[{"intvolume":"        13","publisher":"American Physical Society","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaSe"}],"scopus_import":"1","date_created":"2023-04-16T22:01:09Z","date_published":"2023-03-07T00:00:00Z","external_id":{"isi":["000957625700001"]},"date_updated":"2023-08-01T14:11:28Z","publication":"Physical Review X","article_type":"original","article_number":"011033","oa":1,"year":"2023","file":[{"success":1,"date_updated":"2023-04-17T08:36:53Z","access_level":"open_access","content_type":"application/pdf","checksum":"ee060cea609af79bba7af74b1ce28078","file_name":"2023_PhysReviewX_Ljubotina.pdf","relation":"main_file","creator":"dernst","file_size":1958523,"file_id":"12845","date_created":"2023-04-17T08:36:53Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","volume":13,"has_accepted_license":"1","file_date_updated":"2023-04-17T08:36:53Z","month":"03","ddc":["530"],"day":"07","citation":{"chicago":"Ljubotina, Marko, Jean Yves Desaules, Maksym Serbyn, and Zlatko Papić. “Superdiffusive Energy Transport in Kinetically Constrained Models.” <i>Physical Review X</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevX.13.011033\">https://doi.org/10.1103/PhysRevX.13.011033</a>.","mla":"Ljubotina, Marko, et al. “Superdiffusive Energy Transport in Kinetically Constrained Models.” <i>Physical Review X</i>, vol. 13, no. 1, 011033, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.011033\">10.1103/PhysRevX.13.011033</a>.","apa":"Ljubotina, M., Desaules, J. Y., Serbyn, M., &#38; Papić, Z. (2023). Superdiffusive energy transport in kinetically constrained models. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.13.011033\">https://doi.org/10.1103/PhysRevX.13.011033</a>","ieee":"M. Ljubotina, J. Y. Desaules, M. Serbyn, and Z. Papić, “Superdiffusive energy transport in kinetically constrained models,” <i>Physical Review X</i>, vol. 13, no. 1. American Physical Society, 2023.","ista":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. 2023. Superdiffusive energy transport in kinetically constrained models. Physical Review X. 13(1), 011033.","ama":"Ljubotina M, Desaules JY, Serbyn M, Papić Z. Superdiffusive energy transport in kinetically constrained models. <i>Physical Review X</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.011033\">10.1103/PhysRevX.13.011033</a>","short":"M. Ljubotina, J.Y. Desaules, M. Serbyn, Z. Papić, Physical Review X 13 (2023)."},"oa_version":"Published Version","project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"publication_identifier":{"eissn":["2160-3308"]},"ec_funded":1,"publication_status":"published","acknowledgement":"We would like to thank Alexios Michailidis, Sarang Gopalakrishnan, and Achilleas Lazarides for useful comments. M. L. and M. S. acknowledge support by the European Research Council under the European Union’s Horizon 2020 research and innovation program (Grant\r\nAgreement No. 850899). J.-Y. D. and Z. P. acknowledge support by EPSRC Grant No. EP/R513258/1 and the Leverhulme Trust Research Leadership Grant No. RL2019-015. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. M. S., M. L., and Z. P. acknowledge support by the Erwin Schrödinger International Institute for Mathematics and\r\nPhysics. M. L. and M. S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD\r\nsimulations were performed using the ITENSOR library [54].","status":"public","_id":"12839","author":[{"full_name":"Ljubotina, Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko"},{"full_name":"Desaules, Jean Yves","last_name":"Desaules","first_name":"Jean Yves"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"}],"title":"Superdiffusive energy transport in kinetically constrained models","doi":"10.1103/PhysRevX.13.011033","issue":"1","abstract":[{"lang":"eng","text":"Universal nonequilibrium properties of isolated quantum systems are typically probed by studying transport of conserved quantities, such as charge or spin, while transport of energy has received considerably less attention. Here, we study infinite-temperature energy transport in the kinetically constrained PXP model describing Rydberg atom quantum simulators. Our state-of-the-art numerical simulations, including exact diagonalization and time-evolving block decimation methods, reveal the existence of two distinct transport regimes. At moderate times, the energy-energy correlation function displays periodic oscillations due to families of eigenstates forming different su(2) representations hidden within the spectrum. These families of eigenstates generalize the quantum many-body scarred states found in previous works and leave an imprint on the infinite-temperature energy transport. At later times, we observe a long-lived superdiffusive transport regime that we attribute to the proximity of a nearby integrable point. While generic strong deformations of the PXP model indeed restore diffusive transport, adding a strong chemical potential intriguingly gives rise to a well-converged superdiffusive exponent z≈3/2. Our results suggest constrained models to be potential hosts of novel transport regimes and call for developing an analytic understanding of their energy transport."}]},{"article_number":"2303.14555","acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","status":"public","publication_status":"submitted","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"date_updated":"2023-04-25T06:51:21Z","publication":"arXiv","doi":"10.48550/arXiv.2303.14555","year":"2023","abstract":[{"text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons.","lang":"eng"}],"_id":"12846","author":[{"full_name":"Chern, Albert","last_name":"Chern","first_name":"Albert"},{"full_name":"Ishida, Sadashige","last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige"}],"oa":1,"title":"Area formula for spherical polygons via prequantization","type":"preprint","language":[{"iso":"eng"}],"article_processing_charge":"No","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/2303.14555","open_access":"1"}],"oa_version":"Preprint","date_created":"2023-04-18T19:16:06Z","external_id":{"arxiv":["2303.14555"]},"date_published":"2023-03-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","day":"25","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"citation":{"ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” <i>arXiv</i>. .","apa":"Chern, A., &#38; Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2303.14555\">https://doi.org/10.48550/arXiv.2303.14555</a>","short":"A. Chern, S. Ishida, ArXiv (n.d.).","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2303.14555\">10.48550/arXiv.2303.14555</a>","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2303.14555\">https://doi.org/10.48550/arXiv.2303.14555</a>.","mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” <i>ArXiv</i>, 2303.14555, doi:<a href=\"https://doi.org/10.48550/arXiv.2303.14555\">10.48550/arXiv.2303.14555</a>."}},{"day":"20","citation":{"ama":"Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 13994. Springer Nature; 2023:535-540. doi:<a href=\"https://doi.org/10.1007/978-3-031-30820-8_32\">10.1007/978-3-031-30820-8_32</a>","ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540.","ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Paris, France, 2023, vol. 13994, pp. 535–540.","apa":"Chalupa, M., &#38; Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30820-8_32\">https://doi.org/10.1007/978-3-031-30820-8_32</a>","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 13994:535–40. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30820-8_32\">https://doi.org/10.1007/978-3-031-30820-8_32</a>.","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:<a href=\"https://doi.org/10.1007/978-3-031-30820-8_32\">10.1007/978-3-031-30820-8_32</a>."},"file_date_updated":"2023-04-25T06:58:36Z","month":"04","ddc":["000"],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"2023_LNCS_Chalupa.pdf","relation":"main_file","creator":"dernst","file_size":16096413,"success":1,"date_updated":"2023-04-25T06:58:36Z","access_level":"open_access","content_type":"application/pdf","checksum":"120d2c2a38384058ad0630fdf8288312","file_id":"12864","date_created":"2023-04-25T06:58:36Z"}],"has_accepted_license":"1","volume":13994,"article_processing_charge":"No","author":[{"id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","first_name":"Marek","full_name":"Chalupa, Marek","last_name":"Chalupa"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724"}],"title":"Bubaak: Runtime monitoring of program verifiers","_id":"12854","abstract":[{"lang":"eng","text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP  2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition."}],"doi":"10.1007/978-3-031-30820-8_32","publication_identifier":{"isbn":["9783031308192"],"eisbn":["9783031308208"],"issn":["0302-9743"],"eissn":["1611-3349"]},"project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","status":"public","publication_status":"published","ec_funded":1,"department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-04-20T00:00:00Z","date_created":"2023-04-20T08:22:53Z","intvolume":"     13994","publisher":"Springer Nature","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"year":"2023","alternative_title":["LNCS"],"publication":"Tools and Algorithms for the Construction and Analysis of Systems","date_updated":"2023-04-25T07:02:43Z","page":"535-540"},{"has_accepted_license":"1","volume":13991,"article_processing_charge":"No","file":[{"date_created":"2023-04-25T07:16:36Z","file_id":"12865","checksum":"17a7c8e08be609cf2408d37ea55e322c","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-04-25T07:16:36Z","success":1,"creator":"dernst","relation":"main_file","file_size":580828,"file_name":"2023_LNCS_ChalupaM.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","conference":{"end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22","name":"FASE: Fundamental Approaches to Software Engineering"},"citation":{"ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: <i>Fundamental Approaches to Software Engineering</i>. Vol 13991. Springer Nature; 2023:260-281. doi:<a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">10.1007/978-3-031-30826-0_15</a>","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in <i>Fundamental Approaches to Software Engineering</i>, Paris, France, 2023, vol. 13991, pp. 260–281.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., &#38; Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In <i>Fundamental Approaches to Software Engineering</i> (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">https://doi.org/10.1007/978-3-031-30826-0_15</a>","mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” <i>Fundamental Approaches to Software Engineering</i>, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:<a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">10.1007/978-3-031-30826-0_15</a>.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In <i>Fundamental Approaches to Software Engineering</i>, 13991:260–81. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30826-0_15\">https://doi.org/10.1007/978-3-031-30826-0_15</a>."},"day":"20","file_date_updated":"2023-04-25T07:16:36Z","ddc":["000"],"month":"04","publication_status":"published","status":"public","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","ec_funded":1,"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783031308260"],"isbn":["9783031308253"]},"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"doi":"10.1007/978-3-031-30826-0_15","title":"Vamos: Middleware for best-effort third-party monitoring","author":[{"first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian","full_name":"Mühlböck, Fabian","last_name":"Mühlböck","orcid":"0000-0003-1548-0177"},{"first_name":"Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","last_name":"Muroya Lei","full_name":"Muroya Lei, Stefanie"},{"orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"_id":"12856","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","publisher":"Springer Nature","intvolume":"     13991","date_published":"2023-04-20T00:00:00Z","date_created":"2023-04-20T08:29:42Z","department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"12407"}]},"page":"260-281","publication":"Fundamental Approaches to Software Engineering","date_updated":"2023-04-25T07:19:07Z","alternative_title":["LNCS"],"year":"2023","oa":1},{"month":"10","citation":{"short":"S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776.","ama":"Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:2738-2776.","ista":"Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 2738–2776.","ieee":"S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, HI, United States, 2023, vol. 202, pp. 2738–2776.","apa":"Bombari, S., Kiyani, S., &#38; Mondelli, M. (2023). Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.","chicago":"Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:2738–76. ML Research Press, 2023.","mla":"Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 2738–76."},"day":"27","oa_version":"Preprint","conference":{"name":"ICML: International Conference on Machine Learning","location":"Honolulu, HI, United States","start_date":"2023-07-23","end_date":"2023-07-29"},"arxiv":1,"article_processing_charge":"No","volume":202,"_id":"12859","title":"Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels","author":[{"id":"ca726dda-de17-11ea-bc14-f9da834f63aa","first_name":"Simone","full_name":"Bombari, Simone","last_name":"Bombari"},{"id":"f5a2b424-e339-11ed-8435-ff3b4fe70cf8","first_name":"Shayan","full_name":"Kiyani, Shayan","last_name":"Kiyani"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020"}],"abstract":[{"lang":"eng","text":"Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this \"universal\" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an \"interaction matrix\", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10)."}],"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"acknowledgement":"Simone Bombari and Marco Mondelli were partially supported by the 2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for helpful discussions.\r\n","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"MaMo"}],"date_created":"2023-04-23T16:11:03Z","external_id":{"arxiv":["2302.01629"]},"date_published":"2023-10-27T00:00:00Z","publisher":"ML Research Press","intvolume":"       202","main_file_link":[{"url":"https://arxiv.org/abs/2302.01629","open_access":"1"}],"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"alternative_title":["PMLR"],"year":"2023","date_updated":"2024-09-10T13:03:19Z","publication":"Proceedings of the 40th International Conference on Machine Learning","page":"2738-2776","related_material":{"link":[{"relation":"software","url":"https://github.com/simone-bombari/beyond-universal-robustness"}]}},{"author":[{"last_name":"Schmid","full_name":"Schmid, Laura","first_name":"Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6978-7329"},{"last_name":"Ekbatani","full_name":"Ekbatani, Farbod","first_name":"Farbod"},{"orcid":"0000-0001-5116-955X","last_name":"Hilbe","full_name":"Hilbe, Christian","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}],"title":"Quantitative assessment can stabilize indirect reciprocity under imperfect information","_id":"12861","abstract":[{"lang":"eng","text":"The field of indirect reciprocity investigates how social norms can foster cooperation when individuals continuously monitor and assess each other’s social interactions. By adhering to certain social norms, cooperating individuals can improve their reputation and, in turn, receive benefits from others. Eight social norms, known as the “leading eight,\" have been shown to effectively promote the evolution of cooperation as long as information is public and reliable. These norms categorize group members as either ’good’ or ’bad’. In this study, we examine a scenario where individuals instead assign nuanced reputation scores to each other, and only cooperate with those whose reputation exceeds a certain threshold. We find both analytically and through simulations that such quantitative assessments are error-correcting, thus facilitating cooperation in situations where information is private and unreliable. Moreover, our results identify four specific norms that are robust to such conditions, and may be relevant for helping to sustain cooperation in natural populations."}],"doi":"10.1038/s41467-023-37817-x","publication_identifier":{"eissn":["2041-1723"]},"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"publication_status":"published","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.). L.S. received additional partial support by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and also thanks the support by the Stochastic Analysis and Application Research Center (SAARC) under National Research Foundation of Korea grant NRF-2019R1A5A1028324. The authors additionally thank Stefan Schmid for providing access to his lab infrastructure at the University of Vienna for the purpose of collecting simulation data.","status":"public","ec_funded":1,"day":"12","citation":{"chicago":"Schmid, Laura, Farbod Ekbatani, Christian Hilbe, and Krishnendu Chatterjee. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37817-x\">https://doi.org/10.1038/s41467-023-37817-x</a>.","mla":"Schmid, Laura, et al. “Quantitative Assessment Can Stabilize Indirect Reciprocity under Imperfect Information.” <i>Nature Communications</i>, vol. 14, 2086, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37817-x\">10.1038/s41467-023-37817-x</a>.","apa":"Schmid, L., Ekbatani, F., Hilbe, C., &#38; Chatterjee, K. (2023). Quantitative assessment can stabilize indirect reciprocity under imperfect information. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37817-x\">https://doi.org/10.1038/s41467-023-37817-x</a>","ieee":"L. Schmid, F. Ekbatani, C. Hilbe, and K. Chatterjee, “Quantitative assessment can stabilize indirect reciprocity under imperfect information,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","short":"L. Schmid, F. Ekbatani, C. Hilbe, K. Chatterjee, Nature Communications 14 (2023).","ama":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. Quantitative assessment can stabilize indirect reciprocity under imperfect information. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37817-x\">10.1038/s41467-023-37817-x</a>","ista":"Schmid L, Ekbatani F, Hilbe C, Chatterjee K. 2023. Quantitative assessment can stabilize indirect reciprocity under imperfect information. Nature Communications. 14, 2086."},"file_date_updated":"2023-04-25T09:13:53Z","ddc":["000"],"pmid":1,"month":"04","oa_version":"Published Version","file":[{"date_created":"2023-04-25T09:13:53Z","file_id":"12868","checksum":"a4b3b7b36fbef068cabf4fb99501fef6","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-04-25T09:13:53Z","success":1,"relation":"main_file","creator":"dernst","file_size":1786475,"file_name":"2023_NatureComm_Schmid.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":14,"oa":1,"year":"2023","publication":"Nature Communications","date_updated":"2025-07-14T09:09:52Z","article_type":"original","article_number":"2086","department":[{"_id":"KrCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2023-04-12T00:00:00Z","external_id":{"isi":["001003644100020"],"pmid":["37045828"]},"scopus_import":"1","date_created":"2023-04-23T22:01:03Z","intvolume":"        14","publisher":"Springer Nature","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article"},{"date_updated":"2023-08-01T14:15:16Z","publication":"PLoS Computational Biology","article_number":"e1010983","article_type":"original","related_material":{"link":[{"relation":"software","url":"https://github.com/shervinsafavi/gpla.git"}]},"oa":1,"year":"2023","publisher":"Public Library of Science","intvolume":"        19","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JoCs"}],"date_created":"2023-04-23T22:01:03Z","scopus_import":"1","external_id":{"isi":["000962668700002"]},"date_published":"2023-04-01T00:00:00Z","publication_identifier":{"eissn":["1553-7358"]},"status":"public","acknowledgement":"We thank Britni Crocker for help with preprocessing of the data and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support; Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ","publication_status":"published","_id":"12862","title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","author":[{"first_name":"Shervin","full_name":"Safavi, Shervin","last_name":"Safavi"},{"first_name":"Theofanis I.","last_name":"Panagiotaropoulos","full_name":"Panagiotaropoulos, Theofanis I."},{"first_name":"Vishal","full_name":"Kapoor, Vishal","last_name":"Kapoor"},{"full_name":"Ramirez Villegas, Juan F","last_name":"Ramirez Villegas","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","first_name":"Juan F"},{"last_name":"Logothetis","full_name":"Logothetis, Nikos K.","first_name":"Nikos K."},{"full_name":"Besserve, Michel","last_name":"Besserve","first_name":"Michel"}],"doi":"10.1371/journal.pcbi.1010983","abstract":[{"lang":"eng","text":"Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings."}],"issue":"4","file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"edeb9d09f3e41ba7c0251308b9e372e7","success":1,"date_updated":"2023-04-25T08:59:18Z","file_name":"2023_PLoSCompBio_Safavi.pdf","creator":"dernst","relation":"main_file","file_size":4737671,"file_id":"12867","date_created":"2023-04-25T08:59:18Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","volume":19,"has_accepted_license":"1","file_date_updated":"2023-04-25T08:59:18Z","month":"04","ddc":["570"],"citation":{"ama":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. <i>PLoS Computational Biology</i>. 2023;19(4). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">10.1371/journal.pcbi.1010983</a>","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023).","ista":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.","ieee":"S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N. K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits with Generalized Phase Locking Analysis,” <i>PLoS Computational Biology</i>, vol. 19, no. 4. Public Library of Science, 2023.","apa":"Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F., Logothetis, N. K., &#38; Besserve, M. (2023). Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">https://doi.org/10.1371/journal.pcbi.1010983</a>","chicago":"Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” <i>PLoS Computational Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">https://doi.org/10.1371/journal.pcbi.1010983</a>.","mla":"Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” <i>PLoS Computational Biology</i>, vol. 19, no. 4, e1010983, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">10.1371/journal.pcbi.1010983</a>."},"day":"01","oa_version":"Published Version"},{"article_processing_charge":"No","volume":30,"oa_version":"None","month":"05","pmid":1,"day":"01","citation":{"mla":"Filipović Marijić, Vlatka, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>, vol. 30, Springer Nature, 2023, pp. 63510–21, doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>.","chicago":"Filipović Marijić, Vlatka, Nesrete Krasnici, Damir Valić, Damir Kapetanović, Irena Vardić Smrzlić, Maja Jordanova, Katerina Rebok, et al. “Pollution Impact on Metal and Biomarker Responses in Intestinal Cytosol of Freshwater Fish.” <i>Environmental Science and Pollution Research</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>.","ama":"Filipović Marijić V, Krasnici N, Valić D, et al. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. 2023;30:63510-63521. doi:<a href=\"https://doi.org/10.1007/s11356-023-26844-2\">10.1007/s11356-023-26844-2</a>","ista":"Filipović Marijić V, Krasnici N, Valić D, Kapetanović D, Vardić Smrzlić I, Jordanova M, Rebok K, Ramani S, Kostov V, Nastova R, Dragun Z. 2023. Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. Environmental Science and Pollution Research. 30, 63510–63521.","short":"V. Filipović Marijić, N. Krasnici, D. Valić, D. Kapetanović, I. Vardić Smrzlić, M. Jordanova, K. Rebok, S. Ramani, V. Kostov, R. Nastova, Z. Dragun, Environmental Science and Pollution Research 30 (2023) 63510–63521.","apa":"Filipović Marijić, V., Krasnici, N., Valić, D., Kapetanović, D., Vardić Smrzlić, I., Jordanova, M., … Dragun, Z. (2023). Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish. <i>Environmental Science and Pollution Research</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11356-023-26844-2\">https://doi.org/10.1007/s11356-023-26844-2</a>","ieee":"V. Filipović Marijić <i>et al.</i>, “Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish,” <i>Environmental Science and Pollution Research</i>, vol. 30. Springer Nature, pp. 63510–63521, 2023."},"acknowledgement":"The authors are grateful to Dr. Nevenka Mikac for the opportunity to perform metal measurements on HR ICP-MS. This research was funded by the Ministry of Science, Education and Sport of the Republic of Croatia (projects No. 098–0982934-2721 and 098–1782739-2749). The sampling was carried out as a part of two Croatian-Macedonian bilateral projects: “The assessment of availability and effects of metals on fish in the rivers under the impact of mining activities” and “Bacterial and parasitical communities of chub as indicators of the status of environment exposed to mining activities.”","status":"public","publication_status":"published","publication_identifier":{"issn":["0944-1344"],"eissn":["1614-7499"]},"doi":"10.1007/s11356-023-26844-2","abstract":[{"text":"In the present study, essential and nonessential metal content and biomarker responses were investigated in the intestine of fish collected from the areas polluted by mining. Our objective was to determine metal and biomarker levels in tissue responsible for dietary intake, which is rarely studied in water pollution research. The study was conducted in the Bregalnica River, reference location, and in the Zletovska and Kriva Rivers (the Republic of North Macedonia), which are directly influenced by the active mines Zletovo and Toranica, respectively. Biological responses were analyzed in Vardar chub (Squalius vardarensis; Karaman, 1928), using for the first time intestinal cytosol as a potentially toxic cell fraction, since metal sensitivity is mostly associated with cytosol. Cytosolic metal levels were higher in fish under the influence of mining (Tl, Li, Cs, Mo, Sr, Cd, Rb, and Cu in the Zletovska River and Cr, Pb, and Se in the Kriva River compared to the Bregalnica River in both seasons). The same trend was evident for total proteins, biomarkers of general stress, and metallothioneins, biomarkers of metal exposure, indicating cellular disturbances in the intestine, the primary site of dietary metal uptake. The association of cytosolic Cu and Cd at all locations pointed to similar pathways and homeostasis of these metallothionein-binding metals. Comparison with other indicator tissues showed that metal concentrations were higher in the intestine of fish from mining-affected areas than in the liver and gills. In general, these results indicated the importance of dietary metal pathways, and cytosolic metal fraction in assessing pollution impacts in freshwater ecosystems.","lang":"eng"}],"_id":"12863","author":[{"full_name":"Filipović Marijić, Vlatka","last_name":"Filipović Marijić","first_name":"Vlatka"},{"last_name":"Krasnici","full_name":"Krasnici, Nesrete","first_name":"Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745"},{"last_name":"Valić","full_name":"Valić, Damir","first_name":"Damir"},{"first_name":"Damir","last_name":"Kapetanović","full_name":"Kapetanović, Damir"},{"first_name":"Irena","full_name":"Vardić Smrzlić, Irena","last_name":"Vardić Smrzlić"},{"first_name":"Maja","last_name":"Jordanova","full_name":"Jordanova, Maja"},{"full_name":"Rebok, Katerina","last_name":"Rebok","first_name":"Katerina"},{"last_name":"Ramani","full_name":"Ramani, Sheriban","first_name":"Sheriban"},{"full_name":"Kostov, Vasil","last_name":"Kostov","first_name":"Vasil"},{"first_name":"Rodne","last_name":"Nastova","full_name":"Nastova, Rodne"},{"last_name":"Dragun","full_name":"Dragun, Zrinka","first_name":"Zrinka"}],"title":"Pollution impact on metal and biomarker responses in intestinal cytosol of freshwater fish","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"intvolume":"        30","publisher":"Springer Nature","scopus_import":"1","date_created":"2023-04-23T22:01:03Z","external_id":{"pmid":["37055686"],"isi":["000970917900012"]},"date_published":"2023-05-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LifeSc"}],"article_type":"original","page":"63510-63521","date_updated":"2023-10-04T11:23:10Z","publication":"Environmental Science and Pollution Research","year":"2023"},{"publisher":"Elsevier","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","citation":{"ista":"Currin C, Beyer C. 2023.Altered childhood brain development in autism and epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological Development and Physical Health, , 86–98.","short":"C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.","ama":"Currin C, Beyer C. Altered childhood brain development in autism and epilepsy. In: Halpern-Felsher B, ed. <i>Encyclopedia of Child and Adolescent Health</i>. 1st ed. Elsevier; 2023:86-98. doi:<a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">10.1016/b978-0-12-818872-9.00129-1</a>","ieee":"C. Currin and C. Beyer, “Altered childhood brain development in autism and epilepsy,” in <i>Encyclopedia of Child and Adolescent Health</i>, 1st ed., B. Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.","apa":"Currin, C., &#38; Beyer, C. (2023). Altered childhood brain development in autism and epilepsy. In B. Halpern-Felsher (Ed.), <i>Encyclopedia of Child and Adolescent Health</i> (1st ed., pp. 86–98). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">https://doi.org/10.1016/b978-0-12-818872-9.00129-1</a>","chicago":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” In <i>Encyclopedia of Child and Adolescent Health</i>, edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. <a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">https://doi.org/10.1016/b978-0-12-818872-9.00129-1</a>.","mla":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” <i>Encyclopedia of Child and Adolescent Health</i>, edited by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:<a href=\"https://doi.org/10.1016/b978-0-12-818872-9.00129-1\">10.1016/b978-0-12-818872-9.00129-1</a>."},"department":[{"_id":"TiVo"}],"day":"01","date_created":"2023-04-25T07:52:43Z","oa_version":"None","date_published":"2023-02-01T00:00:00Z","date_updated":"2023-04-25T09:25:40Z","edition":"1","publication_identifier":{"isbn":["9780128188736"]},"publication":"Encyclopedia of Child and Adolescent Health","page":"86-98","publication_status":"published","status":"public","_id":"12866","editor":[{"first_name":"Bonnie","last_name":"Halpern-Felsher","full_name":"Halpern-Felsher, Bonnie"}],"title":"Altered childhood brain development in autism and epilepsy","author":[{"full_name":"Currin, Christopher","last_name":"Currin","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","first_name":"Christopher","orcid":"0000-0002-4809-5059"},{"first_name":"Chad","last_name":"Beyer","full_name":"Beyer, Chad"}],"doi":"10.1016/b978-0-12-818872-9.00129-1","abstract":[{"lang":"eng","text":"Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation.\r\nDecades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain."}],"year":"2023","alternative_title":["Vol. 1: Biological Development and Physical Health"]},{"file_date_updated":"2023-04-26T12:30:06Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","day":"26","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"citation":{"mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. <i>Research Data for: A Stochastic Cellular Automaton Model of Culture Formation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>.","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>.","short":"F.R. Klausen, A.B. Lauritsen, (2023).","ama":"Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>","ista":"Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">10.15479/AT:ISTA:12869</a>.","ieee":"F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12869\">https://doi.org/10.15479/AT:ISTA:12869</a>"},"date_created":"2023-04-26T12:34:49Z","oa_version":"Published Version","date_published":"2023-04-26T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","file":[{"file_id":"12870","date_created":"2023-04-26T12:30:06Z","success":1,"date_updated":"2023-04-26T12:30:06Z","access_level":"open_access","content_type":"application/octet-stream","checksum":"85ede12d38bb8d944022a8cba4d719f5","file_name":"README.md","file_size":4567,"relation":"main_file","creator":"alaurits"},{"creator":"alaurits","file_size":732586731,"relation":"main_file","file_name":"simulations_era=10_flux_varied_europe.zip","date_updated":"2023-04-26T12:27:34Z","success":1,"content_type":"application/x-zip-compressed","checksum":"25bf79452ae895f9c8a20571a096b4c3","access_level":"open_access","date_created":"2023-04-26T12:27:34Z","file_id":"12871"},{"file_id":"12872","date_created":"2023-04-26T12:29:53Z","file_name":"simulations_era=10_flux_varied_torus.zip","file_size":1743893150,"relation":"main_file","creator":"alaurits","access_level":"open_access","content_type":"application/x-zip-compressed","checksum":"bca48d80ece73eb169aee7211a4a751a","success":1,"date_updated":"2023-04-26T12:29:53Z"},{"file_id":"12873","date_created":"2023-04-26T12:29:19Z","file_name":"simulations_era=10_R_varied_torus.zip","relation":"main_file","file_size":878391851,"creator":"alaurits","access_level":"open_access","checksum":"e77a655db15486a387a36362fbf0b665","content_type":"application/x-zip-compressed","success":1,"date_updated":"2023-04-26T12:29:19Z"},{"date_updated":"2023-04-26T12:30:05Z","success":1,"content_type":"application/x-zip-compressed","checksum":"8556406513adc4aa2e0417f46680f627","access_level":"open_access","relation":"main_file","file_size":201652478,"creator":"alaurits","file_name":"simulations_era=100.zip","date_created":"2023-04-26T12:30:05Z","file_id":"12874"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"publisher":"Institute of Science and Technology Austria","type":"research_data","article_processing_charge":"No","has_accepted_license":"1","_id":"12869","author":[{"first_name":"Frederik Ravn","full_name":"Klausen, Frederik Ravn","last_name":"Klausen"},{"orcid":"0000-0003-4476-2288","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard","first_name":"Asbjørn Bækgaard","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1"}],"oa":1,"title":"Research data for: A stochastic cellular automaton model of culture formation","doi":"10.15479/AT:ISTA:12869","year":"2023","abstract":[{"lang":"eng","text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage.  We first analyse the model  with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. "}],"date_updated":"2023-11-13T07:47:29Z","status":"public","acknowledgement":"FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ","related_material":{"record":[{"status":"for_moderation","relation":"used_in_publication","id":"14505"},{"id":"12890","status":"public","relation":"used_in_publication"}]}},{"department":[{"_id":"ToHe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2023-04-03T00:00:00Z","external_id":{"isi":["000976610800001"],"pmid":["37004199"]},"date_created":"2023-04-30T22:01:05Z","scopus_import":"1","publisher":"Oxford Academic","intvolume":"        39","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","oa":1,"year":"2023","publication":"Bioinformatics","date_updated":"2023-08-01T14:27:28Z","related_material":{"link":[{"url":"https://doi.org/10.5281/zenodo.7688740","relation":"software"}]},"article_number":"btad158","article_type":"original","citation":{"mla":"Beneš, Nikola, et al. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” <i>Bioinformatics</i>, vol. 39, no. 4, btad158, Oxford Academic, 2023, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad158\">10.1093/bioinformatics/btad158</a>.","chicago":"Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “Boolean Network Sketches: A Unifying Framework for Logical Model Inference.” <i>Bioinformatics</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad158\">https://doi.org/10.1093/bioinformatics/btad158</a>.","ista":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2023. Boolean network sketches: A unifying framework for logical model inference. Bioinformatics. 39(4), btad158.","ama":"Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. Boolean network sketches: A unifying framework for logical model inference. <i>Bioinformatics</i>. 2023;39(4). doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad158\">10.1093/bioinformatics/btad158</a>","short":"N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, Bioinformatics 39 (2023).","apa":"Beneš, N., Brim, L., Huvar, O., Pastva, S., &#38; Šafránek, D. (2023). Boolean network sketches: A unifying framework for logical model inference. <i>Bioinformatics</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/bioinformatics/btad158\">https://doi.org/10.1093/bioinformatics/btad158</a>","ieee":"N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “Boolean network sketches: A unifying framework for logical model inference,” <i>Bioinformatics</i>, vol. 39, no. 4. Oxford Academic, 2023."},"day":"03","file_date_updated":"2023-05-02T07:39:04Z","month":"04","pmid":1,"ddc":["000"],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2023-05-02T07:39:04Z","file_id":"12886","date_updated":"2023-05-02T07:39:04Z","success":1,"checksum":"2cb90ddf781baefddf47eac4b54e2a03","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":478740,"file_name":"2023_Bioinformatics_Benes.pdf"}],"has_accepted_license":"1","article_processing_charge":"No","volume":39,"title":"Boolean network sketches: A unifying framework for logical model inference","author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"first_name":"Luboš","full_name":"Brim, Luboš","last_name":"Brim"},{"first_name":"Ondřej","last_name":"Huvar","full_name":"Huvar, Ondřej"},{"first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva","full_name":"Pastva, Samuel"},{"full_name":"Šafránek, David","last_name":"Šafránek","first_name":"David"}],"_id":"12876","abstract":[{"text":"Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only.\r\n\r\nResults: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data.","lang":"eng"}],"issue":"4","doi":"10.1093/bioinformatics/btad158","publication_identifier":{"eissn":["1367-4811"]},"project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"acknowledgement":"This work was partially supported by GACR [grant No. GA22-10845S]; and Grant Agency of Masaryk University [grant No. MUNI/G/1771/2020]. This work was partially supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie [Grant Agreement No. 101034413 to S.P.].","status":"public","publication_status":"published","ec_funded":1},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1905.00890"}],"intvolume":"       233","publisher":"Springer Nature","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"VaKa"}],"scopus_import":"1","date_created":"2023-04-30T22:01:05Z","date_published":"2023-08-01T00:00:00Z","external_id":{"isi":["000978887600001"],"arxiv":["1905.00890"]},"date_updated":"2023-10-04T11:25:37Z","publication":"Inventiones Mathematicae","article_type":"original","page":"829-901","oa":1,"year":"2023","arxiv":1,"article_processing_charge":"No","volume":233,"month":"08","day":"01","citation":{"mla":"De Simoi, Jacopo, et al. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” <i>Inventiones Mathematicae</i>, vol. 233, Springer Nature, 2023, pp. 829–901, doi:<a href=\"https://doi.org/10.1007/s00222-023-01191-8\">10.1007/s00222-023-01191-8</a>.","chicago":"De Simoi, Jacopo, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectral Determination of Analytic Chaotic Billiards with Axial Symmetries.” <i>Inventiones Mathematicae</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00222-023-01191-8\">https://doi.org/10.1007/s00222-023-01191-8</a>.","ieee":"J. De Simoi, V. Kaloshin, and M. Leguil, “Marked Length Spectral determination of analytic chaotic billiards with axial symmetries,” <i>Inventiones Mathematicae</i>, vol. 233. Springer Nature, pp. 829–901, 2023.","apa":"De Simoi, J., Kaloshin, V., &#38; Leguil, M. (2023). Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. <i>Inventiones Mathematicae</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00222-023-01191-8\">https://doi.org/10.1007/s00222-023-01191-8</a>","ama":"De Simoi J, Kaloshin V, Leguil M. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. <i>Inventiones Mathematicae</i>. 2023;233:829-901. doi:<a href=\"https://doi.org/10.1007/s00222-023-01191-8\">10.1007/s00222-023-01191-8</a>","short":"J. De Simoi, V. Kaloshin, M. Leguil, Inventiones Mathematicae 233 (2023) 829–901.","ista":"De Simoi J, Kaloshin V, Leguil M. 2023. Marked Length Spectral determination of analytic chaotic billiards with axial symmetries. Inventiones Mathematicae. 233, 829–901."},"oa_version":"Preprint","project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020"}],"publication_identifier":{"eissn":["1432-1297"],"issn":["0020-9910"]},"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"J.D.S. and M.L. have been partially supported by the NSERC Discovery grant, reference number 502617-2017. M.L. was also supported by the ERC project 692925 NUHGD of Sylvain Crovisier, by the ANR AAPG 2021 PRC CoSyDy: Conformally symplectic dynamics, beyond symplectic dynamics (ANR-CE40-0014), and by the ANR JCJC PADAWAN: Parabolic dynamics, bifurcations and wandering domains (ANR-21-CE40-0012). V.K. acknowledges partial support of the NSF grant DMS-1402164 and ERC Grant # 885707.","_id":"12877","author":[{"full_name":"De Simoi, Jacopo","last_name":"De Simoi","first_name":"Jacopo"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628"},{"first_name":"Martin","last_name":"Leguil","full_name":"Leguil, Martin"}],"title":"Marked Length Spectral determination of analytic chaotic billiards with axial symmetries","doi":"10.1007/s00222-023-01191-8","abstract":[{"lang":"eng","text":"We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table."}]},{"article_processing_charge":"No","volume":115,"oa_version":"None","day":"01","citation":{"mla":"Jiang, Lihui, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” <i>Plant Journal</i>, vol. 115, no. 1, Wiley, 2023, pp. 155–74, doi:<a href=\"https://doi.org/10.1111/tpj.16218\">10.1111/tpj.16218</a>.","chicago":"Jiang, Lihui, Baolin Yao, Xiaoyan Zhang, Lixia Wu, Qijing Fu, Yiting Zhao, Yuxin Cao, et al. “Salicylic Acid Inhibits Rice Endocytic Protein Trafficking Mediated by OsPIN3t and Clathrin to Affect Root Growth.” <i>Plant Journal</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/tpj.16218\">https://doi.org/10.1111/tpj.16218</a>.","ama":"Jiang L, Yao B, Zhang X, et al. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. <i>Plant Journal</i>. 2023;115(1):155-174. doi:<a href=\"https://doi.org/10.1111/tpj.16218\">10.1111/tpj.16218</a>","ista":"Jiang L, Yao B, Zhang X, Wu L, Fu Q, Zhao Y, Cao Y, Zhu R, Lu X, Huang W, Zhao J, Li K, Zhao S, Han L, Zhou X, Luo C, Zhu H, Yang J, Huang H, Zhu Z, He X, Friml J, Zhang Z, Liu C, Du Y. 2023. Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. Plant Journal. 115(1), 155–174.","short":"L. Jiang, B. Yao, X. Zhang, L. Wu, Q. Fu, Y. Zhao, Y. Cao, R. Zhu, X. Lu, W. Huang, J. Zhao, K. Li, S. Zhao, L. Han, X. Zhou, C. Luo, H. Zhu, J. Yang, H. Huang, Z. Zhu, X. He, J. Friml, Z. Zhang, C. Liu, Y. Du, Plant Journal 115 (2023) 155–174.","ieee":"L. Jiang <i>et al.</i>, “Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth,” <i>Plant Journal</i>, vol. 115, no. 1. Wiley, pp. 155–174, 2023.","apa":"Jiang, L., Yao, B., Zhang, X., Wu, L., Fu, Q., Zhao, Y., … Du, Y. (2023). Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth. <i>Plant Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/tpj.16218\">https://doi.org/10.1111/tpj.16218</a>"},"month":"07","pmid":1,"publication_status":"published","status":"public","acknowledgement":"The authors thank Professor Jianqiang Wu (Kunming Institute of Botany, Chinese Academy of Sciences) for support with phytohormone measurement. Thanks also go to Professor Pieter. B. F. Ouwerkerk (Leiden University) and Professor Jean-Benoit Morel (Plant Health Institute of Montpellier) for provision of the rice lines NB-7B-70 and NB-7B-76 and wild-type NB-61-WT, Professor Zuhua He (Chinese Academy of Sciences) for provision of the rice OsNPR1-RNAi mutant, and Professor Yinong Yang (The Pennsylvania State University) for provision of the rice line NahG. This work was supported by grants from the National Natural Science Foundation of China (Grant Nos. 32260085, 31460453, 31660501, 31860064, 31970609, 31801792 and 31960554), the Key Projects of the Applied Basic Research Plan of Yunnan Province (202301AS070082), the Major Special Program for Scientific Research, Education Department of Yunnan Province (Grant No. ZD2015005), the Start-up fund from Xishuangbanna Tropical Botanical Garden, and ‘Top Talents Program in Science and Technology’ from Yunnan Province, the SRF for ROCS, SEM (Grant No. [2013] 1792), and the Major Science and Technology Project in Yunnan Province (202102AE090042 and 202202AE090036); and the young and middle-aged academic and technical leaders reserve talent program in Yunnan Province (202205AC160076).","publication_identifier":{"issn":["0960-7412"],"eissn":["1365-313X"]},"issue":"1","abstract":[{"lang":"eng","text":"Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components."}],"doi":"10.1111/tpj.16218","author":[{"first_name":"Lihui","full_name":"Jiang, Lihui","last_name":"Jiang"},{"full_name":"Yao, Baolin","last_name":"Yao","first_name":"Baolin"},{"first_name":"Xiaoyan","full_name":"Zhang, Xiaoyan","last_name":"Zhang"},{"full_name":"Wu, Lixia","last_name":"Wu","first_name":"Lixia"},{"last_name":"Fu","full_name":"Fu, Qijing","first_name":"Qijing"},{"first_name":"Yiting","last_name":"Zhao","full_name":"Zhao, Yiting"},{"full_name":"Cao, Yuxin","last_name":"Cao","first_name":"Yuxin"},{"first_name":"Ruomeng","last_name":"Zhu","full_name":"Zhu, Ruomeng"},{"last_name":"Lu","full_name":"Lu, Xinqi","first_name":"Xinqi"},{"full_name":"Huang, Wuying","last_name":"Huang","first_name":"Wuying"},{"first_name":"Jianping","full_name":"Zhao, Jianping","last_name":"Zhao"},{"first_name":"Kuixiu","last_name":"Li","full_name":"Li, Kuixiu"},{"first_name":"Shuanglu","last_name":"Zhao","full_name":"Zhao, Shuanglu"},{"first_name":"Li","full_name":"Han, Li","last_name":"Han"},{"full_name":"Zhou, Xuan","last_name":"Zhou","first_name":"Xuan"},{"first_name":"Chongyu","full_name":"Luo, Chongyu","last_name":"Luo"},{"first_name":"Haiyan","last_name":"Zhu","full_name":"Zhu, Haiyan"},{"last_name":"Yang","full_name":"Yang, Jing","first_name":"Jing"},{"full_name":"Huang, Huichuan","last_name":"Huang","first_name":"Huichuan"},{"full_name":"Zhu, Zhengge","last_name":"Zhu","first_name":"Zhengge"},{"first_name":"Xiahong","last_name":"He","full_name":"He, Xiahong"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"last_name":"Zhang","full_name":"Zhang, Zhongkai","first_name":"Zhongkai"},{"first_name":"Changning","full_name":"Liu, Changning","last_name":"Liu"},{"last_name":"Du","full_name":"Du, Yunlong","first_name":"Yunlong"}],"title":"Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth","_id":"12878","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       115","publisher":"Wiley","date_published":"2023-07-01T00:00:00Z","external_id":{"pmid":["37025008 "],"isi":["000971861400001"]},"scopus_import":"1","date_created":"2023-04-30T22:01:06Z","department":[{"_id":"JiFr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","page":"155-174","publication":"Plant Journal","date_updated":"2023-08-01T14:16:33Z","year":"2023"},{"citation":{"chicago":"Chen, Ke, Christian Kunkel, Bingqing Cheng, Karsten Reuter, and Johannes T. Margraf. “Physics-Inspired Machine Learning of Localized Intensive Properties.” <i>Chemical Science</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3sc00841j\">https://doi.org/10.1039/d3sc00841j</a>.","mla":"Chen, Ke, et al. “Physics-Inspired Machine Learning of Localized Intensive Properties.” <i>Chemical Science</i>, Royal Society of Chemistry, 2023, doi:<a href=\"https://doi.org/10.1039/d3sc00841j\">10.1039/d3sc00841j</a>.","apa":"Chen, K., Kunkel, C., Cheng, B., Reuter, K., &#38; Margraf, J. T. (2023). Physics-inspired machine learning of localized intensive properties. <i>Chemical Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3sc00841j\">https://doi.org/10.1039/d3sc00841j</a>","ieee":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, and J. T. Margraf, “Physics-inspired machine learning of localized intensive properties,” <i>Chemical Science</i>. Royal Society of Chemistry, 2023.","ama":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. Physics-inspired machine learning of localized intensive properties. <i>Chemical Science</i>. 2023. doi:<a href=\"https://doi.org/10.1039/d3sc00841j\">10.1039/d3sc00841j</a>","short":"K. Chen, C. Kunkel, B. Cheng, K. Reuter, J.T. Margraf, Chemical Science (2023).","ista":"Chen K, Kunkel C, Cheng B, Reuter K, Margraf JT. 2023. Physics-inspired machine learning of localized intensive properties. Chemical Science."},"day":"10","file_date_updated":"2023-05-02T07:17:05Z","ddc":["000","540"],"month":"04","license":"https://creativecommons.org/licenses/by/3.0/","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"file":[{"creator":"dernst","relation":"main_file","file_size":1515446,"file_name":"2023_ChemialScience_Chen.pdf","date_updated":"2023-05-02T07:17:05Z","success":1,"checksum":"5eeec69a51e192dcd94b955d84423836","content_type":"application/pdf","access_level":"open_access","date_created":"2023-05-02T07:17:05Z","file_id":"12883"}],"has_accepted_license":"1","article_processing_charge":"No","title":"Physics-inspired machine learning of localized intensive properties","author":[{"first_name":"Ke","id":"c636c5ca-e8b8-11ed-b2d4-cc2c37613a8d","last_name":"Chen","full_name":"Chen, Ke"},{"last_name":"Kunkel","full_name":"Kunkel, Christian","first_name":"Christian"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","full_name":"Cheng, Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632"},{"last_name":"Reuter","full_name":"Reuter, Karsten","first_name":"Karsten"},{"first_name":"Johannes T.","full_name":"Margraf, Johannes T.","last_name":"Margraf"}],"_id":"12879","abstract":[{"text":"Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations.","lang":"eng"}],"doi":"10.1039/d3sc00841j","publication_identifier":{"eissn":["2041-6539"],"issn":["2041-6520"]},"publication_status":"published","status":"public","acknowledgement":"KC acknowledges funding from the China Scholarship Council. KC is grateful for the TUM graduate school finance support to visit Bingqing Cheng's group in IST for two months. We also thankfully acknowledge computational resources provided by the MPCDF Supercomputing Centre.","department":[{"_id":"BiCh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000971508100001"]},"date_published":"2023-04-10T00:00:00Z","date_created":"2023-04-30T22:01:06Z","scopus_import":"1","publisher":"Royal Society of Chemistry","isi":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"year":"2023","publication":"Chemical Science","date_updated":"2023-08-01T14:18:10Z","article_type":"original"},{"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"checksum":"8e707eda84f64dbad7f03545ae0a83ef","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-05-02T07:24:55Z","success":1,"relation":"main_file","file_size":3811113,"creator":"dernst","file_name":"2023_Nucleus_Kaneshiro.pdf","date_created":"2023-05-02T07:24:55Z","file_id":"12884"}],"volume":14,"article_processing_charge":"No","has_accepted_license":"1","pmid":1,"file_date_updated":"2023-05-02T07:24:55Z","month":"04","ddc":["570"],"citation":{"apa":"Kaneshiro, J. M., Capitanio, J. S., &#38; Hetzer, M. (2023). Lamin B1 overexpression alters chromatin organization and gene expression. <i>Nucleus</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/19491034.2023.2202548\">https://doi.org/10.1080/19491034.2023.2202548</a>","ieee":"J. M. Kaneshiro, J. S. Capitanio, and M. Hetzer, “Lamin B1 overexpression alters chromatin organization and gene expression,” <i>Nucleus</i>, vol. 14, no. 1. Taylor &#38; Francis, 2023.","short":"J.M. Kaneshiro, J.S. Capitanio, M. Hetzer, Nucleus 14 (2023).","ama":"Kaneshiro JM, Capitanio JS, Hetzer M. Lamin B1 overexpression alters chromatin organization and gene expression. <i>Nucleus</i>. 2023;14(1). doi:<a href=\"https://doi.org/10.1080/19491034.2023.2202548\">10.1080/19491034.2023.2202548</a>","ista":"Kaneshiro JM, Capitanio JS, Hetzer M. 2023. Lamin B1 overexpression alters chromatin organization and gene expression. Nucleus. 14(1), 2202548.","chicago":"Kaneshiro, Jeanae M., Juliana S. Capitanio, and Martin Hetzer. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” <i>Nucleus</i>. Taylor &#38; Francis, 2023. <a href=\"https://doi.org/10.1080/19491034.2023.2202548\">https://doi.org/10.1080/19491034.2023.2202548</a>.","mla":"Kaneshiro, Jeanae M., et al. “Lamin B1 Overexpression Alters Chromatin Organization and Gene Expression.” <i>Nucleus</i>, vol. 14, no. 1, 2202548, Taylor &#38; Francis, 2023, doi:<a href=\"https://doi.org/10.1080/19491034.2023.2202548\">10.1080/19491034.2023.2202548</a>."},"day":"18","oa_version":"Published Version","publication_identifier":{"issn":["1949-1034"],"eissn":["1949-1042"]},"status":"public","acknowledgement":"We thank members of the Hetzer lab for critical review of the manuscript; Novogene for mRNA library preparation and sequencing; the Next-Generation Sequencing Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Chapman Foundation, and the Helmsley Charitable Trust, for sequencing Cut&Run libraries; and the Waitt Advanced Biophotonics Core Facility at the Salk Institute, with funding from NIH-NCI CCSG: P30 014195, the Waitt Foundation, and the Chan-Zuckerberg Initiative Imaging Scientist Award, for electron microscopy sample preparation and imaging.","publication_status":"published","_id":"12880","title":"Lamin B1 overexpression alters chromatin organization and gene expression","author":[{"first_name":"Jeanae M.","full_name":"Kaneshiro, Jeanae M.","last_name":"Kaneshiro"},{"first_name":"Juliana S.","full_name":"Capitanio, Juliana S.","last_name":"Capitanio"},{"orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"Hetzer","full_name":"Hetzer, Martin W"}],"doi":"10.1080/19491034.2023.2202548","abstract":[{"text":"Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.","lang":"eng"}],"issue":"1","publisher":"Taylor & Francis","intvolume":"        14","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"MaHe"}],"date_created":"2023-04-30T22:01:06Z","scopus_import":"1","external_id":{"pmid":["37071033"],"isi":["000971629400001"]},"date_published":"2023-04-18T00:00:00Z","date_updated":"2023-08-01T14:18:46Z","publication":"Nucleus","article_number":"2202548","article_type":"original","oa":1,"year":"2023"},{"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_published":"2023-04-28T00:00:00Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"date_created":"2023-05-02T07:58:57Z","department":[{"_id":"GradSch"},{"_id":"MaIb"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10806"},{"relation":"part_of_dissertation","status":"public","id":"10042"},{"id":"12237","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"9118"},{"id":"10123","relation":"part_of_dissertation","status":"public"}]},"page":"82","date_updated":"2023-08-14T07:25:26Z","alternative_title":["ISTA Thesis"],"year":"2023","oa":1,"has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"file_id":"12887","date_created":"2023-05-02T07:43:18Z","date_updated":"2023-05-02T07:43:18Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"9347b0e09425f56fdcede5d3528404dc","file_name":"Thesis_Calcabrini.docx","relation":"source_file","creator":"mcalcabr","file_size":99627036},{"access_level":"open_access","checksum":"2d188b76621086cd384f0b9264b0a576","content_type":"application/pdf","success":1,"date_updated":"2023-05-02T07:42:45Z","file_name":"Thesis_Calcabrini_pdfa.pdf","relation":"main_file","file_size":8742220,"creator":"mcalcabr","file_id":"12888","date_created":"2023-05-02T07:42:45Z"}],"oa_version":"Published Version","day":"28","citation":{"ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023.","apa":"Calcabrini, M. (2023). <i>Nanoparticle-based semiconductor solids: From synthesis to consolidation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12885\">https://doi.org/10.15479/at:ista:12885</a>.","mla":"Calcabrini, Mariano. <i>Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12885\">10.15479/at:ista:12885</a>."},"month":"04","file_date_updated":"2023-05-02T07:43:18Z","ddc":["546","541"],"publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-028-2"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"abstract":[{"text":"High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. ","lang":"eng"}],"doi":"10.15479/at:ista:12885","author":[{"orcid":"0000-0003-4566-5877","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","first_name":"Mariano","full_name":"Calcabrini, Mariano","last_name":"Calcabrini"}],"title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","supervisor":[{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez"}],"_id":"12885"},{"date_created":"2023-05-04T08:35:01Z","scopus_import":"1","date_published":"2023-11-08T00:00:00Z","external_id":{"arxiv":["2305.02153"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"American Physical Society","intvolume":"       108","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.02153"}],"year":"2023","oa":1,"article_number":"054307","article_type":"original","related_material":{"link":[{"relation":"software","url":"https://github.com/FrederikRavnKlausen/model-for-culture-formation"}],"record":[{"status":"public","relation":"research_data","id":"12869"}]},"date_updated":"2023-11-13T07:47:30Z","publication":"Physical Review E","oa_version":"Preprint","month":"11","citation":{"ista":"Klausen FR, Lauritsen AB. 2023. Stochastic cellular automaton model of culture formation. Physical Review E. 108(5), 054307.","ama":"Klausen FR, Lauritsen AB. Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. 2023;108(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>","short":"F.R. Klausen, A.B. Lauritsen, Physical Review E 108 (2023).","ieee":"F. R. Klausen and A. B. Lauritsen, “Stochastic cellular automaton model of culture formation,” <i>Physical Review E</i>, vol. 108, no. 5. American Physical Society, 2023.","apa":"Klausen, F. R., &#38; Lauritsen, A. B. (2023). Stochastic cellular automaton model of culture formation. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>","mla":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>, vol. 108, no. 5, 054307, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">10.1103/PhysRevE.108.054307</a>.","chicago":"Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Stochastic Cellular Automaton Model of Culture Formation.” <i>Physical Review E</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevE.108.054307\">https://doi.org/10.1103/PhysRevE.108.054307</a>."},"day":"08","volume":108,"article_processing_charge":"No","arxiv":1,"doi":"10.1103/PhysRevE.108.054307","abstract":[{"text":"We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.","lang":"eng"}],"issue":"5","_id":"12890","title":"Stochastic cellular automaton model of culture formation","author":[{"first_name":"Frederik Ravn","last_name":"Klausen","full_name":"Klausen, Frederik Ravn"},{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard","last_name":"Lauritsen","orcid":"0000-0003-4476-2288"}],"acknowledgement":"Thanks to Kim Sneppen, Svend Krøjer, Peter Wildemann, Peter Rasmussen and Kent Bækgaard Lauritsen for discussions and suggestions. FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs.","publication_status":"published","status":"public","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]}},{"degree_awarded":"PhD","file":[{"date_updated":"2023-05-05T13:01:14Z","access_level":"closed","checksum":"59b0303dc483f40a96a610a90aab7ee9","content_type":"application/pdf","embargo":"2024-05-05","file_name":"Thesis_Schauer_final.pdf","file_size":31434230,"creator":"aschauer","relation":"main_file","file_id":"12907","date_created":"2023-05-05T13:01:14Z","embargo_to":"open_access"},{"file_name":"Thesis_Schauer_final.docx","relation":"source_file","creator":"aschauer","file_size":43809109,"date_updated":"2023-05-05T13:04:15Z","access_level":"closed","checksum":"25f54e12479b6adaabd129a20568e6c1","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12908","date_created":"2023-05-05T13:04:15Z"}],"has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Schauer, Alexandra. “Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>.","mla":"Schauer, Alexandra. <i>Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>.","ama":"Schauer A. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12891\">10.15479/at:ista:12891</a>","ista":"Schauer A. 2023. Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues. Institute of Science and Technology Austria.","short":"A. Schauer, Mesendoderm Formation in Zebrafish Gastrulation: The Role of Extraembryonic Tissues, Institute of Science and Technology Austria, 2023.","apa":"Schauer, A. (2023). <i>Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12891\">https://doi.org/10.15479/at:ista:12891</a>","ieee":"A. Schauer, “Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues,” Institute of Science and Technology Austria, 2023."},"day":"05","month":"05","file_date_updated":"2023-05-05T13:04:15Z","ddc":["570"],"oa_version":"Published Version","publication_identifier":{"issn":["2663 - 337X"]},"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues"}],"status":"public","publication_status":"published","ec_funded":1,"title":"Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues","supervisor":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"author":[{"last_name":"Schauer","full_name":"Schauer, Alexandra","first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142"}],"_id":"12891","abstract":[{"lang":"eng","text":"The tight spatiotemporal coordination of signaling activity determining embryo\r\npatterning and the physical processes driving embryo morphogenesis renders\r\nembryonic development robust, such that key developmental processes can unfold\r\nrelatively normally even outside of the full embryonic context. For instance, embryonic\r\nstem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry\r\nleading to germ layer formation and morphogenesis, in a very reduced environment.\r\nThis leads to questions on specific contributions of embryo-specific features, such as\r\nthe presence of extraembryonic tissues, which are inherently involved in gastrulation\r\nin the full embryonic context. To address this, we established zebrafish embryonic\r\nexplants without the extraembryonic yolk cell, an important player as a signaling\r\nsource and for morphogenesis during gastrulation, as a model of ex vivo development.\r\nWe found that dorsal-marginal determinants are required and sufficient in these\r\nexplants to form and pattern all three germ layers. However, formation of tissues,\r\nwhich require the highest Nodal-signaling levels, is variable, demonstrating a\r\ncontribution of extraembryonic tissues for reaching peak Nodal signaling levels.\r\nBlastoderm explants also undergo gastrulation-like axis elongation. We found that this\r\nelongation movement shows hallmarks of oriented mesendoderm cell intercalations\r\ntypically associated with dorsal tissues in the intact embryo. These are disrupted by\r\nuniform upregulation of BMP signaling activity and concomitant explant ventralization,\r\nsuggesting that tight spatial control of BMP signaling is a prerequisite for explant\r\nmorphogenesis. This control is achieved by Nodal signaling, which is critical for\r\neffectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal\r\nsignaling is not only directly required for mesendoderm cell fate specification and\r\nmorphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.\r\nCollectively, we provide insights into the capacity and organization of signaling and\r\nmorphogenetic domains to recapitulate features of zebrafish gastrulation outside of\r\nthe full embryonic context."}],"doi":"10.15479/at:ista:12891","publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"CaHe"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2023-05-05T00:00:00Z","date_created":"2023-05-05T08:48:20Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_updated":"2023-08-21T06:25:48Z","related_material":{"record":[{"id":"8966","relation":"part_of_dissertation","status":"public"},{"id":"7888","relation":"part_of_dissertation","status":"public"}]},"page":"190","year":"2023","alternative_title":["ISTA Thesis"]},{"department":[{"_id":"GradSch"},{"_id":"BeBi"}],"user_id":"400429CC-F248-11E8-B48F-1D18A9856A87","date_published":"2023-05-05T00:00:00Z","acknowledged_ssus":[{"_id":"M-Shop"}],"date_created":"2023-05-05T10:40:14Z","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","oa":1,"year":"2023","alternative_title":["ISTA Thesis"],"date_updated":"2024-01-29T10:47:51Z","related_material":{"record":[{"id":"9817","status":"public","relation":"part_of_dissertation"},{"id":"7117","relation":"part_of_dissertation","status":"public"},{"relation":"dissertation_contains","status":"public","id":"13188"}]},"page":"180","day":"05","citation":{"mla":"Hafner, Christian. <i>Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>.","chicago":"Hafner, Christian. “Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>.","apa":"Hafner, C. (2023). <i>Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12897\">https://doi.org/10.15479/at:ista:12897</a>","ieee":"C. Hafner, “Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models,” Institute of Science and Technology Austria, 2023.","ama":"Hafner C. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12897\">10.15479/at:ista:12897</a>","ista":"Hafner C. 2023. Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models. Institute of Science and Technology Austria.","short":"C. Hafner, Inverse Shape Design with Parametric Representations: Kirchhoff Rods and Parametric Surface Models, Institute of Science and Technology Austria, 2023."},"month":"05","ddc":["516","004","518","531"],"file_date_updated":"2023-12-08T23:30:04Z","oa_version":"Published Version","degree_awarded":"PhD","file":[{"file_id":"12942","date_created":"2023-05-11T10:43:20Z","access_level":"open_access","checksum":"cc2094e92fa27000b70eb4bfb76d6b5a","content_type":"application/pdf","date_updated":"2023-12-08T23:30:04Z","file_name":"thesis-hafner-2023may11-a2b.pdf","relation":"main_file","creator":"chafner","file_size":50714445,"embargo":"2023-12-07"},{"file_name":"thesis-release-form.pdf","relation":"source_file","creator":"chafner","file_size":265319,"access_level":"closed","checksum":"a6b51334be2b81672357b1549afab40c","content_type":"application/pdf","date_updated":"2023-12-08T23:30:04Z","embargo_to":"open_access","file_id":"12943","date_created":"2023-05-11T10:43:44Z"}],"has_accepted_license":"1","article_processing_charge":"No","author":[{"last_name":"Hafner","full_name":"Hafner, Christian","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"}],"supervisor":[{"full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385"}],"title":"Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models","_id":"12897","abstract":[{"text":"Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.\r\n\r\nThe first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.\r\n\r\nWe show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. \r\n\r\nThe second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.","lang":"eng"}],"doi":"10.15479/at:ista:12897","publication_identifier":{"isbn":["978-3-99078-031-2"],"issn":["2663-337X"]},"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"status":"public","publication_status":"published","ec_funded":1},{"article_processing_charge":"No","has_accepted_license":"1","file":[{"creator":"rsahu","relation":"source_file","file_size":36767177,"file_name":"thesis.zip","checksum":"8cbdab9c37ee55e591092a6f66b272c4","content_type":"application/x-zip-compressed","access_level":"closed","date_updated":"2023-06-06T22:30:03Z","embargo_to":"open_access","date_created":"2023-05-09T08:45:14Z","file_id":"12928"},{"date_updated":"2023-07-06T11:37:40Z","content_type":"application/pdf","checksum":"439659ead46618147309be39d9dd5a8c","access_level":"closed","relation":"main_file","file_size":17501990,"creator":"rsahu","file_name":"thesis_pdfa_final.pdf","date_created":"2023-05-09T08:51:17Z","file_id":"12929"}],"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"degree_awarded":"PhD","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-07-06T11:37:40Z","month":"05","ddc":["537","535","539"],"citation":{"mla":"Sahu, Rishabh. <i>Cavity Quantum Electrooptics</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>.","chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12900\">10.15479/at:ista:12900</a>","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","apa":"Sahu, R. (2023). <i>Cavity quantum electrooptics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12900\">https://doi.org/10.15479/at:ista:12900</a>"},"day":"05","ec_funded":1,"publication_status":"published","status":"public","project":[{"call_identifier":"H2020","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-030-5"]},"doi":"10.15479/at:ista:12900","abstract":[{"text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"_id":"12900","supervisor":[{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M"}],"title":"Cavity quantum electrooptics","author":[{"full_name":"Sahu, Rishabh","last_name":"Sahu","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh","orcid":"0000-0001-6264-2162"}],"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_created":"2023-05-05T11:08:50Z","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"date_published":"2023-05-05T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"page":"190","related_material":{"record":[{"id":"9114","status":"public","relation":"part_of_dissertation"},{"id":"10924","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"new_edition","id":"13175"}]},"date_updated":"2024-10-29T09:11:05Z","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"year":"2023","alternative_title":["ISTA Thesis"]}]