Navier-Stokes flow with surface tension and the weak solution concept of Laux and Otto (Calc. Var. Partial Differential Equations 55, 2016) to multiphase mean curvature flow (for networks in R^2 or double bubbles in R^3) represents the unique solution to these interface evolution problems within the class of classical solutions, respectively. To the best of the author's knowledge, for interface evolution problems not admitting a geometric comparison principle the derivation of a weak-strong uniqueness principle represented an open problem, so that the works contained in the present thesis constitute the first positive results in this direction. The key ingredient of our approach consists of the introduction of a novel concept of relative entropies for a class of curvature driven interface evolution problems, for which the associated energy contains an interfacial contribution being proportional to the surface area of the evolving (network of) interface(s). The interfacial part of the relative entropy gives sufficient control on the interface error between a weak and a classical solution, and its time evolution can be computed, at least in principle, for any energy dissipating weak solution concept. A resulting stability estimate for the relative entropy essentially entails the above mentioned weak-strong uniqueness principles. The present thesis contains a detailed introduction to our relative entropy approach, which in particular highlights potential applications to other problems in curvature driven interface evolution not treated in this thesis."}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"grant_number":"948819","name":"Bridging Scales in Random Materials","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"day":"14","title":"Curvature driven interface evolution: Uniqueness properties of weak solution concepts","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10012"},{"status":"public","id":"10013","relation":"part_of_dissertation"},{"id":"7489","relation":"part_of_dissertation","status":"public"}]},"year":"2021","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","month":"09","doi":"10.15479/at:ista:10007","_id":"10007","oa_version":"Published Version","file":[{"file_name":"thesis_final_Hensel.zip","file_size":15022154,"relation":"source_file","checksum":"c8475faaf0b680b4971f638f1db16347","creator":"shensel","date_updated":"2021-09-15T14:37:30Z","access_level":"closed","content_type":"application/x-zip-compressed","file_id":"10008","date_created":"2021-09-13T11:03:24Z"},{"checksum":"1a609937aa5275452822f45f2da17f07","creator":"shensel","date_updated":"2021-09-14T09:52:47Z","file_name":"thesis_final_Hensel.pdf","file_size":6583638,"relation":"main_file","file_id":"10014","content_type":"application/pdf","date_created":"2021-09-13T14:18:56Z","access_level":"open_access"}],"ddc":["515"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"has_accepted_license":"1","date_published":"2021-09-14T00:00:00Z","date_updated":"2026-04-08T07:01:01Z","author":[{"first_name":"Sebastian","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian"}],"page":"300","publisher":"Institute of Science and Technology Austria","ec_funded":1,"status":"public","supervisor":[{"last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Hensel, Sebastian. <i>Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10007\">10.15479/at:ista:10007</a>.","apa":"Hensel, S. (2021). <i>Curvature driven interface evolution: Uniqueness properties of weak solution concepts</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10007\">https://doi.org/10.15479/at:ista:10007</a>","short":"S. Hensel, Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts, Institute of Science and Technology Austria, 2021.","ieee":"S. Hensel, “Curvature driven interface evolution: Uniqueness properties of weak solution concepts,” Institute of Science and Technology Austria, 2021.","chicago":"Hensel, Sebastian. “Curvature Driven Interface Evolution: Uniqueness Properties of Weak Solution Concepts.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10007\">https://doi.org/10.15479/at:ista:10007</a>.","ista":"Hensel S. 2021. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. Institute of Science and Technology Austria.","ama":"Hensel S. Curvature driven interface evolution: Uniqueness properties of weak solution concepts. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10007\">10.15479/at:ista:10007</a>"}},{"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","fulldoi":"https://doi.org/10.15479/at:ista:10030","acknowledgement":"The author gratefully acknowledges support by the Austrian Science Fund (FWF), grants No W1245.","date_created":"2021-09-21T09:14:15Z","abstract":[{"text":"This PhD thesis is primarily focused on the study of discrete transport problems, introduced for the first time in the seminal works of Maas [Maa11] and Mielke [Mie11] on finite state Markov chains and reaction-diffusion equations, respectively. More in detail, my research focuses on the study of transport costs on graphs, in particular the convergence and the stability of such problems in the discrete-to-continuum limit. This thesis also includes some results concerning\r\nnon-commutative optimal transport. The first chapter of this thesis consists of a general introduction to the optimal transport problems, both in the discrete, the continuous, and the non-commutative setting. Chapters 2 and 3 present the content of two works, obtained in collaboration with Peter Gladbach, Eva Kopfer, and Jan Maas, where we have been able to show the convergence of discrete transport costs on periodic graphs to suitable continuous ones, which can be described by means of a homogenisation result. We first focus on the particular case of quadratic costs on the real line and then extending the result to more general costs in arbitrary dimension. Our results are the first complete characterisation of limits of transport costs on periodic graphs in arbitrary dimension which do not rely on any additional symmetry. In Chapter 4 we turn our attention to one of the intriguing connection between evolution equations and optimal transport, represented by the theory of gradient flows. We show that discrete gradient flow structures associated to a finite volume approximation of a certain class of diffusive equations (Fokker–Planck) is stable in the limit of vanishing meshes, reproving the convergence of the scheme via the method of evolutionary Γ-convergence and exploiting a more variational point of view on the problem. This is based on a collaboration with Dominik Forkert and Jan Maas. Chapter 5 represents a change of perspective, moving away from the discrete world and reaching the non-commutative one. As in the discrete case, we discuss how classical tools coming from the commutative optimal transport can be translated into the setting of density matrices. In particular, in this final chapter we present a non-commutative version of the Schrödinger problem (or entropic regularised optimal transport problem) and discuss existence and characterisation of minimisers, a duality result, and present a non-commutative version of the well-known Sinkhorn algorithm to compute the above mentioned optimisers. This is based on a joint work with Dario Feliciangeli and Augusto Gerolin. Finally, Appendix A and B contain some additional material and discussions, with particular attention to Harnack inequalities and the regularity of flows on discrete spaces.","lang":"eng"}],"oa":1,"project":[{"_id":"260788DE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Dissipation and dispersion in nonlinear partial differential equations","grant_number":"W1245"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"day":"22","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"OA_place":"publisher","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"file_date_updated":"2022-03-10T12:14:42Z","publication_status":"published","type":"dissertation","oa_version":"Published Version","file":[{"date_updated":"2022-03-10T12:14:42Z","creator":"cchlebak","checksum":"8cd60dcb8762e8f21867e21e8001e183","relation":"source_file","file_name":"tex_and_pictures.zip","file_size":3876668,"date_created":"2021-09-21T09:17:34Z","content_type":"application/x-zip-compressed","file_id":"10032","access_level":"closed"},{"date_updated":"2021-09-27T11:14:31Z","checksum":"9789e9d967c853c1503ec7f307170279","creator":"cchlebak","file_name":"thesis_portinale_Final (1).pdf","file_size":2532673,"relation":"main_file","content_type":"application/pdf","file_id":"10047","date_created":"2021-09-27T11:14:31Z","access_level":"open_access"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ddc":["515"],"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"has_accepted_license":"1","date_published":"2021-09-22T00:00:00Z","date_updated":"2026-04-08T07:00:04Z","author":[{"full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","first_name":"Lorenzo"}],"publisher":"Institute of Science and Technology Austria","status":"public","supervisor":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas"}],"citation":{"chicago":"Portinale, Lorenzo. “Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10030\">https://doi.org/10.15479/at:ista:10030</a>.","ista":"Portinale L. 2021. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. Institute of Science and Technology Austria.","ama":"Portinale L. Discrete-to-continuum limits of transport problems and gradient flows in the space of measures. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10030\">10.15479/at:ista:10030</a>","apa":"Portinale, L. (2021). <i>Discrete-to-continuum limits of transport problems and gradient flows in the space of measures</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10030\">https://doi.org/10.15479/at:ista:10030</a>","short":"L. Portinale, Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures, Institute of Science and Technology Austria, 2021.","ieee":"L. Portinale, “Discrete-to-continuum limits of transport problems and gradient flows in the space of measures,” Institute of Science and Technology Austria, 2021.","mla":"Portinale, Lorenzo. <i>Discrete-to-Continuum Limits of Transport Problems and Gradient Flows in the Space of Measures</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10030\">10.15479/at:ista:10030</a>."},"title":"Discrete-to-continuum limits of transport problems and gradient flows in the space of measures","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"9792"},{"status":"public","relation":"part_of_dissertation","id":"10022"},{"status":"public","id":"7573","relation":"part_of_dissertation"}]},"year":"2021","corr_author":"1","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","doi":"10.15479/at:ista:10030","month":"09","_id":"10030"},{"language":[{"iso":"eng"}],"volume":5,"publication_status":"published","type":"journal_article","file_date_updated":"2021-11-04T07:24:48Z","oa":1,"abstract":[{"lang":"eng","text":"In this work we solve the algorithmic problem of consistency verification for the TSO and PSO memory models given a reads-from map, denoted VTSO-rf and VPSO-rf, respectively. For an execution of n events over k threads and d variables, we establish novel bounds that scale as nk+1 for TSO and as nk+1· min(nk2, 2k· d) for PSO. Moreover, based on our solution to these problems, we develop an SMC algorithm under TSO and PSO that uses the RF equivalence. The algorithm is exploration-optimal, in the sense that it is guaranteed to explore each class of the RF partitioning exactly once, and spends polynomial time per class when k is bounded. Finally, we implement all our algorithms in the SMC tool Nidhugg, and perform a large number of experiments over benchmarks from existing literature. Our experimental results show that our algorithms for VTSO-rf and VPSO-rf provide significant scalability improvements over standard alternatives. Moreover, when used for SMC, the RF partitioning is often much coarser than the standard Shasha-Snir partitioning for TSO/PSO, which yields a significant speedup in the model checking task.\r\n\r\n"}],"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)"},"article_number":"164","date_created":"2021-10-27T15:05:34Z","fulldoi":"https://doi.org/10.1145/3485541","acknowledgement":"The research was partially funded by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science\r\nand Technology Fund (WWTF) through project ICT15-003.","day":"15","issue":"OOPSLA","scopus_import":"1","quality_controlled":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"intvolume":"         5","arxiv":1,"year":"2021","title":"The reads-from equivalence for the TSO and PSO memory models","related_material":{"record":[{"id":"10199","relation":"dissertation_contains","status":"public"}]},"external_id":{"arxiv":["2011.11763"]},"_id":"10191","publication_identifier":{"eissn":["2475-1421"]},"article_processing_charge":"No","month":"10","doi":"10.1145/3485541","ddc":["000"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"has_accepted_license":"1","keyword":["safety","risk","reliability and quality","software"],"date_published":"2021-10-15T00:00:00Z","oa_version":"Published Version","file":[{"date_updated":"2021-11-04T07:24:48Z","checksum":"9d6dce7b611853c529bb7b1915ac579e","creator":"cchlebak","file_size":2903485,"file_name":"2021_ProcACMPL_Bui.pdf","relation":"main_file","file_id":"10215","content_type":"application/pdf","date_created":"2021-11-04T07:24:48Z","access_level":"open_access","success":1}],"publication":"Proceedings of the ACM on Programming Languages","article_type":"original","citation":{"ama":"Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. The reads-from equivalence for the TSO and PSO memory models. <i>Proceedings of the ACM on Programming Languages</i>. 2021;5(OOPSLA). doi:<a href=\"https://doi.org/10.1145/3485541\">10.1145/3485541</a>","ista":"Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. 2021. The reads-from equivalence for the TSO and PSO memory models. Proceedings of the ACM on Programming Languages. 5(OOPSLA), 164.","chicago":"Bui, Truc Lam, Krishnendu Chatterjee, Tushar Gautam, Andreas Pavlogiannis, and Viktor Toman. “The Reads-from Equivalence for the TSO and PSO Memory Models.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3485541\">https://doi.org/10.1145/3485541</a>.","short":"T.L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, V. Toman, Proceedings of the ACM on Programming Languages 5 (2021).","ieee":"T. L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, and V. Toman, “The reads-from equivalence for the TSO and PSO memory models,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5, no. OOPSLA. Association for Computing Machinery, 2021.","apa":"Bui, T. L., Chatterjee, K., Gautam, T., Pavlogiannis, A., &#38; Toman, V. (2021). The reads-from equivalence for the TSO and PSO memory models. <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3485541\">https://doi.org/10.1145/3485541</a>","mla":"Bui, Truc Lam, et al. “The Reads-from Equivalence for the TSO and PSO Memory Models.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5, no. OOPSLA, 164, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3485541\">10.1145/3485541</a>."},"author":[{"full_name":"Bui, Truc Lam","first_name":"Truc Lam","last_name":"Bui"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Tushar","last_name":"Gautam","full_name":"Gautam, Tushar"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-08T07:00:31Z","ec_funded":1,"publisher":"Association for Computing Machinery","status":"public"}]