[{"year":"2022","article_processing_charge":"No","corr_author":"1","oa_version":"Preprint","arxiv":1,"project":[{"call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"author":[{"last_name":"Lechner","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"full_name":"Amini, Alexander","last_name":"Amini","first_name":"Alexander"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"language":[{"iso":"eng"}],"publication":"arXiv","article_number":"2204.07373","publication_status":"draft","citation":{"apa":"Lechner, M., Amini, A., Rus, D., &#38; Henzinger, T. A. (n.d.). Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2204.07373\">https://doi.org/10.48550/arXiv.2204.07373</a>","ista":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. arXiv, 2204.07373.","ieee":"M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial robustness-accuracy tradeoff in robot learning,” <i>arXiv</i>. .","short":"M. Lechner, A. Amini, D. Rus, T.A. Henzinger, ArXiv (n.d.).","mla":"Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>ArXiv</i>, 2204.07373, doi:<a href=\"https://doi.org/10.48550/arXiv.2204.07373\">10.48550/arXiv.2204.07373</a>.","chicago":"Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger. “Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2204.07373\">https://doi.org/10.48550/arXiv.2204.07373</a>.","ama":"Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy tradeoff in robot learning. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2204.07373\">10.48550/arXiv.2204.07373</a>"},"title":"Revisiting the adversarial robustness-accuracy tradeoff in robot learning","oa":1,"month":"04","external_id":{"arxiv":["2204.07373"]},"acknowledgement":"This work was supported in parts by the ERC-2020-AdG 101020093, National Science Foundation (NSF), and JP\r\nMorgan Graduate Fellowships. We thank Christoph Lampert for inspiring this work.\r\n","ec_funded":1,"OA_place":"repository","date_updated":"2026-08-12T06:40:15Z","related_material":{"record":[{"status":"public","id":"11362","relation":"dissertation_contains"},{"relation":"later_version","status":"public","id":"12704"}]},"_id":"11366","status":"public","abstract":[{"lang":"eng","text":"Adversarial training (i.e., training on adversarially perturbed input data) is a well-studied method for making neural networks robust to potential adversarial attacks during inference. However, the improved robustness does not\r\ncome for free but rather is accompanied by a decrease in overall model accuracy and performance. Recent work has shown that, in practical robot learning applications, the effects of adversarial training do not pose a fair trade-off\r\nbut inflict a net loss when measured in holistic robot performance. This work revisits the robustness-accuracy trade-off in robot learning by systematically analyzing if recent advances in robust training methods and theory in\r\nconjunction with adversarial robot learning can make adversarial training suitable for real-world robot applications. We evaluate a wide variety of robot learning tasks ranging from autonomous driving in a high-fidelity environment\r\namenable to sim-to-real deployment, to mobile robot gesture recognition. Our results demonstrate that, while these techniques make incremental improvements on the trade-off on a relative scale, the negative side-effects caused by\r\nadversarial training still outweigh the improvements by an order of magnitude. We conclude that more substantial advances in robust learning methods are necessary before they can benefit robot learning tasks in practice."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.07373","open_access":"1"}],"day":"15","doi":"10.48550/arXiv.2204.07373","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"date_created":"2022-05-12T13:20:17Z","date_published":"2022-04-15T00:00:00Z","type":"preprint"},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2375-1207"],"eisbn":["9781665413169"]},"author":[{"first_name":"Sourav","last_name":"Das","full_name":"Das, Sourav"},{"first_name":"Thomas","last_name":"Yurek","full_name":"Yurek, Thomas"},{"last_name":"Xiang","full_name":"Xiang, Zhuolun","first_name":"Zhuolun"},{"full_name":"Miller, Andrew","last_name":"Miller","first_name":"Andrew"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","orcid":"0000-0002-8827-3382","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Ren, Ling","last_name":"Ren","first_name":"Ling"}],"publication_status":"published","citation":{"ieee":"S. Das, T. Yurek, Z. Xiang, A. Miller, E. Kokoris Kogias, and L. Ren, “Practical asynchronous distributed key generation,” in <i>2022 IEEE Symposium on Security and Privacy</i>, San Francisco, CA, United States, 2022, pp. 2518–2534.","short":"S. Das, T. Yurek, Z. Xiang, A. Miller, E. Kokoris Kogias, L. Ren, in:, 2022 IEEE Symposium on Security and Privacy, IEEE, 2022, pp. 2518–2534.","ista":"Das S, Yurek T, Xiang Z, Miller A, Kokoris Kogias E, Ren L. 2022. Practical asynchronous distributed key generation. 2022 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 2518–2534.","apa":"Das, S., Yurek, T., Xiang, Z., Miller, A., Kokoris Kogias, E., &#38; Ren, L. (2022). Practical asynchronous distributed key generation. In <i>2022 IEEE Symposium on Security and Privacy</i> (pp. 2518–2534). San Francisco, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/sp46214.2022.9833584\">https://doi.org/10.1109/sp46214.2022.9833584</a>","chicago":"Das, Sourav, Thomas Yurek, Zhuolun Xiang, Andrew Miller, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous Distributed Key Generation.” In <i>2022 IEEE Symposium on Security and Privacy</i>, 2518–34. IEEE, 2022. <a href=\"https://doi.org/10.1109/sp46214.2022.9833584\">https://doi.org/10.1109/sp46214.2022.9833584</a>.","ama":"Das S, Yurek T, Xiang Z, Miller A, Kokoris Kogias E, Ren L. Practical asynchronous distributed key generation. In: <i>2022 IEEE Symposium on Security and Privacy</i>. IEEE; 2022:2518-2534. doi:<a href=\"https://doi.org/10.1109/sp46214.2022.9833584\">10.1109/sp46214.2022.9833584</a>","mla":"Das, Sourav, et al. “Practical Asynchronous Distributed Key Generation.” <i>2022 IEEE Symposium on Security and Privacy</i>, IEEE, 2022, pp. 2518–34, doi:<a href=\"https://doi.org/10.1109/sp46214.2022.9833584\">10.1109/sp46214.2022.9833584</a>."},"publication":"2022 IEEE Symposium on Security and Privacy","day":"27","article_processing_charge":"No","conference":{"name":"SP: Symposium on Security and Privacy","start_date":"2022-05-23","location":"San Francisco, CA, United States","end_date":"2022-05-26"},"year":"2022","page":"2518-2534","main_file_link":[{"url":"https://eprint.iacr.org/2021/1591","open_access":"1"}],"abstract":[{"text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted third party and is a building block to decentralized protocols such as randomness beacons, threshold signatures, and general multiparty computation. Until recently, DKG protocols have assumed the synchronous model and thus are vulnerable when their underlying network assumptions do not hold. The recent advancements in asynchronous DKG protocols are insufficient as they either have poor efficiency or limited functionality, resulting in a lack of concrete implementations. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol. In a network of n nodes, our ADKG protocol can tolerate up to t<n/3 malicious nodes and have an expected O(κn3) communication cost, where κ is the security parameter. Our ADKG protocol produces a field element as the secret and is thus compatible with off-the-shelf threshold cryptosystems. We implement our ADKG protocol and evaluate it using a network of up to 128 nodes in geographically distributed AWS instances. Our evaluation shows that our protocol takes as low as 3 and 9.5 seconds to terminate for 32 and 64 nodes, respectively. Also, each node sends only 0.7 Megabytes and 2.9 Megabytes of data during the two experiments, respectively.","lang":"eng"}],"status":"public","oa_version":"Preprint","quality_controlled":"1","date_published":"2022-07-27T00:00:00Z","publisher":"IEEE","date_created":"2023-01-16T10:06:11Z","acknowledgement":"The authors would like to thank Amit Agarwal, Adithya Bhat, Kobi Gurkan, Dakshita Khurana, Nibesh Shrestha, and Gilad Stern for the helpful discussions related to the paper.\r\nAlso, the authors would like to thank Sylvain Bellemare for helping with the hbACSS codebase and Nicolas Gailly for helping with running the Drand experiments.","scopus_import":"1","_id":"12300","type":"conference","date_updated":"2026-08-12T06:40:50Z","title":"Practical asynchronous distributed key generation","department":[{"_id":"ElKo"}],"doi":"10.1109/sp46214.2022.9833584","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07"},{"page":"4901-4948","arxiv":1,"oa_version":"Preprint","corr_author":"1","article_processing_charge":"No","year":"2022","citation":{"ista":"Zhang Y, Vatedka S, Jaggi S, Sarwate AD. 2022. Quadratically constrained myopic adversarial channels. IEEE Transactions on Information Theory. 68(8), 4901–4948.","apa":"Zhang, Y., Vatedka, S., Jaggi, S., &#38; Sarwate, A. D. (2022). Quadratically constrained myopic adversarial channels. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/tit.2022.3167554\">https://doi.org/10.1109/tit.2022.3167554</a>","short":"Y. Zhang, S. Vatedka, S. Jaggi, A.D. Sarwate, IEEE Transactions on Information Theory 68 (2022) 4901–4948.","ieee":"Y. Zhang, S. Vatedka, S. Jaggi, and A. D. Sarwate, “Quadratically constrained myopic adversarial channels,” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 8. IEEE, pp. 4901–4948, 2022.","mla":"Zhang, Yihan, et al. “Quadratically Constrained Myopic Adversarial Channels.” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 8, IEEE, 2022, pp. 4901–48, doi:<a href=\"https://doi.org/10.1109/tit.2022.3167554\">10.1109/tit.2022.3167554</a>.","ama":"Zhang Y, Vatedka S, Jaggi S, Sarwate AD. Quadratically constrained myopic adversarial channels. <i>IEEE Transactions on Information Theory</i>. 2022;68(8):4901-4948. doi:<a href=\"https://doi.org/10.1109/tit.2022.3167554\">10.1109/tit.2022.3167554</a>","chicago":"Zhang, Yihan, Shashank Vatedka, Sidharth Jaggi, and Anand D. Sarwate. “Quadratically Constrained Myopic Adversarial Channels.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2022. <a href=\"https://doi.org/10.1109/tit.2022.3167554\">https://doi.org/10.1109/tit.2022.3167554</a>."},"publication_status":"published","publication":"IEEE Transactions on Information Theory","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"language":[{"iso":"eng"}],"author":[{"full_name":"Zhang, Yihan","last_name":"Zhang","orcid":"0000-0002-6465-6258","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c"},{"full_name":"Vatedka, Shashank","last_name":"Vatedka","first_name":"Shashank"},{"first_name":"Sidharth","last_name":"Jaggi","full_name":"Jaggi, Sidharth"},{"last_name":"Sarwate","full_name":"Sarwate, Anand D.","first_name":"Anand D."}],"external_id":{"isi":["000838527100004"],"arxiv":["1801.05951"]},"month":"08","volume":68,"oa":1,"intvolume":"        68","title":"Quadratically constrained myopic adversarial channels","_id":"12273","date_updated":"2026-08-12T06:41:20Z","abstract":[{"text":"We study communication in the presence of a jamming adversary where quadratic power constraints are imposed on the transmitter and the jammer. The jamming signal is allowed to be a function of the codebook, and a noncausal but noisy observation of the transmitted codeword. For a certain range of the noise-to-signal ratios (NSRs) of the transmitter and the jammer, we are able to characterize the capacity of this channel under deterministic encoding or stochastic encoding, i.e., with no common randomness between the encoder/decoder pair. For the remaining NSR regimes, we determine the capacity under the assumption of a small amount of common randomness (at most 2log(n) bits in one sub-regime, and at most Ω(n) bits in the other sub-regime) available to the encoder-decoder pair. Our proof techniques involve a novel myopic list-decoding result for achievability, and a Plotkin-type push attack for the converse in a subregion of the NSRs, both of which may be of independent interest. We also give bounds on the strong secrecy capacity of this channel assuming that the jammer is simultaneously eavesdropping.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1801.05951","open_access":"1"}],"status":"public","day":"01","isi":1,"article_type":"original","department":[{"_id":"MaMo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1109/tit.2022.3167554","issue":"8","type":"journal_article","quality_controlled":"1","date_published":"2022-08-01T00:00:00Z","scopus_import":"1","publisher":"IEEE","date_created":"2023-01-16T10:01:19Z"},{"title":"Decoding Reed-Muller codes with successive codeword permutations","intvolume":"        70","external_id":{"arxiv":["2109.02122"],"isi":["000937284600006"]},"oa":1,"volume":70,"month":"11","_id":"12233","date_updated":"2026-08-12T06:41:04Z","article_processing_charge":"No","year":"2022","page":"7134-7145","oa_version":"Preprint","arxiv":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0090-6778"],"eissn":["1558-0857"]},"author":[{"first_name":"Nghia","full_name":"Doan, Nghia","last_name":"Doan"},{"first_name":"Seyyed Ali","full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi"},{"orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"last_name":"Gross","full_name":"Gross, Warren J.","first_name":"Warren J."}],"publication_status":"published","citation":{"mla":"Doan, Nghia, et al. “Decoding Reed-Muller Codes with Successive Codeword Permutations.” <i>IEEE Transactions on Communications</i>, vol. 70, no. 11, IEEE, 2022, pp. 7134–45, doi:<a href=\"https://doi.org/10.1109/tcomm.2022.3211101\">10.1109/tcomm.2022.3211101</a>.","ama":"Doan N, Hashemi SA, Mondelli M, Gross WJ. Decoding Reed-Muller codes with successive codeword permutations. <i>IEEE Transactions on Communications</i>. 2022;70(11):7134-7145. doi:<a href=\"https://doi.org/10.1109/tcomm.2022.3211101\">10.1109/tcomm.2022.3211101</a>","chicago":"Doan, Nghia, Seyyed Ali Hashemi, Marco Mondelli, and Warren J. Gross. “Decoding Reed-Muller Codes with Successive Codeword Permutations.” <i>IEEE Transactions on Communications</i>. IEEE, 2022. <a href=\"https://doi.org/10.1109/tcomm.2022.3211101\">https://doi.org/10.1109/tcomm.2022.3211101</a>.","apa":"Doan, N., Hashemi, S. A., Mondelli, M., &#38; Gross, W. J. (2022). Decoding Reed-Muller codes with successive codeword permutations. <i>IEEE Transactions on Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/tcomm.2022.3211101\">https://doi.org/10.1109/tcomm.2022.3211101</a>","ista":"Doan N, Hashemi SA, Mondelli M, Gross WJ. 2022. Decoding Reed-Muller codes with successive codeword permutations. IEEE Transactions on Communications. 70(11), 7134–7145.","ieee":"N. Doan, S. A. Hashemi, M. Mondelli, and W. J. Gross, “Decoding Reed-Muller codes with successive codeword permutations,” <i>IEEE Transactions on Communications</i>, vol. 70, no. 11. IEEE, pp. 7134–7145, 2022.","short":"N. Doan, S.A. Hashemi, M. Mondelli, W.J. Gross, IEEE Transactions on Communications 70 (2022) 7134–7145."},"publication":"IEEE Transactions on Communications","department":[{"_id":"MaMo"}],"article_type":"original","doi":"10.1109/tcomm.2022.3211101","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-11-01T00:00:00Z","quality_controlled":"1","publisher":"IEEE","date_created":"2023-01-16T09:50:38Z","scopus_import":"1","type":"journal_article","issue":"11","abstract":[{"text":"A novel recursive list decoding (RLD) algorithm for Reed-Muller (RM) codes based on successive permutations (SP) of the codeword is presented. A low-complexity SP scheme applied to a subset of the symmetry group of RM codes is first proposed to carefully select a good codeword permutation on the fly. Then, the proposed SP technique is integrated into an improved RLD algorithm that initializes different decoding paths with random codeword permutations, which are sampled from the full symmetry group of RM codes. Finally, efficient latency and complexity reduction schemes are introduced that virtually preserve the error-correction performance of the proposed decoder. Simulation results demonstrate that at the target frame error rate of 10−3 for the RM code of length 256 with 163 information bits, the proposed decoder reduces 6% of the computational complexity and 22% of the decoding latency of the state-of-the-art semi-parallel simplified successive-cancellation decoder with fast Hadamard transform (SSC-FHT) that uses 96 permutations from the full symmetry group of RM codes, while relatively maintaining the error-correction performance and memory consumption of the semi-parallel permuted SSC-FHT decoder.","lang":"eng"}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2109.02122","open_access":"1"}],"status":"public","isi":1,"day":"01"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1109/TWC.2021.3125626","article_type":"original","department":[{"_id":"MaMo"}],"scopus_import":"1","publisher":"IEEE","date_created":"2021-11-28T23:01:29Z","quality_controlled":"1","date_published":"2022-06-01T00:00:00Z","issue":"6","type":"journal_article","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/2012.13378","open_access":"1"}],"abstract":[{"lang":"eng","text":"This paper characterizes the latency of the simplified successive-cancellation (SSC) decoding scheme for polar codes under hardware resource constraints. In particular, when the number of processing elements P that can perform SSC decoding operations in parallel is limited, as is the case in practice, the latency of SSC decoding is O(N1-1/μ + N/P log2 log2 N/P), where N is the block length of the code and μ is the scaling exponent of the channel. Three direct consequences of this bound are presented. First, in a fully-parallel implementation where P = N/2, the latency of SSC decoding is O(N1-1/μ), which is sublinear in the block length. This recovers a result from our earlier work. Second, in a fully-serial implementation where P = 1, the latency of SSC decoding scales as O(N log2 log2 N). The multiplicative constant is also calculated: we show that the latency of SSC decoding when P = 1 is given by (2 + o(1))N log2 log2 N. Third, in a semi-parallel implementation, the smallest P that gives the same latency as that of the fully-parallel implementation is P = N1/μ. The tightness of our bound on SSC decoding latency and the applicability of the foregoing results is validated through extensive simulations."}],"isi":1,"day":"01","intvolume":"        21","title":"Parallelism versus latency in simplified successive-cancellation decoding of polar codes","volume":21,"month":"06","oa":1,"external_id":{"arxiv":["2012.13378"],"isi":["000809406400028"]},"acknowledgement":"S. A. Hashemi is supported by a Postdoctoral Fellowship from the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC) and by Huawei. M. Mondelli is partially\r\nsupported by the 2019 Lopez-Loreta Prize. A. Fazeli and A. Vardy were supported in part by\r\nthe National Science Foundation under Grant CCF-1764104.","date_updated":"2026-08-12T06:43:01Z","related_material":{"record":[{"id":"10053","status":"public","relation":"earlier_version"}]},"_id":"10364","year":"2022","article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"page":"3909-3920","author":[{"full_name":"Hashemi, Seyyed Ali","last_name":"Hashemi","first_name":"Seyyed Ali"},{"orcid":"0000-0002-3242-7020","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"full_name":"Fazeli, Arman","last_name":"Fazeli","first_name":"Arman"},{"first_name":"Alexander","last_name":"Vardy","full_name":"Vardy, Alexander"},{"first_name":"John","full_name":"Cioffi, John","last_name":"Cioffi"},{"first_name":"Andrea","full_name":"Goldsmith, Andrea","last_name":"Goldsmith"}],"publication_identifier":{"issn":["1536-1276"],"eissn":["1558-2248"]},"language":[{"iso":"eng"}],"publication":"IEEE Transactions on Wireless Communications","citation":{"ieee":"S. A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, and A. Goldsmith, “Parallelism versus latency in simplified successive-cancellation decoding of polar codes,” <i>IEEE Transactions on Wireless Communications</i>, vol. 21, no. 6. IEEE, pp. 3909–3920, 2022.","short":"S.A. Hashemi, M. Mondelli, A. Fazeli, A. Vardy, J. Cioffi, A. Goldsmith, IEEE Transactions on Wireless Communications 21 (2022) 3909–3920.","ista":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. 2022. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. IEEE Transactions on Wireless Communications. 21(6), 3909–3920.","apa":"Hashemi, S. A., Mondelli, M., Fazeli, A., Vardy, A., Cioffi, J., &#38; Goldsmith, A. (2022). Parallelism versus latency in simplified successive-cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/TWC.2021.3125626\">https://doi.org/10.1109/TWC.2021.3125626</a>","chicago":"Hashemi, Seyyed Ali, Marco Mondelli, Arman Fazeli, Alexander Vardy, John Cioffi, and Andrea Goldsmith. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>. IEEE, 2022. <a href=\"https://doi.org/10.1109/TWC.2021.3125626\">https://doi.org/10.1109/TWC.2021.3125626</a>.","ama":"Hashemi SA, Mondelli M, Fazeli A, Vardy A, Cioffi J, Goldsmith A. Parallelism versus latency in simplified successive-cancellation decoding of polar codes. <i>IEEE Transactions on Wireless Communications</i>. 2022;21(6):3909-3920. doi:<a href=\"https://doi.org/10.1109/TWC.2021.3125626\">10.1109/TWC.2021.3125626</a>","mla":"Hashemi, Seyyed Ali, et al. “Parallelism versus Latency in Simplified Successive-Cancellation Decoding of Polar Codes.” <i>IEEE Transactions on Wireless Communications</i>, vol. 21, no. 6, IEEE, 2022, pp. 3909–20, doi:<a href=\"https://doi.org/10.1109/TWC.2021.3125626\">10.1109/TWC.2021.3125626</a>."},"publication_status":"published"},{"citation":{"ieee":"K. Bartalska <i>et al.</i>, “A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation,” <i>iScience</i>, vol. 25, no. 7. Elsevier, 2022.","short":"K. Bartalska, V. Hübschmann, M. Korkut, R.J. Cubero, A. Venturino, K. Rössler, T. Czech, S. Siegert, IScience 25 (2022).","ista":"Bartalska K, Hübschmann V, Korkut M, Cubero RJ, Venturino A, Rössler K, Czech T, Siegert S. 2022. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. iScience. 25(7), 104580.","apa":"Bartalska, K., Hübschmann, V., Korkut, M., Cubero, R. J., Venturino, A., Rössler, K., … Siegert, S. (2022). A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>","chicago":"Bartalska, Katarina, Verena Hübschmann, Medina Korkut, Ryan J Cubero, Alessandro Venturino, Karl Rössler, Thomas Czech, and Sandra Siegert. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>.","ama":"Bartalska K, Hübschmann V, Korkut M, et al. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>iScience</i>. 2022;25(7). doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>","mla":"Bartalska, Katarina, et al. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>, vol. 25, no. 7, 104580, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>."},"article_number":"104580","publication_status":"published","publication":"iScience","publication_identifier":{"eissn":["2589-0042"]},"language":[{"iso":"eng"}],"author":[{"last_name":"Bartalska","full_name":"Bartalska, Katarina","id":"4D883232-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"last_name":"Hübschmann","full_name":"Hübschmann, Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87","first_name":"Verena"},{"orcid":"0000-0003-4309-2251","first_name":"Medina","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87","full_name":"Korkut, Medina","last_name":"Korkut"},{"last_name":"Cubero","full_name":"Cubero, Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","first_name":"Ryan J"},{"last_name":"Venturino","full_name":"Venturino, Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","orcid":"0000-0003-2356-9403"},{"last_name":"Rössler","full_name":"Rössler, Karl","first_name":"Karl"},{"first_name":"Thomas","last_name":"Czech","full_name":"Czech, Thomas"},{"full_name":"Siegert, Sandra","last_name":"Siegert","orcid":"0000-0001-8635-0877","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2022-07-04T08:19:25Z","project":[{"call_identifier":"H2020","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","_id":"25D4A630-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"SC19-017","name":"How human microglia shape developing neurons during health and inflammation","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A"}],"oa_version":"Published Version","corr_author":"1","article_processing_charge":"Yes","year":"2022","_id":"11478","related_material":{"record":[{"relation":"other","status":"public","id":"12117"},{"relation":"dissertation_contains","id":"20074","status":"public"}]},"date_updated":"2026-08-12T08:45:16Z","ec_funded":1,"acknowledgement":"We thank the scientific service units at ISTA, specifically the lab support facility and imaging & optics facility for their support; Nicolas Armel for performing the Mass Spectrometry. We thank Alexandra Lang and Tanja Peilnsteiner for their help in human brain tissue collection, Rouven Schulz for his insights into the functional assays We thank all members of the Siegert group for constant feedback on the project and Margaret Maes, Rouven Schulz, and Marco Benevento for feedback on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.).","pmid":1,"external_id":{"isi":["000830428500005"],"pmid":["35789843"]},"month":"07","volume":25,"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["610"],"intvolume":"        25","title":"A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"day":"15","isi":1,"abstract":[{"lang":"eng","text":"Cerebral organoids differentiated from human-induced pluripotent stem cells (hiPSC) provide a unique opportunity to investigate brain development. However, organoids usually lack microglia, brain-resident immune cells, which are present in the early embryonic brain and participate in neuronal circuit development. Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol. Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented, 3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When we guide the retinal organoid differentiation with low-dosed BMP4, we prevent cup development and enhance microglia and 3D-cysts formation. Mass spectrometry identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed this microglia-preferred environment also within the unguided protocol, providing insight into microglial behavior and migration and offer a model to study how they enter and distribute within the human brain."}],"status":"public","issue":"7","type":"journal_article","date_published":"2022-07-15T00:00:00Z","quality_controlled":"1","scopus_import":"1","date_created":"2022-07-03T22:01:33Z","publisher":"Elsevier","article_type":"original","file":[{"checksum":"a470b74e1b3796c710189c81a4cd4329","file_name":"2022_iScience_Bartalska.pdf","relation":"main_file","creator":"cchlebak","access_level":"open_access","file_id":"11480","file_size":19400048,"success":1,"date_created":"2022-07-04T08:19:25Z","content_type":"application/pdf","date_updated":"2022-07-04T08:19:25Z"}],"department":[{"_id":"SaSi"}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.isci.2022.104580"},{"author":[{"first_name":"Hongjie","orcid":"0000-0001-5128-7126","id":"3D7DD9BE-F248-11E8-B48F-1D18A9856A87","full_name":"Yu, Hongjie","last_name":"Yu"}],"publication_identifier":{"eissn":["1945-5844"],"issn":["0030-8730"]},"language":[{"iso":"eng"}],"publication":"Pacific Journal of Mathematics","citation":{"mla":"Yu, Hongjie. “A Coarse Geometric Expansion of a Variant of Arthur’s Truncated Traces and Some Applications.” <i>Pacific Journal of Mathematics</i>, vol. 321, no. 1, Mathematical Sciences Publishers, 2022, pp. 193–237, doi:<a href=\"https://doi.org/10.2140/pjm.2022.321.193\">10.2140/pjm.2022.321.193</a>.","ama":"Yu H. A coarse geometric expansion of a variant of Arthur’s truncated traces and some applications. <i>Pacific Journal of Mathematics</i>. 2022;321(1):193-237. doi:<a href=\"https://doi.org/10.2140/pjm.2022.321.193\">10.2140/pjm.2022.321.193</a>","chicago":"Yu, Hongjie. “A Coarse Geometric Expansion of a Variant of Arthur’s Truncated Traces and Some Applications.” <i>Pacific Journal of Mathematics</i>. Mathematical Sciences Publishers, 2022. <a href=\"https://doi.org/10.2140/pjm.2022.321.193\">https://doi.org/10.2140/pjm.2022.321.193</a>.","ista":"Yu H. 2022. A coarse geometric expansion of a variant of Arthur’s truncated traces and some applications. Pacific Journal of Mathematics. 321(1), 193–237.","apa":"Yu, H. (2022). A coarse geometric expansion of a variant of Arthur’s truncated traces and some applications. <i>Pacific Journal of Mathematics</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/pjm.2022.321.193\">https://doi.org/10.2140/pjm.2022.321.193</a>","short":"H. Yu, Pacific Journal of Mathematics 321 (2022) 193–237.","ieee":"H. Yu, “A coarse geometric expansion of a variant of Arthur’s truncated traces and some applications,” <i>Pacific Journal of Mathematics</i>, vol. 321, no. 1. Mathematical Sciences Publishers, pp. 193–237, 2022."},"publication_status":"published","year":"2022","article_processing_charge":"No","corr_author":"1","arxiv":1,"oa_version":"Preprint","page":"193-237","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"acknowledgement":"I’d like to thank Prof. Chaudouard for introducing me to this area. I’d like to thank Prof. Harris for asking me the question that makes Section 10 possible. I’m grateful for the support of Prof. Hausel and IST Austria. The author was funded by an ISTplus fellowship: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","ec_funded":1,"date_updated":"2026-08-12T08:44:28Z","_id":"12793","intvolume":"       321","title":"A coarse geometric expansion of a variant of Arthur's truncated traces and some applications","month":"08","volume":321,"oa":1,"external_id":{"isi":["000954466300006"],"arxiv":["2109.10245"]},"isi":1,"day":"29","keyword":["Arthur–Selberg trace formula","cuspidal automorphic representations","global function fields"],"status":"public","abstract":[{"lang":"eng","text":"Let F be a global function field with constant field Fq. Let G be a reductive group over Fq. We establish a variant of Arthur's truncated kernel for G and for its Lie algebra which generalizes Arthur's original construction. We establish a coarse geometric expansion for our variant truncation.\r\nAs applications, we consider some existence and uniqueness problems of some cuspidal automorphic representations for the functions field of the projective line P1Fq with two points of ramifications."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2109.10245","open_access":"1"}],"scopus_import":"1","date_created":"2023-04-02T22:01:11Z","publisher":"Mathematical Sciences Publishers","quality_controlled":"1","date_published":"2022-08-29T00:00:00Z","issue":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.2140/pjm.2022.321.193","article_type":"original","department":[{"_id":"TaHa"}]},{"title":"Scaling limit of the homogenization commutator for Gaussian coefficient  fields","intvolume":"        32","oa":1,"volume":32,"month":"04","external_id":{"isi":["000791003700011"],"arxiv":["1910.04088"]},"acknowledgement":"The authors thank Ivan Nourdin and Felix Otto for inspiring discussions. The work of MD is financially supported by the CNRS-Momentum program. Financial support of AG is acknowledged from the European Research Council under the European Community’s Seventh Framework Programme (FP7/2014-2019 Grant Agreement QUANTHOM 335410).","date_updated":"2026-08-12T09:22:31Z","_id":"10548","year":"2022","article_processing_charge":"No","oa_version":"Preprint","corr_author":"1","arxiv":1,"page":"1179-1209","author":[{"first_name":"Mitia","last_name":"Duerinckx","full_name":"Duerinckx, Mitia"},{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L"},{"last_name":"Gloria","full_name":"Gloria, Antoine","first_name":"Antoine"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1050-5164"]},"publication":"Annals of Applied Probability","publication_status":"published","citation":{"chicago":"Duerinckx, Mitia, Julian L Fischer, and Antoine Gloria. “Scaling Limit of the Homogenization Commutator for Gaussian Coefficient  Fields.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AAP1705\">https://doi.org/10.1214/21-AAP1705</a>.","ama":"Duerinckx M, Fischer JL, Gloria A. Scaling limit of the homogenization commutator for Gaussian coefficient  fields. <i>Annals of Applied Probability</i>. 2022;32(2):1179-1209. doi:<a href=\"https://doi.org/10.1214/21-AAP1705\">10.1214/21-AAP1705</a>","mla":"Duerinckx, Mitia, et al. “Scaling Limit of the Homogenization Commutator for Gaussian Coefficient  Fields.” <i>Annals of Applied Probability</i>, vol. 32, no. 2, Institute of Mathematical Statistics, 2022, pp. 1179–209, doi:<a href=\"https://doi.org/10.1214/21-AAP1705\">10.1214/21-AAP1705</a>.","ieee":"M. Duerinckx, J. L. Fischer, and A. Gloria, “Scaling limit of the homogenization commutator for Gaussian coefficient  fields,” <i>Annals of Applied Probability</i>, vol. 32, no. 2. Institute of Mathematical Statistics, pp. 1179–1209, 2022.","short":"M. Duerinckx, J.L. Fischer, A. Gloria, Annals of Applied Probability 32 (2022) 1179–1209.","ista":"Duerinckx M, Fischer JL, Gloria A. 2022. Scaling limit of the homogenization commutator for Gaussian coefficient  fields. Annals of Applied Probability. 32(2), 1179–1209.","apa":"Duerinckx, M., Fischer, J. L., &#38; Gloria, A. (2022). Scaling limit of the homogenization commutator for Gaussian coefficient  fields. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AAP1705\">https://doi.org/10.1214/21-AAP1705</a>"},"doi":"10.1214/21-AAP1705","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JuFi"}],"article_type":"original","date_created":"2021-12-16T12:10:16Z","publisher":"Institute of Mathematical Statistics","scopus_import":"1","date_published":"2022-04-28T00:00:00Z","quality_controlled":"1","type":"journal_article","issue":"2","status":"public","abstract":[{"lang":"eng","text":"Consider a linear elliptic partial differential equation in divergence form with a random coefficient field. The solution operator displays fluctuations around its expectation. The recently developed pathwise theory of fluctuations in stochastic homogenization reduces the characterization of these fluctuations to those of the so-called standard homogenization commutator. In this contribution, we investigate the scaling limit of this key quantity: starting\r\nfrom a Gaussian-like coefficient field with possibly strong correlations, we establish the convergence of the rescaled commutator to a fractional Gaussian field, depending on the decay of correlations of the coefficient field, and we\r\ninvestigate the (non)degeneracy of the limit. This extends to general dimension $d\\ge1$ previous results so far limited to dimension $d=1$, and to the continuum setting with strong correlations recent results in the discrete iid case."}],"main_file_link":[{"url":"https://arxiv.org/abs/1910.04088","open_access":"1"}],"isi":1,"day":"28"},{"date_published":"2022-03-31T00:00:00Z","ec_funded":1,"date_created":"2023-11-23T09:30:02Z","_id":"14597","date_updated":"2026-08-12T09:15:49Z","related_material":{"record":[{"status":"public","id":"14587","relation":"dissertation_contains"},{"status":"public","id":"17481","relation":"later_version"}]},"type":"preprint","title":"Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow","external_id":{"arxiv":["2203.17143"]},"department":[{"_id":"JuFi"}],"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.48550/ARXIV.2203.17143","oa":1,"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-0479-558X","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","last_name":"Fischer"},{"first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","full_name":"Marveggio, Alice","last_name":"Marveggio"}],"citation":{"ama":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>","chicago":"Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">https://doi.org/10.48550/ARXIV.2203.17143</a>.","mla":"Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” <i>ArXiv</i>, 2203.17143, doi:<a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>.","ieee":"J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow,” <i>arXiv</i>. .","short":"J.L. Fischer, A. Marveggio, ArXiv (n.d.).","apa":"Fischer, J. L., &#38; Marveggio, A. (n.d.). Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">https://doi.org/10.48550/ARXIV.2203.17143</a>","ista":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv, 2203.17143."},"publication_status":"draft","article_number":"2203.17143","day":"31","publication":"arXiv","article_processing_charge":"No","year":"2022","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2203.17143"}],"project":[{"grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","name":"Bridging Scales in Random Materials"}],"abstract":[{"lang":"eng","text":"Phase-field models such as the Allen-Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen-Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow.\r\nIn the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: As long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen-Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε1/2).\r\nOur approach is based on the gradient flow structure of the Allen-Cahn equation and its limiting motion: Building on the recent concept of \"gradient flow calibrations\" for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen-Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen-Cahn operator or additional convergence hypotheses for the energy at positive times."}],"corr_author":"1","arxiv":1,"oa_version":"Preprint","status":"public"},{"acknowledgement":"iona intestinalis adults were provided by Dr Yutaka Satou (Kyoto University) and Dr Manabu Yoshida (the University of Tokyo) with support from the National Bio-Resource Project of AMED, Japan. We thank Dr Hidehiko Hashimoto and Dr Yuji Mizotani for technical information about 1P-myosin antibody staining. We thank Dr Kaoru Imai and Dr Yutaka Satou for valuable discussion about Admp and for the DNA construct of Bmp2/4 under the Dlx.b upstream sequence. We thank Ms Maki Kogure for constructing the FUSION360 of the intercalating epidermal cell.\r\nThis work was supported by funding from the Japan Society for the Promotion of Science (JP16H01451, JP21H00440). Open Access funding provided by Keio University: Keio Gijuku Daigaku.","pmid":1,"date_updated":"2026-08-12T09:59:24Z","_id":"12231","title":"Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona","intvolume":"       149","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"oa":1,"volume":149,"month":"11","external_id":{"pmid":["36227591"],"isi":["000903991700002"]},"file_date_updated":"2023-01-27T10:36:50Z","author":[{"first_name":"Yuki S.","last_name":"Kogure","full_name":"Kogure, Yuki S."},{"full_name":"Muraoka, Hiromochi","last_name":"Muraoka","first_name":"Hiromochi"},{"full_name":"Koizumi, Wataru C.","last_name":"Koizumi","first_name":"Wataru C."},{"full_name":"Gelin-alessi, Raphaël","last_name":"Gelin-alessi","first_name":"Raphaël"},{"full_name":"Godard, Benoit G","last_name":"Godard","first_name":"Benoit G","id":"33280250-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Oka","full_name":"Oka, Kotaro","first_name":"Kotaro"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"full_name":"Hotta, Kohji","last_name":"Hotta","first_name":"Kohji"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"publication":"Development","article_number":"dev200215","publication_status":"published","citation":{"mla":"Kogure, Yuki S., et al. “Admp Regulates Tail Bending by Controlling Ventral Epidermal Cell Polarity via Phosphorylated Myosin Localization in Ciona.” <i>Development</i>, vol. 149, no. 21, dev200215, Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200215\">10.1242/dev.200215</a>.","chicago":"Kogure, Yuki S., Hiromochi Muraoka, Wataru C. Koizumi, Raphaël Gelin-alessi, Benoit G Godard, Kotaro Oka, Carl-Philipp J Heisenberg, and Kohji Hotta. “Admp Regulates Tail Bending by Controlling Ventral Epidermal Cell Polarity via Phosphorylated Myosin Localization in Ciona.” <i>Development</i>. Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200215\">https://doi.org/10.1242/dev.200215</a>.","ama":"Kogure YS, Muraoka H, Koizumi WC, et al. Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. <i>Development</i>. 2022;149(21). doi:<a href=\"https://doi.org/10.1242/dev.200215\">10.1242/dev.200215</a>","apa":"Kogure, Y. S., Muraoka, H., Koizumi, W. C., Gelin-alessi, R., Godard, B. G., Oka, K., … Hotta, K. (2022). Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200215\">https://doi.org/10.1242/dev.200215</a>","ista":"Kogure YS, Muraoka H, Koizumi WC, Gelin-alessi R, Godard BG, Oka K, Heisenberg C-PJ, Hotta K. 2022. Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona. Development. 149(21), dev200215.","short":"Y.S. Kogure, H. Muraoka, W.C. Koizumi, R. Gelin-alessi, B.G. Godard, K. Oka, C.-P.J. Heisenberg, K. Hotta, Development 149 (2022).","ieee":"Y. S. Kogure <i>et al.</i>, “Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin localization in Ciona,” <i>Development</i>, vol. 149, no. 21. Company of Biologists, 2022."},"year":"2022","article_processing_charge":"No","corr_author":"1","oa_version":"Published Version","date_created":"2023-01-16T09:50:12Z","publisher":"Company of Biologists","scopus_import":"1","quality_controlled":"1","date_published":"2022-11-01T00:00:00Z","type":"journal_article","issue":"21","doi":"10.1242/dev.200215","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"}],"has_accepted_license":"1","article_type":"original","file":[{"content_type":"application/pdf","date_updated":"2023-01-27T10:36:50Z","date_created":"2023-01-27T10:36:50Z","file_size":9160451,"file_id":"12423","access_level":"open_access","success":1,"file_name":"2022_Development_Kogure.pdf","checksum":"871b9c58eb79b9e60752de25a46938d6","creator":"dernst","relation":"main_file"}],"isi":1,"day":"01","keyword":["Developmental Biology","Molecular Biology"],"status":"public","abstract":[{"text":"Ventral tail bending, which is transient but pronounced, is found in many chordate embryos and constitutes an interesting model of how tissue interactions control embryo shape. Here, we identify one key upstream regulator of ventral tail bending in embryos of the ascidian Ciona. We show that during the early tailbud stages, ventral epidermal cells exhibit a boat-shaped morphology (boat cell) with a narrow apical surface where phosphorylated myosin light chain (pMLC) accumulates. We further show that interfering with the function of the BMP ligand Admp led to pMLC localizing to the basal instead of the apical side of ventral epidermal cells and a reduced number of boat cells. Finally, we show that cutting ventral epidermal midline cells at their apex using an ultraviolet laser relaxed ventral tail bending. Based on these results, we propose a previously unreported function for Admp in localizing pMLC to the apical side of ventral epidermal cells, which causes the tail to bend ventrally by resisting antero-posterior notochord extension at the ventral side of the tail.","lang":"eng"}]},{"title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","intvolume":"       149","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"month":"10","volume":149,"external_id":{"isi":["000918161000003"],"pmid":["36189829"]},"acknowledgement":"We are grateful to Dr Tom Pettini for the advice on smiFISH technique and Dr Laure Bally-Cuif for sharing plasmids. The authors also thank the Biological Services Facility, Bioimaging and Systems Microscopy Facilities of the University of Manchester for technical support.\r\nThis work was supported by a Wellcome Trust Senior Research Fellowship (090868/Z/09/Z) and a Wellcome Trust Investigator Award (224394/Z/21/Z) to N.P. and a Medical Research Council Career Development Award to C.S.M. (MR/V032534/1). J.B. was supported by a Wellcome Trust Four-Year PhD Studentship in Basic Science (219992/Z/19/Z). Open Access funding provided by The University of Manchester. Deposited in PMC for immediate release.","pmid":1,"date_updated":"2026-08-12T09:59:40Z","related_material":{"link":[{"url":" https://github.com/burtonjosh/StepwiseMir9","relation":"software"}]},"_id":"12245","year":"2022","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2023-01-30T08:35:44Z","author":[{"first_name":"Ximena","last_name":"Soto","full_name":"Soto, Ximena"},{"full_name":"Burton, Joshua","last_name":"Burton","first_name":"Joshua"},{"last_name":"Manning","full_name":"Manning, Cerys S.","first_name":"Cerys S."},{"first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","last_name":"Minchington"},{"last_name":"Lea","full_name":"Lea, Robert","first_name":"Robert"},{"first_name":"Jessica","full_name":"Lee, Jessica","last_name":"Lee"},{"first_name":"Jochen","full_name":"Kursawe, Jochen","last_name":"Kursawe"},{"full_name":"Rattray, Magnus","last_name":"Rattray","first_name":"Magnus"},{"first_name":"Nancy","last_name":"Papalopulu","full_name":"Papalopulu, Nancy"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"publication":"Development","publication_status":"published","article_number":"dev200474","citation":{"apa":"Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., … Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>","ista":"Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. 2022. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development. 149(19), dev200474.","ieee":"X. Soto <i>et al.</i>, “Sequential and additive expression of miR-9 precursors control timing of neurogenesis,” <i>Development</i>, vol. 149, no. 19. Company of Biologists, 2022.","short":"X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe, M. Rattray, N. Papalopulu, Development 149 (2022).","mla":"Soto, Ximena, et al. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>, vol. 149, no. 19, dev200474, Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>.","ama":"Soto X, Burton J, Manning CS, et al. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. 2022;149(19). doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>","chicago":"Soto, Ximena, Joshua Burton, Cerys S. Manning, Thomas Minchington, Robert Lea, Jessica Lee, Jochen Kursawe, Magnus Rattray, and Nancy Papalopulu. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>. Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>."},"doi":"10.1242/dev.200474","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"AnKi"}],"has_accepted_license":"1","article_type":"original","file":[{"creator":"dernst","relation":"main_file","checksum":"d7c29b74e9e4032308228cc704a30e88","file_name":"2022_Development_Soto.pdf","success":1,"access_level":"open_access","file_id":"12438","file_size":9348839,"date_created":"2023-01-30T08:35:44Z","date_updated":"2023-01-30T08:35:44Z","content_type":"application/pdf"}],"publisher":"Company of Biologists","date_created":"2023-01-16T09:53:17Z","scopus_import":"1","quality_controlled":"1","date_published":"2022-10-01T00:00:00Z","type":"journal_article","issue":"19","status":"public","abstract":[{"text":"MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.","lang":"eng"}],"isi":1,"day":"01","keyword":["Developmental Biology","Molecular Biology"]},{"doi":"10.1088/1361-648X/ac484d","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","department":[{"_id":"KiMo"}],"file":[{"success":1,"access_level":"open_access","file_id":"10741","file_size":1742414,"creator":"cchlebak","relation":"main_file","checksum":"b6c705c7f03dcb1dbcb06b1b4d4938d6","file_name":"2022_JPhysCondensMatter_Nauman.pdf","date_updated":"2022-02-07T10:35:28Z","content_type":"application/pdf","date_created":"2022-02-07T10:35:28Z"}],"article_type":"original","publisher":"IOP Publishing","date_created":"2022-02-06T23:01:31Z","scopus_import":"1","date_published":"2022-01-20T00:00:00Z","quality_controlled":"1","type":"journal_article","issue":"13","status":"public","abstract":[{"text":"Magnetic anisotropy in strontium iridate (Sr2IrO4) is essential because of its strong spin–orbit coupling and crystal field effect. In this paper, we present a detailed mapping of the out-of-plane (OOP) magnetic anisotropy in Sr2IrO4 for different sample orientations using torque magnetometry measurements in the low-magnetic-field region before the isospins are completely ordered. Dominant in-plane anisotropy was identified at low fields, confirming the b axis as an easy magnetization axis. Based on the fitting analysis of the strong uniaxial magnetic anisotropy, we observed that the main anisotropic effect arises from a spin–orbit-coupled magnetic exchange interaction affecting the OOP interaction. The effect of interlayer exchange interaction results in additional anisotropic terms owing to the tilting of the isospins. The results are relevant for understanding OOP magnetic anisotropy and provide a new way to analyze the effects of spin–orbit-coupling and interlayer magnetic exchange interactions. This study provides insight into the understanding of bulk magnetic, magnetotransport, and spintronic behavior on Sr2IrO4 for future studies.","lang":"eng"}],"isi":1,"day":"20","title":"Low-field magnetic anisotropy of Sr2IrO4","intvolume":"        34","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"oa":1,"month":"01","volume":34,"external_id":{"isi":["000775191800001"],"pmid":["34986467"]},"pmid":1,"acknowledgement":"YJ was supported by the National Research Foundation of Korea (NRF) (Grant Nos. NRF-2018K2A9A1A06069211 and NRF-2019R1A2C1089017). The work at Yonsei was supported by the NRF (Grant Nos. NRF-2017R1A5A-1014862 (SRC program: vdWMRC center), NRF-2019R1A2C2002601, and NRF-2021R1A2C1006375). WK acknowledges the support by the NRF (Grant Nos. 2018R1D1A1B07050087, 2018R1A6A1A03025340).","date_updated":"2026-08-12T14:03:01Z","_id":"10735","year":"2022","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2022-02-07T10:35:28Z","author":[{"full_name":"Nauman, Muhammad","last_name":"Nauman","first_name":"Muhammad","orcid":"0000-0002-2111-4846","id":"32c21954-2022-11eb-9d5f-af9f93c24e71"},{"full_name":"Hussain, Tayyaba","last_name":"Hussain","first_name":"Tayyaba"},{"first_name":"Joonyoung","full_name":"Choi, Joonyoung","last_name":"Choi"},{"last_name":"Lee","full_name":"Lee, Nara","first_name":"Nara"},{"first_name":"Young Jai","full_name":"Choi, Young Jai","last_name":"Choi"},{"first_name":"Woun","last_name":"Kang","full_name":"Kang, Woun"},{"first_name":"Younjung","full_name":"Jo, Younjung","last_name":"Jo"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1361-648X"]},"publication":"Journal of Physics: Condensed Matter","publication_status":"published","article_number":"135802","citation":{"ama":"Nauman M, Hussain T, Choi J, et al. Low-field magnetic anisotropy of Sr2IrO4. <i>Journal of Physics: Condensed Matter</i>. 2022;34(13). doi:<a href=\"https://doi.org/10.1088/1361-648X/ac484d\">10.1088/1361-648X/ac484d</a>","chicago":"Nauman, Muhammad, Tayyaba Hussain, Joonyoung Choi, Nara Lee, Young Jai Choi, Woun Kang, and Younjung Jo. “Low-Field Magnetic Anisotropy of Sr2IrO4.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1361-648X/ac484d\">https://doi.org/10.1088/1361-648X/ac484d</a>.","mla":"Nauman, Muhammad, et al. “Low-Field Magnetic Anisotropy of Sr2IrO4.” <i>Journal of Physics: Condensed Matter</i>, vol. 34, no. 13, 135802, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1361-648X/ac484d\">10.1088/1361-648X/ac484d</a>.","ieee":"M. Nauman <i>et al.</i>, “Low-field magnetic anisotropy of Sr2IrO4,” <i>Journal of Physics: Condensed Matter</i>, vol. 34, no. 13. IOP Publishing, 2022.","short":"M. Nauman, T. Hussain, J. Choi, N. Lee, Y.J. Choi, W. Kang, Y. Jo, Journal of Physics: Condensed Matter 34 (2022).","ista":"Nauman M, Hussain T, Choi J, Lee N, Choi YJ, Kang W, Jo Y. 2022. Low-field magnetic anisotropy of Sr2IrO4. Journal of Physics: Condensed Matter. 34(13), 135802.","apa":"Nauman, M., Hussain, T., Choi, J., Lee, N., Choi, Y. J., Kang, W., &#38; Jo, Y. (2022). Low-field magnetic anisotropy of Sr2IrO4. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-648X/ac484d\">https://doi.org/10.1088/1361-648X/ac484d</a>"}},{"language":[{"iso":"eng"}],"author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","orcid":"0000-0002-5372-7890","last_name":"Biswas","full_name":"Biswas, Ranita"},{"full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza"}],"file_date_updated":"2022-07-27T09:30:30Z","citation":{"ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. LIPIcs.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs,” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs (n.d.).","mla":"Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>."},"publication_status":"submitted","publication":"LIPIcs","article_processing_charge":"No","year":"2022","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183"},{"name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"corr_author":"1","oa_version":"Submitted Version","ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35. ","_id":"11660","date_updated":"2026-08-13T09:41:58Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"15094"},{"relation":"later_version","id":"13182","status":"public"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510"],"title":"A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs","month":"07","oa":1,"day":"25","alternative_title":["LIPIcs"],"abstract":[{"text":"We characterize critical points of 1-dimensional maps paired in persistent homology geometrically and this way get elementary proofs of theorems about the symmetry of persistence diagrams and the variation of such maps. In particular, we identify branching points and endpoints of networks as the sole source of asymmetry and relate the cycle basis in persistent homology with a version of the stable marriage problem. Our analysis provides the foundations of fast algorithms for maintaining collections of interrelated sorted lists together with their persistence diagrams. ","lang":"eng"}],"status":"public","quality_controlled":"1","date_published":"2022-07-25T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2022-07-27T09:31:15Z","type":"journal_article","file":[{"date_created":"2022-07-27T09:30:30Z","date_updated":"2022-07-27T09:30:30Z","content_type":"application/pdf","creator":"scultrer","relation":"main_file","file_name":"window 1.pdf","checksum":"95903f9d1649e8e437a967b6f2f64730","access_level":"open_access","file_size":564836,"file_id":"11661"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"ec_funded":1,"acknowledgement":"We acknowledge K. Kubiasová for excellent technical assistance, J. Neuhold, A. Lehner and A. Sedivy for technical assistance with protein production and purification at Vienna Biocenter Core Facilities; Creoptix for performing GCI; and the Bioimaging, Electron Microscopy and Life Science Facilities at ISTA, the Plant Sciences Core Facility of CEITEC Masaryk University, the Core Facility CELLIM (MEYS CR, LM2018129 Czech-BioImaging) and J. Sprakel for their assistance. J.F. is grateful to R. Napier for many insightful suggestions and support. We thank all past and present members of the Friml group for their support and for other contributions to this effort to clarify the controversial role of ABP1 over the past seven years. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 742985 to J.F. and 833867 to D.W.); the Austrian Science Fund (FWF; P29988 to J.F.); the Netherlands Organization for Scientific Research (NWO; VICI grant 865.14.001 to D.W. and VENI grant VI.Veni.212.003 to A.K.); the Ministry of Education, Science and Technological Development of the Republic of Serbia (contract no. 451-03-68/2022-14/200053 to B.D.Ž.); and the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910).","pmid":1,"_id":"12291","date_updated":"2026-08-14T09:33:45Z","related_material":{"record":[{"relation":"dissertation_contains","id":"20364","status":"public"},{"status":"public","id":"19395","relation":"dissertation_contains"}]},"ddc":["580"],"title":"ABP1–TMK auxin perception for global phosphorylation and auxin canalization","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"intvolume":"       609","external_id":{"pmid":["36071161"],"isi":["000851357500002"]},"oa":1,"volume":609,"month":"09","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"file_date_updated":"2023-11-02T17:12:37Z","author":[{"last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"first_name":"Michelle C","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","last_name":"Gallei"},{"last_name":"Gelová","full_name":"Gelová, Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425","orcid":"0000-0003-4783-1752","first_name":"Zuzana"},{"last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J"},{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"full_name":"Monzer, Aline","last_name":"Monzer","first_name":"Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425"},{"full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","orcid":"0000-0002-7244-7237","first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"full_name":"Verstraeten, Inge","last_name":"Verstraeten","orcid":"0000-0001-7241-2328","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Branka D.","full_name":"Živanović, Branka D.","last_name":"Živanović"},{"full_name":"Zou, Minxia","last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas","last_name":"Fiedler","full_name":"Fiedler, Lukas"},{"last_name":"Giannini","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina"},{"first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"id":"45A71A74-F248-11E8-B48F-1D18A9856A87","first_name":"Mónika","last_name":"Hrtyan","full_name":"Hrtyan, Mónika"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Andre","last_name":"Kuhn","full_name":"Kuhn, Andre"},{"full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Randuch","full_name":"Randuch, Marek","id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","first_name":"Marek"},{"full_name":"Rýdza, Nikola","last_name":"Rýdza","first_name":"Nikola"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"last_name":"Tan","full_name":"Tan, Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285"},{"first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia","last_name":"Teplova"},{"full_name":"Kinoshita, Toshinori","last_name":"Kinoshita","first_name":"Toshinori"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"}],"publication_status":"published","citation":{"chicago":"Friml, Jiří, Michelle C Gallei, Zuzana Gelová, Alexander J Johnson, Ewa Mazur, Aline Monzer, Lesia Rodriguez Solovey, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>.","ama":"Friml J, Gallei MC, Gelová Z, et al. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. 2022;609(7927):575-581. doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>","mla":"Friml, Jiří, et al. “ABP1–TMK Auxin Perception for Global Phosphorylation and Auxin Canalization.” <i>Nature</i>, vol. 609, no. 7927, Springer Nature, 2022, pp. 575–81, doi:<a href=\"https://doi.org/10.1038/s41586-022-05187-x\">10.1038/s41586-022-05187-x</a>.","ieee":"J. Friml <i>et al.</i>, “ABP1–TMK auxin perception for global phosphorylation and auxin canalization,” <i>Nature</i>, vol. 609, no. 7927. Springer Nature, pp. 575–581, 2022.","short":"J. Friml, M.C. Gallei, Z. Gelová, A.J. Johnson, E. Mazur, A. Monzer, L. Rodriguez Solovey, M. Roosjen, I. Verstraeten, B.D. Živanović, M. Zou, L. Fiedler, C. Giannini, P. Grones, M. Hrtyan, W. Kaufmann, A. Kuhn, M. Narasimhan, M. Randuch, N. Rýdza, K. Takahashi, S. Tan, A. Teplova, T. Kinoshita, D. Weijers, H. Rakusová, Nature 609 (2022) 575–581.","apa":"Friml, J., Gallei, M. C., Gelová, Z., Johnson, A. J., Mazur, E., Monzer, A., … Rakusová, H. (2022). ABP1–TMK auxin perception for global phosphorylation and auxin canalization. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-022-05187-x\">https://doi.org/10.1038/s41586-022-05187-x</a>","ista":"Friml J, Gallei MC, Gelová Z, Johnson AJ, Mazur E, Monzer A, Rodriguez Solovey L, Roosjen M, Verstraeten I, Živanović BD, Zou M, Fiedler L, Giannini C, Grones P, Hrtyan M, Kaufmann W, Kuhn A, Narasimhan M, Randuch M, Rýdza N, Takahashi K, Tan S, Teplova A, Kinoshita T, Weijers D, Rakusová H. 2022. ABP1–TMK auxin perception for global phosphorylation and auxin canalization. Nature. 609(7927), 575–581."},"publication":"Nature","article_processing_charge":"No","year":"2022","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"grant_number":"P29988","call_identifier":"FWF","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425"}],"page":"575-581","oa_version":"Submitted Version","corr_author":"1","date_published":"2022-09-15T00:00:00Z","quality_controlled":"1","publisher":"Springer Nature","date_created":"2023-01-16T10:04:48Z","scopus_import":"1","type":"journal_article","issue":"7927","has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"GradSch"},{"_id":"EvBe"},{"_id":"EM-Fac"}],"file":[{"checksum":"a6055c606aefb900bf62ae3e7d15f921","file_name":"Friml Nature 2022_merged.pdf","relation":"main_file","creator":"amally","access_level":"open_access","file_size":79774945,"file_id":"14483","success":1,"date_created":"2023-11-02T17:12:37Z","content_type":"application/pdf","date_updated":"2023-11-02T17:12:37Z"}],"article_type":"original","doi":"10.1038/s41586-022-05187-x","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"day":"15","abstract":[{"text":"The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.","lang":"eng"}],"status":"public"},{"status":"public","abstract":[{"text":"Deep learning has enabled breakthroughs in challenging computing problems and has emerged as the standard problem-solving tool for computer vision and natural language processing tasks.\r\nOne exception to this trend is safety-critical tasks where robustness and resilience requirements contradict the black-box nature of neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital to provide guarantees on neural network agents' safety and robustness criteria. \r\nThis can be achieved by developing formal verification methods to verify the safety and robustness properties of neural networks.\r\n\r\nOur goal is to design, develop and assess safety verification methods for neural networks to improve their reliability and trustworthiness in real-world applications.\r\nThis thesis establishes techniques for the verification of compressed and adversarially trained models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst, we establish the problem of verifying quantized neural networks. Quantization is a technique that trades numerical precision for the computational efficiency of running a neural network and is widely adopted in industry.\r\nWe show that neglecting the reduced precision when verifying a neural network can lead to wrong conclusions about the robustness and safety of the network, highlighting that novel techniques for quantized network verification are necessary. We introduce several bit-exact verification methods explicitly designed for quantized neural networks and experimentally confirm on realistic networks that the network's robustness and other formal properties are affected by the quantization.\r\n\r\nFurthermore, we perform a case study providing evidence that adversarial training, a standard technique for making neural networks more robust, has detrimental effects on the network's performance. This robustness-accuracy tradeoff has been studied before regarding the accuracy obtained on classification datasets where each data point is independent of all other data points. On the other hand, we investigate the tradeoff empirically in robot learning settings where a both, a high accuracy and a high robustness, are desirable.\r\nOur results suggest that the negative side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally, we consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with systems over the infinite time horizon. Bayesian neural networks are probabilistic models for learning uncertainties in the data and are therefore often used on robotic and healthcare applications where data is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian neural networks so that they yield probability distributions over safe decisions only.\r\nOur method learns a safety certificate that guarantees safety over the infinite time horizon to determine which decisions are safe in every possible state of the system.\r\nWe demonstrate the effectiveness of our approach on a series of reinforcement learning benchmarks.","lang":"eng"}],"supervisor":[{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"alternative_title":["ISTA Thesis"],"keyword":["neural networks","verification","machine learning"],"day":"12","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:11362","file":[{"content_type":"application/zip","date_updated":"2022-05-13T12:49:00Z","date_created":"2022-05-13T12:33:26Z","access_level":"closed","file_size":13210143,"file_id":"11378","file_name":"src.zip","checksum":"8eefa9c7c10ca7e1a2ccdd731962a645","relation":"source_file","creator":"mlechner"},{"checksum":"1b9e1e5a9a83ed9d89dad2f5133dc026","file_name":"thesis_main-a2.pdf","creator":"mlechner","relation":"main_file","access_level":"open_access","file_id":"11382","file_size":2732536,"date_created":"2022-05-16T08:02:28Z","content_type":"application/pdf","date_updated":"2022-05-17T15:19:39Z"}],"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"has_accepted_license":"1","type":"dissertation","publisher":"Institute of Science and Technology Austria","date_created":"2022-05-12T07:14:01Z","date_published":"2022-05-12T00:00:00Z","corr_author":"1","oa_version":"Published Version","project":[{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"},{"grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"page":"124","year":"2022","article_processing_charge":"No","citation":{"short":"M. Lechner, Learning Verifiable Representations, Institute of Science and Technology Austria, 2022.","ieee":"M. Lechner, “Learning verifiable representations,” Institute of Science and Technology Austria, 2022.","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>","ista":"Lechner M. 2022. Learning verifiable representations. Institute of Science and Technology Austria.","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>","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>."},"publication_status":"published","author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2022-05-17T15:19:39Z","publication_identifier":{"isbn":["978-3-99078-017-6"]},"language":[{"iso":"eng"}],"month":"05","oa":1,"degree_awarded":"PhD","title":"Learning verifiable representations","tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"ddc":["004"],"date_updated":"2026-08-19T09:28:05Z","related_material":{"record":[{"id":"11366","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"7808","relation":"part_of_dissertation"},{"id":"10666","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10667","status":"public"},{"id":"10665","status":"public","relation":"part_of_dissertation"}]},"_id":"11362","OA_place":"publisher","ec_funded":1},{"acknowledgement":"We are grateful to Mikhail Borovoi, Zeev Rudnick and Olivier Wienberg for their interest in our\r\nwork. We would like to address our gratitude to Ulrich Derenthal for his generous support at Leibniz Universitat Hannover. We are in debt to Tim Browning for an enlightening discussion and to the anonymous referees for critical comments, which lead to overall improvements of various preliminary versions of this paper. Part of this work was carried out and reported during a visit to the University of Science and Technology of China. We thank Yongqi Liang for offering warm hospitality. The first author was supported by a Humboldt-Forschungsstipendium. The second author was supported by grant DE 1646/4-2 of the Deutsche Forschungsgemeinschaft.","_id":"10765","date_updated":"2026-08-19T13:00:41Z","intvolume":"       398","title":"Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics","external_id":{"isi":["000792517300014"],"arxiv":["2003.07287"]},"volume":398,"supplementarymaterial":"no","month":"03","oa":1,"publication_identifier":{"issn":["0001-8708"],"eissn":["1090-2082"]},"language":[{"iso":"eng"}],"author":[{"full_name":"Cao, Yang","last_name":"Cao","first_name":"Yang"},{"first_name":"Zhizhong","id":"21f1b52f-2fd1-11eb-a347-a4cdb9b18a51","full_name":"Huang, Zhizhong","last_name":"Huang"}],"citation":{"apa":"Cao, Y., &#38; Huang, Z. (2022). Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2022.108236\">https://doi.org/10.1016/j.aim.2022.108236</a>","ista":"Cao Y, Huang Z. 2022. Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. Advances in Mathematics. 398(3), 108236.","ieee":"Y. Cao and Z. Huang, “Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics,” <i>Advances in Mathematics</i>, vol. 398, no. 3. Elsevier, 2022.","short":"Y. Cao, Z. Huang, Advances in Mathematics 398 (2022).","mla":"Cao, Yang, and Zhizhong Huang. “Arithmetic Purity of the Hardy-Littlewood Property and Geometric Sieve for Affine Quadrics.” <i>Advances in Mathematics</i>, vol. 398, no. 3, 108236, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108236\">10.1016/j.aim.2022.108236</a>.","chicago":"Cao, Yang, and Zhizhong Huang. “Arithmetic Purity of the Hardy-Littlewood Property and Geometric Sieve for Affine Quadrics.” <i>Advances in Mathematics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.aim.2022.108236\">https://doi.org/10.1016/j.aim.2022.108236</a>.","ama":"Cao Y, Huang Z. Arithmetic purity of the Hardy-Littlewood property and geometric sieve for affine quadrics. <i>Advances in Mathematics</i>. 2022;398(3). doi:<a href=\"https://doi.org/10.1016/j.aim.2022.108236\">10.1016/j.aim.2022.108236</a>"},"publication_status":"published","article_number":"108236","publication":"Advances in Mathematics","article_processing_charge":"No","researchdata_availability":"no","year":"2022","oa_version":"Preprint","arxiv":1,"corr_author":"1","date_published":"2022-03-26T00:00:00Z","quality_controlled":"1","scopus_import":"1","date_created":"2022-02-20T23:01:30Z","publisher":"Elsevier","issue":"3","type":"journal_article","article_type":"original","department":[{"_id":"TiBr"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1016/j.aim.2022.108236","isi":1,"day":"26","abstract":[{"lang":"eng","text":"We establish the Hardy-Littlewood property (à la Borovoi-Rudnick) for Zariski open subsets in affine quadrics of the form q(x1,...,xn)=m, where q is a non-degenerate integral quadratic form in  n>3 variables and m is a non-zero integer. This gives asymptotic formulas for the density of integral points taking coprime polynomial values, which is a quantitative version of the arithmetic purity of strong approximation property off infinity for affine quadrics."}],"main_file_link":[{"url":"https://arxiv.org/abs/2003.07287","open_access":"1"}],"das_tickbox":"0","status":"public"},{"scopus_import":"1","publisher":"Institute of Mathematics","date_created":"2024-05-28T13:39:26Z","date_published":"2022-08-22T00:00:00Z","quality_controlled":"1","issue":"4","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.4064/aa210430-1-7","article_type":"original","department":[{"_id":"TiBr"}],"isi":1,"day":"22","das_tickbox":"0","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2104.14946"}],"abstract":[{"lang":"eng","text":"We compare the Manin-type conjecture for Campana points recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado with an alternative prediction of Browning and Van Valckenborgh in the special case of the orbifold (P1,D), where D=1/2[0]+1/2[1]+1/2[∞]. We find that the two predicted leading constants do not agree, and we discuss whether thin sets could explain this discrepancy. Motivated by this, we provide a counterexample to the Manin-type conjecture for Campana points, by considering orbifolds corresponding to squareful values of binary quadratic forms."}],"related_material":{"record":[{"relation":"earlier_version","id":"12077","status":"public"}]},"date_updated":"2026-08-19T12:54:59Z","_id":"17058","intvolume":"       204","title":"On the leading constant in the Manin-type conjecture for Campana points","month":"08","supplementarymaterial":"no","volume":204,"oa":1,"external_id":{"isi":["000844789100001"],"arxiv":["2104.14946"]},"author":[{"first_name":"Alec L","orcid":"0000-0002-1812-2810","id":"440EB050-F248-11E8-B48F-1D18A9856A87","full_name":"Shute, Alec L","last_name":"Shute"}],"publication_identifier":{"eissn":["1730-6264"],"issn":["0065-1036"]},"language":[{"iso":"eng"}],"publication":"Acta Arithmetica","citation":{"ama":"Shute AL. On the leading constant in the Manin-type conjecture for Campana points. <i>Acta Arithmetica</i>. 2022;204(4):317-346. doi:<a href=\"https://doi.org/10.4064/aa210430-1-7\">10.4064/aa210430-1-7</a>","chicago":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>Acta Arithmetica</i>. Institute of Mathematics, 2022. <a href=\"https://doi.org/10.4064/aa210430-1-7\">https://doi.org/10.4064/aa210430-1-7</a>.","mla":"Shute, Alec L. “On the Leading Constant in the Manin-Type Conjecture for Campana Points.” <i>Acta Arithmetica</i>, vol. 204, no. 4, Institute of Mathematics, 2022, pp. 317–46, doi:<a href=\"https://doi.org/10.4064/aa210430-1-7\">10.4064/aa210430-1-7</a>.","ieee":"A. L. Shute, “On the leading constant in the Manin-type conjecture for Campana points,” <i>Acta Arithmetica</i>, vol. 204, no. 4. Institute of Mathematics, pp. 317–346, 2022.","short":"A.L. Shute, Acta Arithmetica 204 (2022) 317–346.","ista":"Shute AL. 2022. On the leading constant in the Manin-type conjecture for Campana points. Acta Arithmetica. 204(4), 317–346.","apa":"Shute, A. L. (2022). On the leading constant in the Manin-type conjecture for Campana points. <i>Acta Arithmetica</i>. Institute of Mathematics. <a href=\"https://doi.org/10.4064/aa210430-1-7\">https://doi.org/10.4064/aa210430-1-7</a>"},"publication_status":"published","year":"2022","article_processing_charge":"No","researchdata_availability":"no","corr_author":"1","oa_version":"Preprint","arxiv":1,"page":"317-346"},{"ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work.","_id":"12109","related_material":{"record":[{"relation":"dissertation_contains","id":"20203","status":"public"},{"status":"public","id":"22684","relation":"dissertation_contains"}]},"date_updated":"2026-08-27T11:42:43Z","intvolume":"         6","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"external_id":{"isi":["000908384800001"],"arxiv":["2209.01889"]},"volume":6,"month":"12","oa":1,"publication_identifier":{"eissn":["2475-9953"]},"language":[{"iso":"eng"}],"author":[{"full_name":"Pertl, Felix","last_name":"Pertl","first_name":"Felix","orcid":"0000-0003-0463-5794","id":"6313aec0-15b2-11ec-abd3-ed67d16139af"},{"full_name":"Sobarzo Ponce, Juan Carlos A","last_name":"Sobarzo Ponce","first_name":"Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425"},{"first_name":"Lubuna B","orcid":"0000-0001-7180-6050","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","full_name":"Shafeek, Lubuna B","last_name":"Shafeek"},{"last_name":"Cramer","full_name":"Cramer, Tobias","first_name":"Tobias"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R","orcid":"0000-0002-2299-3176","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"}],"citation":{"apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., &#38; Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>","ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605.","ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” <i>Physical Review Materials</i>, vol. 6, no. 12. American Physical Society, 2022.","short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>.","ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. <i>Physical Review Materials</i>. 2022;6(12). doi:<a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">10.1103/PhysRevMaterials.6.125605</a>","chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” <i>Physical Review Materials</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevMaterials.6.125605\">https://doi.org/10.1103/PhysRevMaterials.6.125605</a>."},"article_number":"125605","publication_status":"published","publication":"Physical Review Materials","article_processing_charge":"No","year":"2022","project":[{"grant_number":"949120","call_identifier":"H2020","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"}],"arxiv":1,"oa_version":"Preprint","corr_author":"1","date_published":"2022-12-29T00:00:00Z","quality_controlled":"1","scopus_import":"1","date_created":"2023-01-08T23:00:53Z","publisher":"American Physical Society","issue":"12","type":"journal_article","article_type":"original","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1103/PhysRevMaterials.6.125605","isi":1,"day":"29","abstract":[{"text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2209.01889"}],"status":"public"},{"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"author":[{"full_name":"Kim, Olena","last_name":"Kim","orcid":"0000-0003-2344-1039","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-04-20T22:30:03Z","citation":{"ieee":"O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022.","short":"O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022.","ista":"Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria.","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>","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>","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>."},"publication_status":"published","article_processing_charge":"No","year":"2022","project":[{"call_identifier":"H2020","grant_number":"708497","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692","call_identifier":"H2020"},{"grant_number":"W01205","call_identifier":"FWF","name":"Zellkommunikation in Gesundheit und Krankheit","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits"}],"page":"132","oa_version":"Published Version","corr_author":"1","OA_place":"publisher","ec_funded":1,"_id":"11196","date_updated":"2026-06-18T10:49:27Z","related_material":{"record":[{"status":"public","id":"7473","relation":"part_of_dissertation"},{"id":"11222","status":"public","relation":"part_of_dissertation"}]},"ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"}],"title":"Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses","month":"04","oa":1,"day":"20","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n"}],"supervisor":[{"first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas"}],"status":"public","date_published":"2022-04-20T00:00:00Z","publisher":"Institute of Science and Technology Austria","date_created":"2022-04-20T09:47:12Z","type":"dissertation","file":[{"embargo":"2023-04-19","file_name":"Olena_KIM_thesis_final.pdf","checksum":"1616a8bf6f13a57c892dac873dcd0936","creator":"okim","relation":"main_file","access_level":"open_access","file_id":"11220","file_size":21273537,"date_created":"2022-04-20T14:21:56Z","content_type":"application/pdf","date_updated":"2023-04-20T22:30:03Z"},{"file_id":"11221","file_size":59248569,"access_level":"closed","creator":"okim","relation":"source_file","file_name":"KIM_thesis_final.zip","checksum":"1acb433f98dc42abb0b4b0cbb0c4b918","date_updated":"2023-04-20T22:30:03Z","embargo_to":"open_access","content_type":"application/x-zip-compressed","date_created":"2022-04-20T14:22:56Z"}],"has_accepted_license":"1","department":[{"_id":"PeJo"},{"_id":"GradSch"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:11196"},{"publication_status":"published","citation":{"ieee":"C. Artner, “Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature,” Institute of Science and Technology Austria, 2022.","short":"C. Artner, Modulation of Auxin Transport via ZF Proteins Adjust Plant Response to High Ambient Temperature, Institute of Science and Technology Austria, 2022.","apa":"Artner, C. (2022). <i>Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11879\">https://doi.org/10.15479/at:ista:11879</a>","ista":"Artner C. 2022. Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature. Institute of Science and Technology Austria.","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>.","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>."},"file_date_updated":"2023-09-09T22:30:03Z","author":[{"full_name":"Artner, Christina","last_name":"Artner","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-022-0"],"issn":["2663-337X"]},"oa_version":"Published Version","corr_author":"1","page":"128","project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"year":"2022","article_processing_charge":"No","date_updated":"2026-04-07T14:30:39Z","_id":"11879","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).","OA_place":"publisher","oa":1,"month":"08","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"SSU"}],"title":"Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature","degree_awarded":"PhD","ddc":["580"],"day":"17","keyword":["high ambient temperature","auxin","PINs","Zinc-Finger proteins","thermomorphogenesis","stress"],"status":"public","supervisor":[{"last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva"}],"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."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","publisher":"Institute of Science and Technology Austria","date_created":"2022-08-17T07:58:53Z","date_published":"2022-08-17T00:00:00Z","doi":"10.15479/at:ista:11879","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"EvBe"}],"file":[{"access_level":"open_access","file_id":"11907","file_size":11113608,"embargo":"2023-09-08","checksum":"a2c2fdc28002538840490bfa6a08b2cb","file_name":"ChristinaArtner_PhD_Thesis_2022.pdf","relation":"main_file","creator":"cartner","content_type":"application/pdf","date_updated":"2023-09-09T22:30:03Z","date_created":"2022-08-17T12:08:49Z"},{"file_id":"11908","file_size":19097730,"access_level":"closed","checksum":"66b461c074b815fbe63481b3f46a9f43","file_name":"ChristinaArtner_PhD_Thesis_2022.7z","relation":"source_file","creator":"cartner","embargo_to":"open_access","content_type":"application/octet-stream","date_updated":"2023-09-09T22:30:03Z","date_created":"2022-08-17T12:08:59Z"}]}]