[{"abstract":[{"text":"The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and\r\nvisual complexity. The small-scale interactions of yarns colliding with and pulling on each\r\nother result in drastically different large-scale stretching and bending behavior, introducing\r\nanisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this\r\ncomplexity and match the quality of real fabric, it may be too computationally expensive for\r\nlarge fabrics. On the other hand, continuum-based approaches do not need to discretize the\r\ncloth at a stitch-level, but it is non-trivial to find a material model that would replicate the\r\nlarge-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,\r\nwe discuss three methods to try and bridge the gap between small-scale and large-scale yarn\r\nmechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively\r\nfitting yarn parameters to physical measurements of real fabric.\r\nTo start, we present a method for animating yarn-level cloth effects using a thin-shell solver.\r\nWe first use a large number of periodic yarn-level simulations to build a model of the potential\r\nenergy density of the cloth, and then use it to compute forces in a thin-shell simulator. The\r\nresulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics\r\nand the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of\r\nfull yarn-level simulation.\r\nWhile our thin-shell simulations are able to capture large-scale yarn mechanics, they lack\r\nthe rich visual detail of yarn-level simulations. Therefore, we propose a method to animate\r\nyarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware\r\nfashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are\r\nable to reproduce effects such as knit loops tightening under stretching at negligible cost.\r\nFinally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,\r\nbased on the mechanical response of fabrics in the real world. We compile a database from\r\nphysical tests of several knitted fabrics used in the textile industry spanning diverse physical\r\nproperties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized\r\nshell models to speed up computation and adding some small-but-necessary extensions to\r\nyarn-level models used in computer graphics.\r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"project":[{"call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"ec_funded":1,"oa_version":"Published Version","day":"22","title":"Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting","month":"09","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"date_updated":"2026-04-16T08:31:54Z","doi":"10.15479/at:ista:12103","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-020-6"]},"degree_awarded":"PhD","publication_status":"published","citation":{"ieee":"G. Sperl, “Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting,” Institute of Science and Technology Austria, 2022.","mla":"Sperl, Georg. <i>Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>.","ista":"Sperl G. 2022. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. Institute of Science and Technology Austria.","ama":"Sperl G. Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:12103\">10.15479/at:ista:12103</a>","chicago":"Sperl, Georg. “Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>.","short":"G. Sperl, Homogenizing Yarn Simulations: Large-Scale Mechanics, Small-Scale Detail, and Quantitative Fitting, Institute of Science and Technology Austria, 2022.","apa":"Sperl, G. (2022). <i>Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12103\">https://doi.org/10.15479/at:ista:12103</a>"},"date_published":"2022-09-22T00:00:00Z","year":"2022","page":"138","ddc":["000","620"],"file":[{"file_id":"12371","creator":"cchlebak","title":"Thesis","content_type":"application/pdf","description":"This is the main PDF file of the thesis. 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Information-flow properties are hyperproperties, as they compare different traces of a system. Sequential information-flow properties can express changes, over time, in the information-flow constraints. For example, information-flow constraints during an initialization phase of a system may be different from information-flow constraints that are required during the operation phase. We formalize several variants of interpreting sequential information-flow constraints, which arise from different assumptions about what can be observed of the system. For this purpose, we introduce a first-order logic, called Hypertrace Logic, with both trace and time quantifiers for specifying linear-time hyperproperties. We prove that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted quantifier prefixes, cannot specify the majority of the studied variants of sequential information flow, including all variants in which the transition between sequential phases (such as initialization and operation) happens asynchronously. Our results rely on new equivalences between sets of traces that cannot be distinguished by certain classes of formulas from Hypertrace Logic. This presents a new approach to proving inexpressiveness results for HyperLTL.","lang":"eng"}],"publication_status":"published","publisher":"Springer Nature","article_processing_charge":"No","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783030945831"],"issn":["0302-9743"],"isbn":["9783030945824"]},"doi":"10.1007/978-3-030-94583-1_1","year":"2022","date_published":"2022-01-14T00:00:00Z","citation":{"short":"E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2022, pp. 1–19.","apa":"Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., &#38; Da Costa, A. O. (2022). Flavors of sequential information flow. In <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 13182, pp. 1–19). Philadelphia, PA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">https://doi.org/10.1007/978-3-030-94583-1_1</a>","ama":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Flavors of sequential information flow. In: <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 13182. Springer Nature; 2022:1-19. doi:<a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">10.1007/978-3-030-94583-1_1</a>","chicago":"Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira Da Costa. “Flavors of Sequential Information Flow.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, 13182:1–19. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">https://doi.org/10.1007/978-3-030-94583-1_1</a>.","ista":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Flavors of sequential information flow. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 13182, 1–19.","ieee":"E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa, “Flavors of sequential information flow,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Philadelphia, PA, United States, 2022, vol. 13182, pp. 1–19.","mla":"Bartocci, Ezio, et al. “Flavors of Sequential Information Flow.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, vol. 13182, Springer Nature, 2022, pp. 1–19, doi:<a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">10.1007/978-3-030-94583-1_1</a>."},"title":"Flavors of sequential information flow","isi":1,"date_updated":"2026-04-16T09:13:43Z","month":"01","department":[{"_id":"ToHe"}]},{"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Journal of Graph Algorithms and Applications","status":"public","date_created":"2022-08-21T22:01:56Z","scopus_import":"1","intvolume":"        26","page":"225-240","file":[{"file_size":694538,"relation":"main_file","access_level":"open_access","success":1,"checksum":"dc6e255e3558faff924fd9e370886c11","date_created":"2022-08-22T06:42:42Z","creator":"dernst","file_id":"11940","content_type":"application/pdf","date_updated":"2022-08-22T06:42:42Z","file_name":"2022_JourGraphAlgorithmsApplic_Aichholzer.pdf"}],"ddc":["000"],"_id":"11938","arxiv":1,"related_material":{"record":[{"relation":"earlier_version","id":"9296","status":"public"}]},"oa":1,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Oswin","full_name":"Aichholzer, Oswin","last_name":"Aichholzer"},{"first_name":"Alan M","orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","last_name":"Arroyo Guevara"},{"orcid":"0000-0002-6660-1322","first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","full_name":"Masárová, Zuzana","last_name":"Masárová"},{"first_name":"Irene","full_name":"Parada, Irene","last_name":"Parada"},{"last_name":"Perz","full_name":"Perz, Daniel","first_name":"Daniel"},{"last_name":"Pilz","full_name":"Pilz, Alexander","first_name":"Alexander"},{"first_name":"Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"}],"acknowledgement":"A.A. funded by the Marie Sklodowska-Curie grant agreement No 754411. Z.M. partially funded by Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31. I.P., D.P., and B.V. partially supported by FWF within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. A.P. supported by a Schrödinger fellowship of the FWF: J-3847-N35. J.T. partially supported by ERC Start grant no. (279307: Graph Games), FWF grant no. P23499-N23 and S11407-N23 (RiSE).","file_date_updated":"2022-08-22T06:42:42Z","issue":"2","corr_author":"1","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"Z00342","call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"}],"quality_controlled":"1","external_id":{"arxiv":["2101.03928"]},"volume":26,"oa_version":"Published Version","day":"01","ec_funded":1,"abstract":[{"text":"A matching is compatible to two or more labeled point sets of size n with labels {1, . . . , n} if its straight-line drawing on each of these point sets is crossing-free. We study the maximum number of edges in a matching compatible to two or more labeled point sets in general position in the plane. We show that for any two labeled sets of n points in convex position there exists a compatible matching with ⌊√2n + 1 − 1⌋ edges. More generally, for any ℓ labeled point sets we construct compatible matchings of size Ω(n1/ℓ). As a corresponding upper bound, we use probabilistic arguments to show that for any ℓ given sets of n points there exists a labeling of each set such that the largest compatible matching has O(n2/(ℓ+1)) edges. Finally, we show that Θ(log n) copies of any set of n points are necessary and sufficient for the existence of labelings of these point sets such that any compatible matching consists only of a single edge.","lang":"eng"}],"article_type":"original","publication_status":"published","doi":"10.7155/jgaa.00591","article_processing_charge":"No","publication_identifier":{"issn":["1526-1719"]},"publisher":"Brown University","citation":{"ista":"Aichholzer O, Arroyo Guevara AM, Masárová Z, Parada I, Perz D, Pilz A, Tkadlec J, Vogtenhuber B. 2022. On compatible matchings. Journal of Graph Algorithms and Applications. 26(2), 225–240.","mla":"Aichholzer, Oswin, et al. “On Compatible Matchings.” <i>Journal of Graph Algorithms and Applications</i>, vol. 26, no. 2, Brown University, 2022, pp. 225–40, doi:<a href=\"https://doi.org/10.7155/jgaa.00591\">10.7155/jgaa.00591</a>.","ieee":"O. Aichholzer <i>et al.</i>, “On compatible matchings,” <i>Journal of Graph Algorithms and Applications</i>, vol. 26, no. 2. Brown University, pp. 225–240, 2022.","apa":"Aichholzer, O., Arroyo Guevara, A. M., Masárová, Z., Parada, I., Perz, D., Pilz, A., … Vogtenhuber, B. (2022). On compatible matchings. <i>Journal of Graph Algorithms and Applications</i>. Brown University. <a href=\"https://doi.org/10.7155/jgaa.00591\">https://doi.org/10.7155/jgaa.00591</a>","short":"O. Aichholzer, A.M. Arroyo Guevara, Z. Masárová, I. Parada, D. Perz, A. Pilz, J. Tkadlec, B. Vogtenhuber, Journal of Graph Algorithms and Applications 26 (2022) 225–240.","chicago":"Aichholzer, Oswin, Alan M Arroyo Guevara, Zuzana Masárová, Irene Parada, Daniel Perz, Alexander Pilz, Josef Tkadlec, and Birgit Vogtenhuber. “On Compatible Matchings.” <i>Journal of Graph Algorithms and Applications</i>. Brown University, 2022. <a href=\"https://doi.org/10.7155/jgaa.00591\">https://doi.org/10.7155/jgaa.00591</a>.","ama":"Aichholzer O, Arroyo Guevara AM, Masárová Z, et al. On compatible matchings. <i>Journal of Graph Algorithms and Applications</i>. 2022;26(2):225-240. doi:<a href=\"https://doi.org/10.7155/jgaa.00591\">10.7155/jgaa.00591</a>"},"year":"2022","date_published":"2022-06-01T00:00:00Z","title":"On compatible matchings","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"month":"06","department":[{"_id":"UlWa"},{"_id":"HeEd"},{"_id":"KrCh"}],"date_updated":"2026-04-16T09:18:20Z"},{"abstract":[{"lang":"eng","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."}],"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","day":"12","ec_funded":1,"title":"Learning verifiable representations","license":"https://creativecommons.org/licenses/by-nd/4.0/","tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"date_updated":"2026-04-16T09:46:06Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"month":"05","publication_status":"published","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","publication_identifier":{"isbn":["978-3-99078-017-6"]},"article_processing_charge":"No","doi":"10.15479/at:ista:11362","year":"2022","date_published":"2022-05-12T00:00:00Z","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>","short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","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.","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>.","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022."},"page":"124","file":[{"content_type":"application/zip","file_name":"src.zip","date_updated":"2022-05-13T12:49:00Z","file_id":"11378","creator":"mlechner","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","date_created":"2022-05-13T12:33:26Z","file_size":13210143,"relation":"source_file","access_level":"closed"},{"date_updated":"2022-05-17T15:19:39Z","file_name":"thesis_main-a2.pdf","content_type":"application/pdf","file_id":"11382","creator":"mlechner","date_created":"2022-05-16T08:02:28Z","checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","access_level":"open_access","file_size":2732536,"relation":"main_file"}],"ddc":["004"],"has_accepted_license":"1","language":[{"iso":"eng"}],"supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A"}],"date_created":"2022-05-12T07:14:01Z","status":"public","keyword":["neural networks","verification","machine learning"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Mathias","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner"}],"type":"dissertation","file_date_updated":"2022-05-17T15:19:39Z","corr_author":"1","_id":"11362","OA_place":"publisher","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11366"},{"relation":"part_of_dissertation","status":"public","id":"10665"},{"relation":"part_of_dissertation","id":"10667","status":"public"},{"id":"10666","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7808"}]},"oa":1},{"intvolume":"       221","pmid":1,"file":[{"date_updated":"2023-02-21T23:30:39Z","file_name":"2022_JCB_Enshoji.pdf","embargo":"2023-02-20","content_type":"application/pdf","creator":"dernst","file_id":"12321","date_created":"2023-01-20T09:32:53Z","checksum":"f2e581e66b5cdab9df81b56e850b3eaa","access_level":"open_access","relation":"main_file","file_size":7816875}],"ddc":["570"],"has_accepted_license":"1","publication":"Journal of Cell Biology","language":[{"iso":"eng"}],"date_created":"2022-09-11T22:01:54Z","scopus_import":"1","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Enshoji, Mariko","last_name":"Enshoji","first_name":"Mariko"},{"first_name":"Yoshiko","last_name":"Miyano","full_name":"Miyano, Yoshiko"},{"first_name":"Nao","last_name":"Yoshida","full_name":"Yoshida, Nao"},{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"first_name":"Minami","full_name":"Watanabe, Minami","last_name":"Watanabe"},{"first_name":"Mayumi","last_name":"Kunihiro","full_name":"Kunihiro, Mayumi"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353"},{"full_name":"Toshima, Junko Y.","last_name":"Toshima","first_name":"Junko Y."},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"acknowledgement":"This work was supported by JSPS KAKENHI GRANT #18K062291, and the Takeda Science Foundation to J.Y. Toshima, as well as JSPS KAKENHI GRANT #19K065710, the Uehara Memorial Foundation, and Life Science Foundation of JAPAN to J. Toshima.","type":"journal_article","file_date_updated":"2023-02-21T23:30:39Z","issue":"10","_id":"12080","oa":1,"abstract":[{"text":"Endocytosis is a multistep process involving the sequential recruitment and action of numerous proteins. This process can be divided into two phases: an early phase, in which sites of endocytosis are formed, and a late phase in which clathrin-coated vesicles are formed and internalized into the cytosol, but how these phases link to each other remains unclear. In this study, we demonstrate that anchoring the yeast Eps15-like protein Pan1p to the peroxisome triggers most of the events occurring during the late phase at the peroxisome. At this ectopic location, Pan1p recruits most proteins that function in the late phases—including actin nucleation promoting factors—and then initiates actin polymerization. Pan1p also recruited Prk1 kinase and actin depolymerizing factors, thereby triggering disassembly immediately after actin assembly and inducing dissociation of endocytic proteins from the peroxisome. These observations suggest that Pan1p is a key regulator for initiating, processing, and completing the late phase of endocytosis.","lang":"eng"}],"article_type":"original","external_id":{"pmid":["35984332"],"isi":["000932770500001"]},"quality_controlled":"1","day":"19","volume":221,"oa_version":"Published Version","title":"Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway","article_number":"e202112138","isi":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"date_updated":"2023-08-03T13:49:07Z","month":"08","department":[{"_id":"DaSi"}],"publication_status":"published","article_processing_charge":"No","publisher":"Rockefeller University Press","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"doi":"10.1083/jcb.202112138","year":"2022","date_published":"2022-08-19T00:00:00Z","citation":{"ama":"Enshoji M, Miyano Y, Yoshida N, et al. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. <i>Journal of Cell Biology</i>. 2022;221(10). doi:<a href=\"https://doi.org/10.1083/jcb.202112138\">10.1083/jcb.202112138</a>","chicago":"Enshoji, Mariko, Yoshiko Miyano, Nao Yoshida, Makoto Nagano, Minami Watanabe, Mayumi Kunihiro, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202112138\">https://doi.org/10.1083/jcb.202112138</a>.","short":"M. Enshoji, Y. Miyano, N. Yoshida, M. Nagano, M. Watanabe, M. Kunihiro, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Biology 221 (2022).","apa":"Enshoji, M., Miyano, Y., Yoshida, N., Nagano, M., Watanabe, M., Kunihiro, M., … Toshima, J. (2022). Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202112138\">https://doi.org/10.1083/jcb.202112138</a>","ieee":"M. Enshoji <i>et al.</i>, “Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway,” <i>Journal of Cell Biology</i>, vol. 221, no. 10. Rockefeller University Press, 2022.","mla":"Enshoji, Mariko, et al. “Eps15/Pan1p Is a Master Regulator of the Late Stages of the Endocytic Pathway.” <i>Journal of Cell Biology</i>, vol. 221, no. 10, e202112138, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202112138\">10.1083/jcb.202112138</a>.","ista":"Enshoji M, Miyano Y, Yoshida N, Nagano M, Watanabe M, Kunihiro M, Siekhaus DE, Toshima JY, Toshima J. 2022. Eps15/Pan1p is a master regulator of the late stages of the endocytic pathway. Journal of Cell Biology. 221(10), e202112138."}},{"abstract":[{"lang":"eng","text":"Understanding the properties of neural networks trained via stochastic gradient descent (SGD) is at the heart of the theory of deep learning. In this work, we take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD for a univariate regularized regression problem. Our main result is that SGD with vanishingly small noise injected in the gradients is biased towards a simple solution: at convergence, the ReLU network implements a piecewise linear map of the inputs, and the number of “knot” points -- i.e., points where the tangent of the ReLU network estimator changes -- between two consecutive training inputs is at most three. In particular, as the number of neurons of the network grows, the SGD dynamics is captured by the solution of a gradient flow and, at convergence, the distribution of the weights approaches the unique minimizer of a related free energy, which has a Gibbs form. Our key technical contribution consists in the analysis of the estimator resulting from this minimizer: we show that its second derivative vanishes everywhere, except at some specific locations which represent the “knot” points. We also provide empirical evidence that knots at locations distinct from the data points might occur, as predicted by our theory."}],"article_type":"original","day":"01","volume":23,"oa_version":"Published Version","quality_controlled":"1","external_id":{"arxiv":["2111.02278"]},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2026-04-22T22:30:08Z","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"month":"04","title":"Mean-field analysis of piecewise linear solutions for wide ReLU networks","date_published":"2022-04-01T00:00:00Z","year":"2022","citation":{"chicago":"Shevchenko, Alexander, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2022.","ama":"Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. 2022;23(130):1-55.","apa":"Shevchenko, A., Kungurtsev, V., &#38; Mondelli, M. (2022). Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","short":"A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 1–55.","mla":"Shevchenko, Alexander, et al. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130, Journal of Machine Learning Research, 2022, pp. 1–55.","ieee":"A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise linear solutions for wide ReLU networks,” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022.","ista":"Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. 23(130), 1–55."},"publication_status":"published","publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"publisher":"Journal of Machine Learning Research","article_processing_charge":"No","file":[{"checksum":"d4ff5d1affb34848b5c5e4002483fc62","date_created":"2022-05-30T08:22:55Z","relation":"main_file","file_size":1521701,"success":1,"access_level":"open_access","content_type":"application/pdf","date_updated":"2022-05-30T08:22:55Z","file_name":"21-1365.pdf","file_id":"11422","creator":"cchlebak"}],"ddc":["000"],"intvolume":"        23","page":"1-55","scopus_import":"1","status":"public","date_created":"2022-05-29T22:01:54Z","has_accepted_license":"1","publication":"Journal of Machine Learning Research","language":[{"iso":"eng"}],"file_date_updated":"2022-05-30T08:22:55Z","corr_author":"1","issue":"130","acknowledgement":"We would like to thank Mert Pilanci for several exploratory discussions in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765 Research Center for Informatics.\r\n","author":[{"last_name":"Shevchenko","full_name":"Shevchenko, Aleksandr","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr"},{"first_name":"Vyacheslav","last_name":"Kungurtsev","full_name":"Kungurtsev, Vyacheslav"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","related_material":{"record":[{"id":"17465","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://www.jmlr.org/papers/v23/21-1365.html","relation":"other"}]},"oa":1,"_id":"11420","arxiv":1},{"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:11653","_id":"11653","related_material":{"record":[{"status":"public","id":"12248","relation":"used_in_publication"}]},"year":"2022","oa":1,"date_published":"2022-08-05T00:00:00Z","citation":{"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>.","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.","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>.","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>","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>","short":"M.N. Elkrewi, (2022)."},"author":[{"first_name":"Marwan N","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","corr_author":"1","date_updated":"2025-04-15T08:34:17Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"contributor":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","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"},{"first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"first_name":"Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"first_name":"Luca","last_name":"Sax"},{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans"},{"last_name":"Hontoria ","first_name":"Francisco"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"month":"08","file_date_updated":"2022-08-08T22:30:04Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"has_accepted_license":"1","status":"public","date_created":"2022-07-26T11:01:47Z","oa_version":"Published Version","day":"05","ddc":["570"],"file":[{"file_name":"Data.zip","date_updated":"2022-08-08T22:30:04Z","embargo":"2022-08-07","content_type":"application/x-zip-compressed","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","file_id":"11655","creator":"melkrewi","title":"Supplementary Datasets","date_created":"2022-07-26T12:37:52Z","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","access_level":"open_access","relation":"main_file","file_size":2209382998}],"abstract":[{"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.","lang":"eng"}]},{"external_id":{"isi":["000712198000001"]},"quality_controlled":"1","project":[{"grant_number":"Z00342","name":"Mathematics, Computer Science","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","volume":13,"day":"01","article_type":"original","abstract":[{"lang":"eng","text":"It is practical to collect a huge amount of movement data and environmental context information along with the health signals of individuals because there is the emergence of new generations of positioning and tracking technologies and rapid advancements of health sensors. The study of the relations between these datasets and their sequence similarity analysis is of interest to many applications such as health monitoring and recommender systems. However, entering all movement parameters and health signals can lead to the complexity of the problem and an increase in its computational load. In this situation, dimension reduction techniques can be used to avoid consideration of simultaneous dependent parameters in the process of similarity measurement of the trajectories. The present study provides a framework, named CaDRAW, to use spatial–temporal data and movement parameters along with independent context information in the process of measuring the similarity of trajectories. In this regard, the omission of dependent movement characteristic signals is conducted by using an unsupervised feature selection dimension reduction technique. To evaluate the effectiveness of the proposed framework, it was applied to a real contextualized movement and related health signal datasets of individuals. The results indicated the capability of the proposed framework in measuring the similarity and in decreasing the characteristic signals in such a way that the similarity results -before and after reduction of dependent characteristic signals- have small differences. The mean differences between the obtained results before and after reducing the dimension were 0.029 and 0.023 for the round path, respectively."}],"publication_identifier":{"eissn":["1868-5145"],"issn":["1868-5137"]},"publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1007/s12652-021-03569-z","publication_status":"published","year":"2022","date_published":"2022-05-01T00:00:00Z","citation":{"ieee":"S. Goudarzi, M. Sharif, and F. Karimipour, “A context-aware dimension reduction framework for trajectory and health signal analyses,” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13. Springer Nature, pp. 2621–2635, 2022.","mla":"Goudarzi, Samira, et al. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>, vol. 13, Springer Nature, 2022, pp. 2621–2635, doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>.","ista":"Goudarzi S, Sharif M, Karimipour F. 2022. A context-aware dimension reduction framework for trajectory and health signal analyses. Journal of Ambient Intelligence and Humanized Computing. 13, 2621–2635.","ama":"Goudarzi S, Sharif M, Karimipour F. A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. 2022;13:2621–2635. doi:<a href=\"https://doi.org/10.1007/s12652-021-03569-z\">10.1007/s12652-021-03569-z</a>","chicago":"Goudarzi, Samira, Mohammad Sharif, and Farid Karimipour. “A Context-Aware Dimension Reduction Framework for Trajectory and Health Signal Analyses.” <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>.","short":"S. Goudarzi, M. Sharif, F. Karimipour, Journal of Ambient Intelligence and Humanized Computing 13 (2022) 2621–2635.","apa":"Goudarzi, S., Sharif, M., &#38; Karimipour, F. (2022). A context-aware dimension reduction framework for trajectory and health signal analyses. <i>Journal of Ambient Intelligence and Humanized Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12652-021-03569-z\">https://doi.org/10.1007/s12652-021-03569-z</a>"},"isi":1,"title":"A context-aware dimension reduction framework for trajectory and health signal analyses","date_updated":"2025-04-15T07:16:55Z","month":"05","department":[{"_id":"HeEd"}],"publication":"Journal of Ambient Intelligence and Humanized Computing","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","status":"public","keyword":["general computer science"],"date_created":"2021-11-02T09:28:55Z","intvolume":"        13","page":"2621–2635","ddc":["000"],"file":[{"file_name":"A Context‑aware Dimension Reduction Framework - Journal of Ambient Intelligence 2021 (Preprint version).pdf","date_updated":"2022-12-20T23:30:08Z","content_type":"application/pdf","embargo":"2022-11-12","creator":"fkarimip","file_id":"10279","date_created":"2021-11-12T19:38:05Z","checksum":"0a8961416a9bb2be5a1cebda65468bcf","access_level":"open_access","file_size":1634958,"relation":"main_file"}],"_id":"10208","oa":1,"acknowledgement":"The third author acknowledges the funding received from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. 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Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” <i>Applicable Analysis</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>.","short":"Y. Shehu, O.S. Iyiola, Applicable Analysis 101 (2022) 192–216.","apa":"Shehu, Y., &#38; Iyiola, O. S. (2022). Weak convergence for variational inequalities with inertial-type method. <i>Applicable Analysis</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>"},"publication_identifier":{"eissn":["1563-504X"],"issn":["0003-6811"]},"article_processing_charge":"No","publisher":"Taylor & Francis","doi":"10.1080/00036811.2020.1736287","publication_status":"published","date_updated":"2024-11-04T13:52:44Z","month":"01","department":[{"_id":"VlKo"}],"isi":1,"title":"Weak convergence for variational inequalities with inertial-type method","ec_funded":1,"oa_version":"Submitted Version","volume":101,"day":"01","quality_controlled":"1","external_id":{"isi":["000518364100001"],"arxiv":["2101.08057"]},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"article_type":"original","abstract":[{"text":"Weak convergence of inertial iterative method for solving variational inequalities is the focus of this paper. The cost function is assumed to be non-Lipschitz and monotone. We propose a projection-type method with inertial terms and give weak convergence analysis under appropriate conditions. Some test results are performed and compared with relevant methods in the literature to show the efficiency and advantages given by our proposed methods.","lang":"eng"}]},{"ddc":["530"],"file":[{"relation":"main_file","file_size":4231591,"success":1,"access_level":"open_access","checksum":"a7706b28d24a0e32a55ea04b82a2df43","date_created":"2022-06-30T07:14:48Z","creator":"dernst","file_id":"11472","content_type":"application/pdf","date_updated":"2022-06-30T07:14:48Z","file_name":"2022_PRXQuantum_Sack.pdf"}],"intvolume":"         3","scopus_import":"1","keyword":["General Medicine"],"date_created":"2022-06-29T20:21:32Z","status":"public","publication":"PRX Quantum","language":[{"iso":"eng"}],"has_accepted_license":"1","corr_author":"1","issue":"2","file_date_updated":"2022-06-30T07:14:48Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","full_name":"Sack, Stefan","last_name":"Sack","first_name":"Stefan","orcid":"0000-0001-5400-8508"},{"last_name":"Medina Ramos","id":"CE680B90-D85A-11E9-B684-C920E6697425","full_name":"Medina Ramos, Raimel A","orcid":"0000-0002-5383-2869","first_name":"Raimel A"},{"last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios","first_name":"Alexios","orcid":"0000-0002-8443-1064"},{"first_name":"Richard","full_name":"Kueng, Richard","last_name":"Kueng"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S., R.A.M., A.A.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","id":"17208","status":"public"},{"relation":"dissertation_contains","id":"14622","status":"public"}]},"oa":1,"arxiv":1,"_id":"11471","article_type":"original","abstract":[{"text":"Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. ","lang":"eng"}],"ec_funded":1,"day":"29","volume":3,"oa_version":"Published Version","quality_controlled":"1","external_id":{"isi":["000822564300001"],"arxiv":["2201.08194"]},"project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"date_updated":"2026-04-22T22:30:25Z","department":[{"_id":"MaSe"}],"month":"06","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"isi":1,"article_number":"020365","title":"Avoiding barren plateaus using classical shadows","year":"2022","date_published":"2022-06-29T00:00:00Z","citation":{"apa":"Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., &#38; Serbyn, M. (2022). Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>","short":"S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022).","chicago":"Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng, and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>.","ama":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>","ista":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 020365.","mla":"Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>.","ieee":"S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding barren plateaus using classical shadows,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022."},"publication_identifier":{"issn":["2691-3399"]},"article_processing_charge":"No","publisher":"American Physical Society","doi":"10.1103/prxquantum.3.020365","publication_status":"published"},{"issue":"8","corr_author":"1","file_date_updated":"2023-01-30T10:39:34Z","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","last_name":"Stopp"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"oa":1,"related_material":{"record":[{"id":"14697","status":"public","relation":"dissertation_contains"}]},"_id":"12272","ddc":["570"],"file":[{"date_updated":"2023-01-30T10:39:34Z","file_name":"2022_JourCellBiology_Stopp.pdf","content_type":"application/pdf","file_id":"12451","creator":"dernst","date_created":"2023-01-30T10:39:34Z","checksum":"6b1620743669679b48b9389bb40f5a11","success":1,"access_level":"open_access","relation":"main_file","file_size":969969}],"pmid":1,"intvolume":"       221","scopus_import":"1","date_created":"2023-01-16T10:01:08Z","keyword":["Cell Biology"],"status":"public","language":[{"iso":"eng"}],"publication":"Journal of Cell Biology","has_accepted_license":"1","month":"07","department":[{"_id":"MiSi"}],"date_updated":"2026-04-22T22:30:27Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"isi":1,"article_number":"e202206127","title":"Plan your trip before you leave: The neutrophils’ search-and-run journey","citation":{"mla":"Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>, vol. 221, no. 8, e202206127, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>.","ieee":"J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’ search-and-run journey,” <i>Journal of Cell Biology</i>, vol. 221, no. 8. Rockefeller University Press, 2022.","ista":"Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 221(8), e202206127.","chicago":"Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>.","ama":"Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. 2022;221(8). doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>","apa":"Stopp, J. A., &#38; Sixt, M. K. (2022). Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>","short":"J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022)."},"year":"2022","date_published":"2022-07-20T00:00:00Z","doi":"10.1083/jcb.202206127","publisher":"Rockefeller University Press","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"article_processing_charge":"No","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant."}],"oa_version":"Published Version","volume":221,"day":"20","external_id":{"isi":["000874717200001"],"pmid":["35856919"]},"quality_controlled":"1"},{"title":"In vitro reconstitution of Escherichia coli divisome activation","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"month":"04","contributor":[{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","first_name":"Martin","orcid":"0000-0001-7309-9724"},{"last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Christoph M"},{"contributor_type":"researcher","first_name":"Paulo","last_name":"Caldas"},{"first_name":"David","contributor_type":"researcher","id":"B9577E20-AA38-11E9-AC9A-0930E6697425","last_name":"Michalik"},{"last_name":"Baranova","first_name":"Natalia","contributor_type":"researcher"}],"date_updated":"2026-04-22T22:30:28Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.15479/AT:ISTA:10934","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"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>.","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>","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>","short":"P. Radler, (2022).","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>.","ieee":"P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022.","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>."},"date_published":"2022-04-05T00:00:00Z","year":"2022","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":[{"grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"}],"ec_funded":1,"day":"05","oa_version":"Submitted Version","type":"research_data","author":[{"full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp","orcid":" 0000-0001-9198-2182 "}],"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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","file_date_updated":"2022-04-22T10:15:19Z","_id":"10934","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11373"},{"status":"public","id":"14280","relation":"used_in_publication"}],"link":[{"relation":"software","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. 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activation","date_published":"2022-05-12T00:00:00Z","year":"2022","citation":{"short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>","chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>.","ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>."},"publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"No","publisher":"Springer Nature","doi":"10.1038/s41467-022-30301-y","publication_status":"published","article_type":"original","abstract":[{"text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ.","lang":"eng"}],"ec_funded":1,"oa_version":"Published Version","day":"12","volume":13,"external_id":{"isi":["000795171100037"]},"quality_controlled":"1","project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"grant_number":"P34607","name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"}],"corr_author":"1","file_date_updated":"2022-05-13T09:10:51Z","author":[{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","last_name":"Radler","orcid":"0000-0001-9198-2182 ","first_name":"Philipp"},{"full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","orcid":"0000-0002-3086-9124","first_name":"Natalia S."},{"last_name":"Dos Santos Caldas","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","full_name":"Dos Santos Caldas, Paulo R","first_name":"Paulo R","orcid":"0000-0001-6730-4461"},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"first_name":"Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Pelegrin, Maria D","last_name":"Lopez Pelegrin"},{"last_name":"Michalik","full_name":"Michalik, David","id":"B9577E20-AA38-11E9-AC9A-0930E6697425","first_name":"David"},{"orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"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) and 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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","oa":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"10934"},{"relation":"dissertation_contains","status":"public","id":"14280"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-34485-1"}]},"_id":"11373","ddc":["570"],"file":[{"file_size":6945191,"relation":"main_file","success":1,"access_level":"open_access","checksum":"5af863ee1b95a0710f6ee864d68dc7a6","date_created":"2022-05-13T09:10:51Z","file_id":"11374","creator":"dernst","content_type":"application/pdf","date_updated":"2022-05-13T09:10:51Z","file_name":"2022_NatureCommunications_Radler.pdf"}],"intvolume":"        13","date_created":"2022-05-13T09:06:28Z","scopus_import":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"status":"public","publication":"Nature Communications","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"has_accepted_license":"1"},{"language":[{"iso":"eng"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"date_created":"2022-04-20T09:47:12Z","status":"public","supervisor":[{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"}],"page":"132","ddc":["570"],"file":[{"checksum":"1616a8bf6f13a57c892dac873dcd0936","date_created":"2022-04-20T14:21:56Z","relation":"main_file","file_size":21273537,"access_level":"open_access","embargo":"2023-04-19","content_type":"application/pdf","date_updated":"2023-04-20T22:30:03Z","file_name":"Olena_KIM_thesis_final.pdf","creator":"okim","file_id":"11220"},{"file_id":"11221","creator":"okim","embargo_to":"open_access","content_type":"application/x-zip-compressed","date_updated":"2023-04-20T22:30:03Z","file_name":"KIM_thesis_final.zip","file_size":59248569,"relation":"source_file","access_level":"closed","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","date_created":"2022-04-20T14:22:56Z"}],"_id":"11196","OA_place":"publisher","oa":1,"related_material":{"record":[{"status":"public","id":"7473","relation":"part_of_dissertation"},{"status":"public","id":"11222","relation":"part_of_dissertation"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena","last_name":"Kim","orcid":"0000-0003-2344-1039","first_name":"Olena"}],"type":"dissertation","corr_author":"1","file_date_updated":"2023-04-20T22:30:03Z","alternative_title":["ISTA Thesis"],"project":[{"grant_number":"708497","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"692692"},{"grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit","call_identifier":"FWF","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"}],"ec_funded":1,"oa_version":"Published Version","day":"20","abstract":[{"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","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","doi":"10.15479/at:ista:11196","degree_awarded":"PhD","publication_status":"published","year":"2022","date_published":"2022-04-20T00:00:00Z","citation":{"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>.","ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","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>","short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022.","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>"},"title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","date_updated":"2026-04-07T14:22:20Z","month":"04","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"}},{"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"}],"alternative_title":["ISTA Thesis"],"project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ec_funded":1,"oa_version":"Published Version","day":"07","title":"Pathogen-mediated sexual selection and immunization in ant colonies","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"month":"02","date_updated":"2026-04-07T14:30:18Z","doi":"10.15479/AT:ISTA:10727","publisher":"Institute of Science and Technology Austria","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","degree_awarded":"PhD","publication_status":"published","citation":{"ista":"Metzler S. 2022. Pathogen-mediated sexual selection and immunization in ant colonies. Institute of Science and Technology Austria.","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>.","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>","short":"S. Metzler, Pathogen-Mediated Sexual Selection and Immunization in Ant Colonies, Institute of Science and Technology Austria, 2022.","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>.","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>"},"year":"2022","date_published":"2022-02-07T00:00:00Z","ddc":["570"],"file":[{"date_created":"2022-02-04T15:36:12Z","checksum":"47ba18bb270dd6cc266e0a3f7c69d0e4","access_level":"closed","file_size":6757886,"relation":"source_file","date_updated":"2023-02-03T23:30:03Z","file_name":"Thesis_Sina_Metzler.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"10728","embargo_to":"open_access","creator":"smetzler"},{"access_level":"open_access","file_size":6314921,"relation":"main_file","date_created":"2022-02-04T15:36:43Z","checksum":"f3ec07d5d6b20ae6e46bfeedebce9027","file_id":"10730","creator":"smetzler","file_name":"Thesis_Sina_Metzler_A2.pdf","date_updated":"2023-02-03T23:30:03Z","content_type":"application/pdf","embargo":"2023-02-02"},{"embargo":"2023-02-02","content_type":"application/pdf","file_name":"Thesis_Sina_Metzler_print.pdf","date_updated":"2023-02-04T23:30:03Z","creator":"smetzler","file_id":"10742","checksum":"dedd14b7be7a75d63018dbfc68dd8113","date_created":"2022-02-07T10:35:02Z","relation":"main_file","file_size":6882557,"access_level":"open_access"}],"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"has_accepted_license":"1","date_created":"2022-02-04T15:45:12Z","status":"public","supervisor":[{"last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Metzler, Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","orcid":"0000-0002-9547-2494","first_name":"Sina"}],"corr_author":"1","file_date_updated":"2023-02-04T23:30:03Z","OA_place":"publisher","_id":"10727","oa":1},{"oa":1,"OA_place":"publisher","_id":"11879","file_date_updated":"2023-09-09T22:30:03Z","corr_author":"1","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","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).","author":[{"first_name":"Christina","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87","last_name":"Artner"}],"supervisor":[{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva"}],"keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"date_created":"2022-08-17T07:58:53Z","status":"public","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"language":[{"iso":"eng"}],"file":[{"relation":"main_file","file_size":11113608,"access_level":"open_access","checksum":"a2c2fdc28002538840490bfa6a08b2cb","date_created":"2022-08-17T12:08:49Z","creator":"cartner","file_id":"11907","embargo":"2023-09-08","content_type":"application/pdf","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","date_updated":"2023-09-09T22:30:03Z"},{"file_size":19097730,"relation":"source_file","access_level":"closed","checksum":"66b461c074b815fbe63481b3f46a9f43","date_created":"2022-08-17T12:08:59Z","creator":"cartner","embargo_to":"open_access","file_id":"11908","content_type":"application/octet-stream","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","date_updated":"2023-09-09T22:30:03Z"}],"ddc":["580"],"page":"128","citation":{"ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","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>.","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>","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>","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>."},"year":"2022","date_published":"2022-08-17T00:00:00Z","degree_awarded":"PhD","publication_status":"published","doi":"10.15479/at:ista:11879","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","publication_identifier":{"isbn":["978-3-99078-022-0"],"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"EvBe"}],"month":"08","date_updated":"2026-04-07T14:30:39Z","title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","day":"17","oa_version":"Published Version","project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"alternative_title":["ISTA Thesis"],"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."}]},{"doi":"10.1038/s41586-022-05199-7","article_processing_charge":"No","publisher":"Springer Nature","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication_status":"published","citation":{"short":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, L.A. Sazanov, Nature 609 (2022) 808–814.","apa":"Kravchuk, V., Petrova, O., Kampjut, D., Wojciechowska-Bason, A., Breese, Z., &#38; Sazanov, L. A. (2022). A universal coupling mechanism of respiratory complex I. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>","ama":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. A universal coupling mechanism of respiratory complex I. <i>Nature</i>. 2022;609(7928):808-814. doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>","chicago":"Kravchuk, Vladyslav, Olga Petrova, Domen Kampjut, Anna Wojciechowska-Bason, Zara Breese, and Leonid A Sazanov. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05199-7\">https://doi.org/10.1038/s41586-022-05199-7</a>.","ista":"Kravchuk V, Petrova O, Kampjut D, Wojciechowska-Bason A, Breese Z, Sazanov LA. 2022. A universal coupling mechanism of respiratory complex I. Nature. 609(7928), 808–814.","ieee":"V. Kravchuk, O. Petrova, D. Kampjut, A. Wojciechowska-Bason, Z. Breese, and L. A. Sazanov, “A universal coupling mechanism of respiratory complex I,” <i>Nature</i>, vol. 609, no. 7928. Springer Nature, pp. 808–814, 2022.","mla":"Kravchuk, Vladyslav, et al. “A Universal Coupling Mechanism of Respiratory Complex I.” <i>Nature</i>, vol. 609, no. 7928, Springer Nature, 2022, pp. 808–14, doi:<a href=\"https://doi.org/10.1038/s41586-022-05199-7\">10.1038/s41586-022-05199-7</a>."},"year":"2022","date_published":"2022-09-22T00:00:00Z","isi":1,"title":"A universal coupling mechanism of respiratory complex I","department":[{"_id":"LeSa"}],"month":"09","date_updated":"2026-04-22T22:30:31Z","project":[{"grant_number":"25541","name":"Structural characterization of E. coli complex I: an important mechanistic model","_id":"238A0A5A-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"101020697","call_identifier":"H2020","name":"Structure and mechanism of respiratory chain molecular machines","_id":"627abdeb-2b32-11ec-9570-ec31a97243d3"}],"quality_controlled":"1","external_id":{"isi":["000854788200001"],"pmid":["36104567"]},"ec_funded":1,"day":"22","volume":609,"oa_version":"Submitted Version","article_type":"original","abstract":[{"lang":"eng","text":"Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria1. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane2, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues3, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a ‘domino effect’ series of proton transfers and electrostatic interactions: the forward wave (‘dominoes stacking’) primes the pump, and the reverse wave (‘dominoes falling’) results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes."}],"_id":"12138","oa":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-022-05457-8"},{"relation":"press_release","url":"https://ista.ac.at/en/news/proton-dominos-kick-off-life/","description":"News on ISTA website"}],"record":[{"relation":"dissertation_contains","status":"public","id":"12781"}]},"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster. We thank V.-V. Hodirnau from IST Austria EMF, M. Babiak from CEITEC for assistance with collecting cryo-EM data and A. Charnagalov for the assistance with protein purification. V.K. was a recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. V.K. and O.P. are funded by the ERC Advanced Grant 101020697 RESPICHAIN to L.S. This work was also supported by the Medical Research Council (UK).","author":[{"first_name":"Vladyslav","orcid":"0000-0001-9523-9089","last_name":"Kravchuk","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","full_name":"Kravchuk, Vladyslav"},{"first_name":"Olga","last_name":"Petrova","id":"5D8C9660-5D49-11EA-8188-567B3DDC885E","full_name":"Petrova, Olga"},{"id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen","last_name":"Kampjut","first_name":"Domen","orcid":"0000-0002-6018-3422"},{"last_name":"Wojciechowska-Bason","full_name":"Wojciechowska-Bason, Anna","first_name":"Anna"},{"full_name":"Breese, Zara","last_name":"Breese","first_name":"Zara"},{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A"}],"issue":"7928","corr_author":"1","file_date_updated":"2023-05-30T17:07:05Z","language":[{"iso":"eng"}],"publication":"Nature","has_accepted_license":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"status":"public","date_created":"2023-01-12T12:04:33Z","keyword":["Multidisciplinary"],"scopus_import":"1","intvolume":"       609","page":"808-814","pmid":1,"ddc":["572"],"file":[{"file_size":1425655,"relation":"main_file","success":1,"access_level":"open_access","checksum":"d42a93e24f59e883ef0b5429832391d0","date_created":"2023-05-30T17:05:31Z","file_id":"13104","creator":"lsazanov","content_type":"application/pdf","date_updated":"2023-05-30T17:05:31Z","file_name":"EcCxI_manuscript_rev3_noSI_updated_withFigs_opt.pdf"},{"success":1,"access_level":"open_access","relation":"main_file","file_size":9842513,"date_created":"2023-05-30T17:07:05Z","checksum":"5422bc0a73b3daadafa262c7ea6deae3","file_id":"13105","creator":"lsazanov","date_updated":"2023-05-30T17:07:05Z","file_name":"EcCxI_manuscript_rev3_SI_All_opt_upd.pdf","content_type":"application/pdf"}]},{"oa_version":"Published Version","day":"05","volume":39,"ec_funded":1,"project":[{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"call_identifier":"FWF","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy","_id":"2690FEAC-B435-11E9-9278-68D0E5697425","grant_number":"I04205"}],"external_id":{"pmid":["35385734"],"isi":["000785983900003"]},"quality_controlled":"1","abstract":[{"text":"Mutations in the chromodomain helicase DNA-binding 8 (CHD8) gene are a frequent cause of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly, implicating cortical abnormalities, how CHD8 haploinsufficiency affects neurodevelopmental is unclear. Here, employing human cerebral organoids, we find that CHD8 haploinsufficiency disrupted neurodevelopmental trajectories with an accelerated and delayed generation of, respectively, inhibitory and excitatory neurons that yields, at days 60 and 120, symmetrically opposite expansions in their proportions. This imbalance is consistent with an enlargement of cerebral organoids as an in vitro correlate of patients’ macrocephaly. Through an isogenic design of patient-specific mutations and mosaic organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Our results define cell-type-specific CHD8-dependent molecular defects related to an abnormal program of proliferation and alternative splicing. By identifying cell-type-specific effects of CHD8 mutations, our study uncovers reproducible developmental alterations that may be employed for neurodevelopmental disease modeling.","lang":"eng"}],"article_type":"original","citation":{"ama":"Villa CE, Cheroni C, Dotter C, et al. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. 2022;39(1). doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>","chicago":"Villa, Carlo Emanuele, Cristina Cheroni, Christoph Dotter, Alejandro López-Tóbon, Bárbara Oliveira, Roberto Sacco, Aysan Çerağ Yahya, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>.","short":"C.E. Villa, C. Cheroni, C. Dotter, A. López-Tóbon, B. Oliveira, R. Sacco, A.Ç. Yahya, J. Morandell, M. Gabriele, M. Tavakoli, J. Lyudchik, C.M. Sommer, M. Gabitto, J.G. Danzl, G. Testa, G. Novarino, Cell Reports 39 (2022).","apa":"Villa, C. E., Cheroni, C., Dotter, C., López-Tóbon, A., Oliveira, B., Sacco, R., … Novarino, G. (2022). CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">https://doi.org/10.1016/j.celrep.2022.110615</a>","ieee":"C. E. Villa <i>et al.</i>, “CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories,” <i>Cell Reports</i>, vol. 39, no. 1. Elsevier, 2022.","mla":"Villa, Carlo Emanuele, et al. “CHD8 Haploinsufficiency Links Autism to Transient Alterations in Excitatory and Inhibitory Trajectories.” <i>Cell Reports</i>, vol. 39, no. 1, 110615, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.celrep.2022.110615\">10.1016/j.celrep.2022.110615</a>.","ista":"Villa CE, Cheroni C, Dotter C, López-Tóbon A, Oliveira B, Sacco R, Yahya AÇ, Morandell J, Gabriele M, Tavakoli M, Lyudchik J, Sommer CM, Gabitto M, Danzl JG, Testa G, Novarino G. 2022. CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories. Cell Reports. 39(1), 110615."},"year":"2022","date_published":"2022-04-05T00:00:00Z","publication_status":"published","doi":"10.1016/j.celrep.2022.110615","publication_identifier":{"issn":["2211-1247"]},"publisher":"Elsevier","article_processing_charge":"Yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"JoDa"},{"_id":"GaNo"}],"month":"04","date_updated":"2026-04-22T22:30:32Z","title":"CHD8 haploinsufficiency links autism to transient alterations in excitatory and inhibitory trajectories","isi":1,"article_number":"110615","status":"public","scopus_import":"1","keyword":["General Biochemistry","Genetics and Molecular Biology"],"date_created":"2022-04-15T09:03:10Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Cell Reports","file":[{"checksum":"b4e8d68f0268dec499af333e6fd5d8e1","date_created":"2022-04-15T09:06:25Z","relation":"main_file","file_size":"7808644","access_level":"open_access","success":1,"content_type":"application/pdf","date_updated":"2022-04-15T09:06:25Z","file_name":"2022_CellReports_Villa.pdf","file_id":"11164","creator":"dernst"}],"ddc":["570"],"intvolume":"        39","pmid":1,"oa":1,"related_material":{"record":[{"id":"18681","status":"public","relation":"dissertation_contains"},{"status":"public","id":"18674","relation":"dissertation_contains"},{"status":"public","id":"12364","relation":"dissertation_contains"}]},"_id":"11160","file_date_updated":"2022-04-15T09:06:25Z","issue":"1","corr_author":"1","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Villa","full_name":"Villa, Carlo Emanuele","first_name":"Carlo Emanuele"},{"first_name":"Cristina","full_name":"Cheroni, Cristina","last_name":"Cheroni"},{"orcid":"0000-0002-9033-9096","first_name":"Christoph","full_name":"Dotter, Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter"},{"full_name":"López-Tóbon, Alejandro","last_name":"López-Tóbon","first_name":"Alejandro"},{"first_name":"Bárbara","full_name":"Oliveira, Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","last_name":"Oliveira"},{"last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","full_name":"Sacco, Roberto","first_name":"Roberto"},{"first_name":"Aysan Çerağ","last_name":"Yahya","full_name":"Yahya, Aysan Çerağ","id":"365A65F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","full_name":"Morandell, Jasmin","last_name":"Morandell"},{"first_name":"Michele","full_name":"Gabriele, Michele","last_name":"Gabriele"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","last_name":"Tavakoli","orcid":"0000-0002-7667-6854","first_name":"Mojtaba"},{"first_name":"Julia","last_name":"Lyudchik","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M"},{"last_name":"Gabitto","full_name":"Gabitto, Mariano","first_name":"Mariano"},{"last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","first_name":"Johann G"},{"full_name":"Testa, Giuseppe","last_name":"Testa","first_name":"Giuseppe"},{"first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We thank Farnaz Freeman for technical assistance. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF) and the Life Science Facility (LSF). This work supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 to G.N. (REVERSEAUTISM) and grant 825759 to G.T. (ENDpoiNTs); the Fondazione Cariplo 2017-0886 to A.L.T.; E-Rare-3 JTC 2018 IMPACT to M. Gabriele; and the Austrian Science Fund FWF I 4205-B to G.N. Graphical abstract and figures were created using BioRender.com."},{"file_date_updated":"2023-09-20T22:30:03Z","corr_author":"1","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Dotter","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","first_name":"Christoph","orcid":"0000-0002-9033-9096"}],"oa":1,"related_material":{"record":[{"id":"11160","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"3","relation":"part_of_dissertation"}]},"OA_place":"publisher","_id":"12364","file":[{"embargo":"2023-09-19","content_type":"application/pdf","file_name":"220923_Thesis_CDotter_Final.pdf","date_updated":"2023-09-20T22:30:03Z","creator":"cchlebak","file_id":"12365","checksum":"896f4cac9adb6d3f26a6605772f4e1a3","date_created":"2023-01-24T13:15:45Z","relation":"main_file","file_size":20457465,"access_level":"open_access"},{"checksum":"ad01bb20da163be6893b7af832e58419","date_created":"2023-02-02T09:15:35Z","file_size":22433512,"relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"latex_source_CDotter_Thesis_2022.zip","date_updated":"2023-09-20T22:30:03Z","creator":"cchlebak","embargo_to":"open_access","file_id":"12482"}],"ddc":["570"],"page":"152","supervisor":[{"last_name":"Novarino","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178"}],"status":"public","date_created":"2023-01-24T13:09:57Z","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"GaNo"}],"month":"09","date_updated":"2026-04-07T14:30:57Z","title":"Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder","citation":{"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>","short":"C. Dotter, Transcriptional Consequences of Mutations in Genes Associated with Autism Spectrum Disorder, Institute of Science and Technology Austria, 2022.","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>.","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>","ista":"Dotter C. 2022. Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder. Institute of Science and Technology Austria.","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>.","ieee":"C. Dotter, “Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder,” Institute of Science and Technology Austria, 2022."},"year":"2022","date_published":"2022-09-19T00:00:00Z","degree_awarded":"PhD","publication_status":"published","doi":"10.15479/at:ista:12094","publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","day":"19","ec_funded":1,"project":[{"grant_number":"401299","name":"Probing development and reversibility of autism spectrum disorders","_id":"254BA948-B435-11E9-9278-68D0E5697425"},{"grant_number":"707964","_id":"9B91375C-BA93-11EA-9121-9846C619BF3A","name":"Critical windows and reversibility of ASD associated with mutations in chromatin remodelers"},{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508"},{"grant_number":"I04205","call_identifier":"FWF","_id":"2690FEAC-B435-11E9-9278-68D0E5697425","name":"Identification of converging Molecular Pathways Across Chromatinopathies as Targets for Therapy"}],"alternative_title":["ISTA Thesis"]},{"alternative_title":["ISTA Thesis"],"oa_version":"Published Version","day":"16","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"}],"doi":"10.15479/at:ista:11393","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","citation":{"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.","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>.","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>.","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>"},"date_published":"2022-05-16T00:00:00Z","year":"2022","title":"Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus","month":"05","department":[{"_id":"GradSch"},{"_id":"RySh"}],"date_updated":"2026-04-07T14:31:19Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"has_accepted_license":"1","status":"public","date_created":"2022-05-17T08:57:41Z","supervisor":[{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"page":"108","ddc":["570"],"file":[{"access_level":"closed","file_size":56427603,"relation":"source_file","date_created":"2022-05-17T09:08:06Z","checksum":"8fc695d88020d70d231dad0e9f10b138","embargo_to":"open_access","file_id":"11395","creator":"cchlebak","file_name":"MJ thesis.docx","date_updated":"2023-05-17T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_name":"MJ_thesis_PDFA.pdf","date_updated":"2023-05-17T22:30:03Z","content_type":"application/pdf","embargo":"2023-05-16","file_id":"11397","creator":"cchlebak","date_created":"2022-05-17T12:09:25Z","checksum":"c1dd20a1aece521b3500607b00e463d6","access_level":"open_access","file_size":4351981,"relation":"main_file"}],"OA_place":"publisher","_id":"11393","oa":1,"related_material":{"record":[{"status":"public","id":"7391","relation":"part_of_dissertation"}]},"type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"full_name":"Jevtic, Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","last_name":"Jevtic","first_name":"Marijo"}],"corr_author":"1","file_date_updated":"2023-05-17T22:30:03Z"}]