[{"file_date_updated":"2022-08-08T06:58:22Z","volume":106,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"article_number":"045302","file":[{"checksum":"115aff9e0cde2f806cb26953d7262791","date_updated":"2022-08-08T06:58:22Z","access_level":"open_access","file_name":"2022_PhysRevB_Dziom.pdf","file_size":774455,"creator":"dernst","date_created":"2022-08-08T06:58:22Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"11743"}],"_id":"11737","date_published":"2022-07-15T00:00:00Z","abstract":[{"text":"Spin-orbit coupling in thin HgTe quantum wells results in a relativistic-like electron band structure, making it a versatile solid state platform to observe and control nontrivial electrodynamic phenomena. Here we report an observation of universal terahertz (THz) transparency determined by fine-structure constant α≈1/137 in 6.5-nm-thick HgTe layer, close to the critical thickness separating phases with topologically different electronic band structure. Using THz spectroscopy in a magnetic field we obtain direct evidence of asymmetric spin splitting of the Dirac cone. This particle-hole asymmetry facilitates optical control of edge spin currents in the quantum wells.","lang":"eng"}],"issue":"4","article_processing_charge":"No","date_updated":"2023-08-03T12:38:57Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000834349200010"]},"scopus_import":"1","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"article_type":"original","oa_version":"Published Version","has_accepted_license":"1","year":"2022","department":[{"_id":"ZhAl"}],"quality_controlled":"1","publication":"Physical Review B","status":"public","intvolume":"       106","publisher":"American Physical Society","isi":1,"month":"07","date_created":"2022-08-07T22:01:58Z","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.106.045302","ddc":["530"],"acknowledgement":"This work was supported by the Austrian Science Funds (W 1243, I 3456-N27, I 5539-N).","day":"15","author":[{"id":"6A9A37C2-8C5C-11E9-AE53-F2FDE5697425","orcid":"0000-0002-1648-0999","first_name":"Uladzislau","full_name":"Dziom, Uladzislau","last_name":"Dziom"},{"first_name":"A.","full_name":"Shuvaev, A.","last_name":"Shuvaev"},{"first_name":"J.","full_name":"Gospodarič, J.","last_name":"Gospodarič"},{"last_name":"Novik","first_name":"E. G.","full_name":"Novik, E. G."},{"last_name":"Dobretsova","first_name":"A. A.","full_name":"Dobretsova, A. A."},{"last_name":"Mikhailov","first_name":"N. N.","full_name":"Mikhailov, N. N."},{"last_name":"Kvon","first_name":"Z. D.","full_name":"Kvon, Z. D."},{"orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek"},{"last_name":"Pimenov","first_name":"A.","full_name":"Pimenov, A."}],"type":"journal_article","citation":{"chicago":"Dziom, Uladzislau, A. Shuvaev, J. Gospodarič, E. G. Novik, A. A. Dobretsova, N. N. Mikhailov, Z. D. Kvon, Zhanybek Alpichshev, and A. Pimenov. “Universal Transparency and Asymmetric Spin Splitting near the Dirac Point in HgTe Quantum Wells.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">https://doi.org/10.1103/PhysRevB.106.045302</a>.","ieee":"U. Dziom <i>et al.</i>, “Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells,” <i>Physical Review B</i>, vol. 106, no. 4. American Physical Society, 2022.","ista":"Dziom U, Shuvaev A, Gospodarič J, Novik EG, Dobretsova AA, Mikhailov NN, Kvon ZD, Alpichshev Z, Pimenov A. 2022. Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. Physical Review B. 106(4), 045302.","mla":"Dziom, Uladzislau, et al. “Universal Transparency and Asymmetric Spin Splitting near the Dirac Point in HgTe Quantum Wells.” <i>Physical Review B</i>, vol. 106, no. 4, 045302, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">10.1103/PhysRevB.106.045302</a>.","short":"U. Dziom, A. Shuvaev, J. Gospodarič, E.G. Novik, A.A. Dobretsova, N.N. Mikhailov, Z.D. Kvon, Z. Alpichshev, A. Pimenov, Physical Review B 106 (2022).","ama":"Dziom U, Shuvaev A, Gospodarič J, et al. Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. <i>Physical Review B</i>. 2022;106(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">10.1103/PhysRevB.106.045302</a>","apa":"Dziom, U., Shuvaev, A., Gospodarič, J., Novik, E. G., Dobretsova, A. A., Mikhailov, N. N., … Pimenov, A. (2022). Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.106.045302\">https://doi.org/10.1103/PhysRevB.106.045302</a>"},"title":"Universal transparency and asymmetric spin splitting near the Dirac point in HgTe quantum wells"},{"abstract":[{"text":"We consider finite-volume approximations of Fokker--Planck equations on bounded convex domains in $\\mathbb{R}^d$ and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker--Planck equation via the method of evolutionary $\\Gamma$-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalizing the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality.","lang":"eng"}],"_id":"11739","date_published":"2022-07-18T00:00:00Z","issue":"4","article_processing_charge":"No","arxiv":1,"volume":54,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2008.10962","open_access":"1"}],"oa":1,"publication_status":"published","oa_version":"Preprint","year":"2022","article_type":"original","publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:37:21Z","scopus_import":"1","external_id":{"isi":["000889274600001"],"arxiv":["2008.10962"]},"date_created":"2022-08-07T22:01:59Z","month":"07","page":"4297-4333","status":"public","intvolume":"        54","quality_controlled":"1","department":[{"_id":"JaMa"}],"publication":"SIAM Journal on Mathematical Analysis","isi":1,"publisher":"Society for Industrial and Applied Mathematics","type":"journal_article","author":[{"id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L","full_name":"Forkert, Dominik L","last_name":"Forkert"},{"first_name":"Jan","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Portinale, Lorenzo","first_name":"Lorenzo","last_name":"Portinale"}],"day":"18","title":"Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","ec_funded":1,"citation":{"chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>.","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4. Society for Industrial and Applied Mathematics, pp. 4297–4333, 2022.","ista":"Forkert DL, Maas J, Portinale L. 2022. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. SIAM Journal on Mathematical Analysis. 54(4), 4297–4333.","mla":"Forkert, Dominik L., et al. “Evolutionary $\\Gamma$-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 4, Society for Industrial and Applied Mathematics, 2022, pp. 4297–333, doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>.","short":"D.L. Forkert, J. Maas, L. Portinale, SIAM Journal on Mathematical Analysis 54 (2022) 4297–4333.","ama":"Forkert DL, Maas J, Portinale L. Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(4):4297-4333. doi:<a href=\"https://doi.org/10.1137/21M1410968\">10.1137/21M1410968</a>","apa":"Forkert, D. L., Maas, J., &#38; Portinale, L. (2022). Evolutionary $\\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1410968\">https://doi.org/10.1137/21M1410968</a>"},"doi":"10.1137/21M1410968","language":[{"iso":"eng"}],"keyword":["Fokker--Planck equation","gradient flow","evolutionary $\\Gamma$-convergence"],"acknowledgement":"This work was supported by the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme grant 716117 and by the AustrianScience Fund (FWF) through grants F65 and W1245.","related_material":{"record":[{"relation":"earlier_version","id":"10022","status":"public"}]},"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425"}]},{"date_created":"2022-08-07T22:01:59Z","month":"07","intvolume":"        29","status":"public","publication":"Electronic Journal of Combinatorics","quality_controlled":"1","department":[{"_id":"MaKw"}],"isi":1,"publisher":"Electronic Journal of Combinatorics","author":[{"id":"43f4ddd0-a46b-11ec-8df6-ef3703bd721d","first_name":"Oliver","full_name":"Cooley, Oliver","last_name":"Cooley"},{"first_name":"Nicola","full_name":"Del Giudice, Nicola","last_name":"Del Giudice"},{"last_name":"Kang","first_name":"Mihyun","full_name":"Kang, Mihyun"},{"last_name":"Sprüssel","first_name":"Philipp","full_name":"Sprüssel, Philipp"}],"type":"journal_article","day":"29","title":"Phase transition in cohomology groups of non-uniform random simplicial complexes","citation":{"ieee":"O. Cooley, N. Del Giudice, M. Kang, and P. Sprüssel, “Phase transition in cohomology groups of non-uniform random simplicial complexes,” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3. Electronic Journal of Combinatorics, 2022.","ista":"Cooley O, Del Giudice N, Kang M, Sprüssel P. 2022. Phase transition in cohomology groups of non-uniform random simplicial complexes. Electronic Journal of Combinatorics. 29(3), P3.27.","chicago":"Cooley, Oliver, Nicola Del Giudice, Mihyun Kang, and Philipp Sprüssel. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2022. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>.","mla":"Cooley, Oliver, et al. “Phase Transition in Cohomology Groups of Non-Uniform Random Simplicial Complexes.” <i>Electronic Journal of Combinatorics</i>, vol. 29, no. 3, P3.27, Electronic Journal of Combinatorics, 2022, doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>.","short":"O. Cooley, N. Del Giudice, M. Kang, P. Sprüssel, Electronic Journal of Combinatorics 29 (2022).","apa":"Cooley, O., Del Giudice, N., Kang, M., &#38; Sprüssel, P. (2022). Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/10607\">https://doi.org/10.37236/10607</a>","ama":"Cooley O, Del Giudice N, Kang M, Sprüssel P. Phase transition in cohomology groups of non-uniform random simplicial complexes. <i>Electronic Journal of Combinatorics</i>. 2022;29(3). doi:<a href=\"https://doi.org/10.37236/10607\">10.37236/10607</a>"},"ddc":["510"],"doi":"10.37236/10607","language":[{"iso":"eng"}],"acknowledgement":"Supported by Austrian Science Fund (FWF): I3747, W1230.","date_published":"2022-07-29T00:00:00Z","_id":"11740","abstract":[{"lang":"eng","text":"We consider a generalised model of a random simplicial complex, which arises from a random hypergraph. Our model is generated by taking the downward-closure of a non-uniform binomial random hypergraph, in which for each k, each set of k+1 vertices forms an edge with some probability pk independently. As a special case, this contains an extensively studied model of a (uniform) random simplicial complex, introduced by Meshulam and Wallach [Random Structures & Algorithms 34 (2009), no. 3, pp. 408–417].\r\nWe consider a higher-dimensional notion of connectedness on this new model according to the vanishing of cohomology groups over an arbitrary abelian group R. We prove that this notion of connectedness displays a phase transition and determine the threshold. We also prove a hitting time result for a natural process interpretation, in which simplices and their downward-closure are added one by one. In addition, we determine the asymptotic behaviour of cohomology groups inside the critical window around the time of the phase transition."}],"article_number":"P3.27","file":[{"relation":"main_file","file_id":"11742","content_type":"application/pdf","date_created":"2022-08-08T06:28:52Z","success":1,"file_size":1768663,"creator":"dernst","file_name":"2022_ElecJournCombinatorics_Cooley.pdf","checksum":"057c676dcee70236aa234d4ce6138c69","access_level":"open_access","date_updated":"2022-08-08T06:28:52Z"}],"article_processing_charge":"No","issue":"3","arxiv":1,"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)"},"volume":29,"file_date_updated":"2022-08-08T06:28:52Z","oa":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","publication_status":"published","oa_version":"Published Version","year":"2022","has_accepted_license":"1","article_type":"original","publication_identifier":{"eissn":["1077-8926"]},"external_id":{"isi":["000836200300001"],"arxiv":["2005.07103"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:37:54Z"},{"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This work was supported in part by the ERC-2020-AdG 101020093.","project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"language":[{"iso":"eng"}],"ddc":["000"],"doi":"10.1007/978-3-031-17196-3_11","ec_funded":1,"citation":{"mla":"Henzinger, Thomas A., et al. “Abstract Monitors for Quantitative Specifications.” <i>22nd International Conference on Runtime Verification</i>, vol. 13498, Springer Nature, 2022, pp. 200–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>.","ieee":"T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Abstract monitors for quantitative specifications,” in <i>22nd International Conference on Runtime Verification</i>, Tbilisi, Georgia, 2022, vol. 13498, pp. 200–220.","ista":"Henzinger TA, Mazzocchi NA, Sarac NE. 2022. Abstract monitors for quantitative specifications. 22nd International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 13498, 200–220.","chicago":"Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Abstract Monitors for Quantitative Specifications.” In <i>22nd International Conference on Runtime Verification</i>, 13498:200–220. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>.","apa":"Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2022). Abstract monitors for quantitative specifications. In <i>22nd International Conference on Runtime Verification</i> (Vol. 13498, pp. 200–220). Tbilisi, Georgia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">https://doi.org/10.1007/978-3-031-17196-3_11</a>","ama":"Henzinger TA, Mazzocchi NA, Sarac NE. Abstract monitors for quantitative specifications. In: <i>22nd International Conference on Runtime Verification</i>. Vol 13498. Springer Nature; 2022:200-220. doi:<a href=\"https://doi.org/10.1007/978-3-031-17196-3_11\">10.1007/978-3-031-17196-3_11</a>","short":"T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 22nd International Conference on Runtime Verification, Springer Nature, 2022, pp. 200–220."},"conference":{"name":"RV: Runtime Verification","end_date":"2022-09-30","start_date":"2022-09-28","location":"Tbilisi, Georgia"},"title":"Abstract monitors for quantitative specifications","day":"23","alternative_title":["LNCS"],"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Mazzocchi","full_name":"Mazzocchi, Nicolas Adrien","first_name":"Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"last_name":"Sarac","first_name":"Naci E","full_name":"Sarac, Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"type":"conference","publisher":"Springer Nature","isi":1,"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"quality_controlled":"1","publication":"22nd International Conference on Runtime Verification","status":"public","intvolume":"     13498","page":"200-220","month":"09","date_created":"2022-08-08T17:09:09Z","date_updated":"2023-08-03T13:38:46Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000866539700011"]},"scopus_import":"1","publication_identifier":{"issn":["0302-9743"]},"oa_version":"Published Version","year":"2022","has_accepted_license":"1","publication_status":"published","oa":1,"file_date_updated":"2023-01-20T07:34:50Z","volume":13498,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"Yes","file":[{"success":1,"date_created":"2023-01-20T07:34:50Z","content_type":"application/pdf","relation":"main_file","file_id":"12317","date_updated":"2023-01-20T07:34:50Z","access_level":"open_access","checksum":"05c7dcfbb9053a98f46441fb2eccb213","file_name":"2022_LNCS_RV_Henzinger.pdf","file_size":477110,"creator":"dernst"}],"_id":"11775","date_published":"2022-09-23T00:00:00Z","abstract":[{"lang":"eng","text":"Quantitative monitoring can be universal and approximate: For every finite sequence of observations, the specification provides a value and the monitor outputs a best-effort approximation of it. The quality of the approximation may depend on the resources that are available to the monitor. By taking to the limit the sequences of specification values and monitor outputs, we obtain precision-resource trade-offs also for limit monitoring. This paper provides a formal framework for studying such trade-offs using an abstract interpretation for monitors: For each natural number n, the aggregate semantics of a monitor at time n is an equivalence relation over all sequences of at most n observations so that two equivalent sequences are indistinguishable to the monitor and thus mapped to the same output. This abstract interpretation of quantitative monitors allows us to measure the number of equivalence classes (or “resource use”) that is necessary for a certain precision up to a certain time, or at any time. Our framework offers several insights. For example, we identify a family of specifications for which any resource-optimal exact limit monitor is independent of any error permitted over finite traces. Moreover, we present a specification for which any resource-optimal approximate limit monitor does not minimize its resource use at any time. "}]},{"title":"High-dimensional expansion and crossing numbers of simplicial complexes","ec_funded":1,"citation":{"ama":"Wild P. High-dimensional expansion and crossing numbers of simplicial complexes. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>","apa":"Wild, P. (2022). <i>High-dimensional expansion and crossing numbers of simplicial complexes</i>. Institute of Science and Technology. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>","short":"P. Wild, High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes, Institute of Science and Technology, 2022.","mla":"Wild, Pascal. <i>High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes</i>. Institute of Science and Technology, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11777\">10.15479/at:ista:11777</a>.","chicago":"Wild, Pascal. “High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes.” Institute of Science and Technology, 2022. <a href=\"https://doi.org/10.15479/at:ista:11777\">https://doi.org/10.15479/at:ista:11777</a>.","ieee":"P. Wild, “High-dimensional expansion and crossing numbers of simplicial complexes,” Institute of Science and Technology, 2022.","ista":"Wild P. 2022. High-dimensional expansion and crossing numbers of simplicial complexes. Institute of Science and Technology."},"alternative_title":["ISTA Thesis"],"author":[{"first_name":"Pascal","full_name":"Wild, Pascal","last_name":"Wild","id":"4C20D868-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","day":"11","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"ddc":["500","516","514"],"doi":"10.15479/at:ista:11777","language":[{"iso":"eng"}],"page":"170","date_created":"2022-08-10T15:51:19Z","supervisor":[{"last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"month":"08","degree_awarded":"PhD","publisher":"Institute of Science and Technology","status":"public","department":[{"_id":"GradSch"},{"_id":"UlWa"}],"oa_version":"Published Version","year":"2022","has_accepted_license":"1","publication_identifier":{"isbn":["978-3-99078-021-3"],"issn":["2663-337X"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-06-22T09:56:36Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.\r\nOur main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.\r\nFor the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\\in \\mathbb{N}}$ and $(H_n)_{n\\in\\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).\r\nVia the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\\mathrm{PGL}_{d+2}(\\mathbb{F}_q)$ for any $\\varepsilon>0$ and sufficiently large $q=q(\\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.\r\nBy improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\\mathrm{PGL}_{2}(\\mathbb{F}_q)$ is not tight.\r\nIn a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise."}],"_id":"11777","date_published":"2022-08-11T00:00:00Z","file":[{"file_name":"flags.py","file_size":16828,"creator":"pwild","date_updated":"2022-08-10T15:34:04Z","access_level":"open_access","description":"Code for computer-assisted proofs in Section 8.4.7 in Thesis","checksum":"f5f3af1fb7c8a24b71ddc88ad7f7c5b4","content_type":"text/x-python","relation":"supplementary_material","file_id":"11780","date_created":"2022-08-10T15:34:04Z"},{"date_created":"2022-08-10T15:34:10Z","relation":"supplementary_material","file_id":"11781","content_type":"text/x-c++src","checksum":"1f7c12dfe3bdaa9b147e4fbc3d34e3d5","description":"Code for proof of Lemma 8.20 in Thesis","access_level":"open_access","date_updated":"2022-08-10T15:34:10Z","file_size":12226,"creator":"pwild","file_name":"lowerbound.cpp"},{"checksum":"4cf81455c49e5dec3b9b2e3980137eeb","description":"Code for proof of Proposition 7.9 in Thesis","access_level":"open_access","date_updated":"2022-08-10T15:34:17Z","file_size":3240,"creator":"pwild","file_name":"upperbound.py","date_created":"2022-08-10T15:34:17Z","file_id":"11782","relation":"supplementary_material","content_type":"text/x-python"},{"file_name":"finalthesisPascalWildPDFA.pdf","file_size":5086282,"creator":"pwild","date_updated":"2022-08-11T16:08:33Z","access_level":"open_access","checksum":"4e96575b10cbe4e0d0db2045b2847774","content_type":"application/pdf","file_id":"11809","relation":"main_file","title":"High-Dimensional Expansion and Crossing Numbers of Simplicial Complexes","date_created":"2022-08-11T16:08:33Z"},{"content_type":"application/zip","relation":"source_file","file_id":"11810","date_created":"2022-08-11T16:09:19Z","file_name":"ThesisSubmission.zip","file_size":18150068,"creator":"pwild","date_updated":"2022-08-11T16:09:19Z","access_level":"closed","checksum":"92d94842a1fb6dca5808448137573b2e"}],"oa":1,"publication_status":"published","file_date_updated":"2022-08-11T16:09:19Z"},{"volume":63,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2022-08-11T07:03:02Z","oa":1,"publication_status":"published","date_published":"2022-06-10T00:00:00Z","_id":"11783","abstract":[{"lang":"eng","text":"We consider a gas of N bosons with interactions in the mean-field scaling regime. We review the proof of an asymptotic expansion of its low-energy spectrum, eigenstates, and dynamics, which provides corrections to Bogoliubov theory to all orders in 1/ N. This is based on joint works with Petrat, Pickl, Seiringer, and Soffer. In addition, we derive a full asymptotic expansion of the ground state one-body reduced density matrix."}],"article_number":"061102","file":[{"checksum":"d0d32c338c1896680174be88c70968fa","date_updated":"2022-08-11T07:03:02Z","access_level":"open_access","file_name":"2022_JourMathPhysics_Bossmann.pdf","file_size":5957888,"creator":"dernst","date_created":"2022-08-11T07:03:02Z","success":1,"content_type":"application/pdf","relation":"main_file","file_id":"11784"}],"issue":"6","article_processing_charge":"Yes (via OA deal)","arxiv":1,"publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"date_updated":"2023-08-03T12:46:28Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2203.00730"],"isi":["000809648100002"]},"scopus_import":"1","has_accepted_license":"1","year":"2022","oa_version":"Published Version","article_type":"original","status":"public","intvolume":"        63","quality_controlled":"1","department":[{"_id":"RoSe"}],"publication":"Journal of Mathematical Physics","isi":1,"publisher":"AIP Publishing","date_created":"2022-08-11T06:37:52Z","month":"06","doi":"10.1063/5.0089983","ddc":["530"],"language":[{"iso":"eng"}],"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"acknowledgement":"The author thanks Nataˇsa Pavlovic, Sören Petrat, Peter Pickl, Robert Seiringer, and Avy Soffer for the collaboration on Refs. 1, 2 and 21. Funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skℓodowska-Curie Grant Agreement\r\nNo. 754411 is gratefully acknowledged.","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"type":"journal_article","author":[{"orcid":"0000-0002-6854-1343","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","last_name":"Bossmann","full_name":"Bossmann, Lea","first_name":"Lea"}],"day":"10","title":"Low-energy spectrum and dynamics of the weakly interacting Bose gas","ec_funded":1,"citation":{"short":"L. Bossmann, Journal of Mathematical Physics 63 (2022).","ama":"Bossmann L. Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. 2022;63(6). doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>","apa":"Bossmann, L. (2022). Low-energy spectrum and dynamics of the weakly interacting Bose gas. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>","chicago":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0089983\">https://doi.org/10.1063/5.0089983</a>.","ista":"Bossmann L. 2022. Low-energy spectrum and dynamics of the weakly interacting Bose gas. Journal of Mathematical Physics. 63(6), 061102.","ieee":"L. Bossmann, “Low-energy spectrum and dynamics of the weakly interacting Bose gas,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6. AIP Publishing, 2022.","mla":"Bossmann, Lea. “Low-Energy Spectrum and Dynamics of the Weakly Interacting Bose Gas.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 6, 061102, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0089983\">10.1063/5.0089983</a>."}},{"department":[{"_id":"HeEd"}],"quality_controlled":"1","publication":"European Journal of Mathematics","status":"public","intvolume":"         8","publisher":"Springer Nature","month":"12","date_created":"2020-05-03T22:00:48Z","page":"1309 - 1312","language":[{"iso":"eng"}],"doi":"10.1007/s40879-020-00405-0","ddc":["510"],"acknowledgement":"AA was supported by European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). RK was supported by the Federal professorship program Grant 1.456.2016/1.4 and the Russian Foundation for Basic Research Grants 18-01-00036 and 19-01-00169. Open access funding provided by Institute of Science and Technology (IST Austria). The authors thank Alexey Balitskiy, Milena Radnović, and Serge Tabachnikov for useful discussions.","project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"day":"01","author":[{"last_name":"Akopyan","full_name":"Akopyan, Arseniy","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"first_name":"Roman","full_name":"Karasev, Roman","last_name":"Karasev"}],"type":"journal_article","ec_funded":1,"citation":{"short":"A. Akopyan, R. Karasev, European Journal of Mathematics 8 (2022) 1309–1312.","apa":"Akopyan, A., &#38; Karasev, R. (2022). When different norms lead to same billiard trajectories? <i>European Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40879-020-00405-0\">https://doi.org/10.1007/s40879-020-00405-0</a>","ama":"Akopyan A, Karasev R. When different norms lead to same billiard trajectories? <i>European Journal of Mathematics</i>. 2022;8(4):1309-1312. doi:<a href=\"https://doi.org/10.1007/s40879-020-00405-0\">10.1007/s40879-020-00405-0</a>","ieee":"A. Akopyan and R. Karasev, “When different norms lead to same billiard trajectories?,” <i>European Journal of Mathematics</i>, vol. 8, no. 4. Springer Nature, pp. 1309–1312, 2022.","ista":"Akopyan A, Karasev R. 2022. When different norms lead to same billiard trajectories? European Journal of Mathematics. 8(4), 1309–1312.","chicago":"Akopyan, Arseniy, and Roman Karasev. “When Different Norms Lead to Same Billiard Trajectories?” <i>European Journal of Mathematics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40879-020-00405-0\">https://doi.org/10.1007/s40879-020-00405-0</a>.","mla":"Akopyan, Arseniy, and Roman Karasev. “When Different Norms Lead to Same Billiard Trajectories?” <i>European Journal of Mathematics</i>, vol. 8, no. 4, Springer Nature, 2022, pp. 1309–12, doi:<a href=\"https://doi.org/10.1007/s40879-020-00405-0\">10.1007/s40879-020-00405-0</a>."},"title":"When different norms lead to same billiard trajectories?","file_date_updated":"2020-07-14T12:48:03Z","volume":8,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"file":[{"date_created":"2020-05-04T10:33:42Z","content_type":"application/pdf","relation":"main_file","file_id":"7796","date_updated":"2020-07-14T12:48:03Z","access_level":"open_access","checksum":"f53e71fd03744075adcd0b8fc1b8423d","file_name":"2020_EuropMathematics_Akopyan.pdf","file_size":263926,"creator":"dernst"}],"_id":"7791","date_published":"2022-12-01T00:00:00Z","abstract":[{"text":"Extending a result of Milena Radnovic and Serge Tabachnikov, we establish conditionsfor two different non-symmetric norms to define the same billiard reflection law.","lang":"eng"}],"arxiv":1,"issue":"4","article_processing_charge":"Yes (via OA deal)","date_updated":"2024-02-22T15:58:42Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","external_id":{"arxiv":["1912.12685"]},"publication_identifier":{"eissn":["2199-6768"],"issn":["2199-675X"]},"article_type":"original","has_accepted_license":"1","year":"2022","oa_version":"Published Version"},{"day":"21","oa_version":"Preprint","year":"2022","author":[{"orcid":"0000-0001-6619-7502","full_name":"Podlaski, William F.","first_name":"William F.","last_name":"Podlaski"},{"first_name":"Everton J.","full_name":"Agnes, Everton J.","last_name":"Agnes","orcid":"0000-0001-7184-7311"},{"orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","full_name":"Vogels, Tim P","last_name":"Vogels"}],"type":"preprint","citation":{"short":"W.F. Podlaski, E.J. Agnes, T.P. Vogels, BioRxiv (2022).","ama":"Podlaski WF, Agnes EJ, Vogels TP. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. <i>bioRxiv</i>. 2022. doi:<a href=\"https://doi.org/10.1101/2020.01.08.898528\">10.1101/2020.01.08.898528</a>","apa":"Podlaski, W. F., Agnes, E. J., &#38; Vogels, T. P. (2022). High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.01.08.898528\">https://doi.org/10.1101/2020.01.08.898528</a>","chicago":"Podlaski, William F., Everton J. Agnes, and Tim P Vogels. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2022. <a href=\"https://doi.org/10.1101/2020.01.08.898528\">https://doi.org/10.1101/2020.01.08.898528</a>.","ieee":"W. F. Podlaski, E. J. Agnes, and T. P. Vogels, “High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2022.","ista":"Podlaski WF, Agnes EJ, Vogels TP. 2022. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. bioRxiv, <a href=\"https://doi.org/10.1101/2020.01.08.898528\">10.1101/2020.01.08.898528</a>.","mla":"Podlaski, William F., et al. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2022, doi:<a href=\"https://doi.org/10.1101/2020.01.08.898528\">10.1101/2020.01.08.898528</a>."},"title":"High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2024-03-06T12:03:59Z","doi":"10.1101/2020.01.08.898528","month":"12","_id":"8125","date_published":"2022-12-21T00:00:00Z","abstract":[{"text":"Context, such as behavioral state, is known to modulate memory formation and retrieval, but is usually ignored in associative memory models. Here, we propose several types of contextual modulation for associative memory networks that greatly increase their performance. In these networks, context inactivates specific neurons and connections, which modulates the effective connectivity of the network. Memories are stored only by the active components, thereby reducing interference from memories acquired in other contexts. Such networks exhibit several beneficial characteristics, including enhanced memory capacity, high robustness to noise, increased robustness to memory overloading, and better memory retention during continual learning. Furthermore, memories can be biased to have different relative strengths, or even gated on or off, according to contextual cues, providing a candidate model for cognitive control of memory and efficient memory search. An external context-encoding network can dynamically switch the memory network to a desired state, which we liken to experimentally observed contextual signals in prefrontal cortex and hippocampus. Overall, our work illustrates the benefits of organizing memory around context, and provides an important link between behavioral studies of memory and mechanistic details of neural circuits.</jats:p><jats:sec><jats:title>SIGNIFICANCE</jats:title><jats:p>Memory is context dependent — both encoding and recall vary in effectiveness and speed depending on factors like location and brain state during a task. We apply this idea to a simple computational model of associative memory through contextual gating of neurons and synaptic connections. Intriguingly, this results in several advantages, including vastly enhanced memory capacity, better robustness, and flexible memory gating. Our model helps to explain (i) how gating and inhibition contribute to memory processes, (ii) how memory access dynamically changes over time, and (iii) how context representations, such as those observed in hippocampus and prefrontal cortex, may interact with and control memory processes.","lang":"eng"}],"date_created":"2020-07-16T12:24:28Z","locked":"1","article_processing_charge":"No","department":[{"_id":"TiVo"}],"publication":"bioRxiv","status":"public","publication_status":"published","publisher":"Cold Spring Harbor Laboratory","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/2020.01.08.898528 ","open_access":"1"}]},{"project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"acknowledgement":"The project of the first author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","language":[{"iso":"eng"}],"ddc":["510","515","518"],"doi":"10.1080/00036811.2020.1736287","citation":{"short":"Y. Shehu, O.S. Iyiola, Applicable Analysis 101 (2022) 192–216.","apa":"Shehu, Y., &#38; Iyiola, O. S. (2022). Weak convergence for variational inequalities with inertial-type method. <i>Applicable Analysis</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>","ama":"Shehu Y, Iyiola OS. Weak convergence for variational inequalities with inertial-type method. <i>Applicable Analysis</i>. 2022;101(1):192-216. doi:<a href=\"https://doi.org/10.1080/00036811.2020.1736287\">10.1080/00036811.2020.1736287</a>","ista":"Shehu Y, Iyiola OS. 2022. Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. 101(1), 192–216.","ieee":"Y. Shehu and O. S. Iyiola, “Weak convergence for variational inequalities with inertial-type method,” <i>Applicable Analysis</i>, vol. 101, no. 1. Taylor &#38; Francis, pp. 192–216, 2022.","chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” <i>Applicable Analysis</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/00036811.2020.1736287\">https://doi.org/10.1080/00036811.2020.1736287</a>.","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” <i>Applicable Analysis</i>, vol. 101, no. 1, Taylor &#38; Francis, 2022, pp. 192–216, doi:<a href=\"https://doi.org/10.1080/00036811.2020.1736287\">10.1080/00036811.2020.1736287</a>."},"ec_funded":1,"title":"Weak convergence for variational inequalities with inertial-type method","day":"01","author":[{"id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","last_name":"Shehu","first_name":"Yekini","full_name":"Shehu, Yekini"},{"first_name":"Olaniyi S.","full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola"}],"type":"journal_article","publisher":"Taylor & Francis","isi":1,"publication":"Applicable Analysis","department":[{"_id":"VlKo"}],"quality_controlled":"1","status":"public","intvolume":"       101","page":"192-216","month":"01","date_created":"2020-03-09T07:06:52Z","external_id":{"isi":["000518364100001"],"arxiv":["2101.08057"]},"scopus_import":"1","date_updated":"2024-03-05T14:01:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0003-6811"],"eissn":["1563-504X"]},"article_type":"original","oa_version":"Submitted Version","has_accepted_license":"1","year":"2022","publication_status":"published","oa":1,"file_date_updated":"2021-03-16T23:30:06Z","volume":101,"arxiv":1,"article_processing_charge":"No","issue":"1","file":[{"file_name":"2020_ApplicAnalysis_Shehu.pdf","file_size":4282586,"creator":"dernst","embargo":"2021-03-15","checksum":"869efe8cb09505dfa6012f67d20db63d","date_updated":"2021-03-16T23:30:06Z","access_level":"open_access","content_type":"application/pdf","file_id":"8648","relation":"main_file","date_created":"2020-10-12T10:42:54Z"}],"abstract":[{"lang":"eng","text":"Weak convergence of inertial iterative method for solving variational inequalities is the focus of this paper. The cost function is assumed to be non-Lipschitz and monotone. We propose a projection-type method with inertial terms and give weak convergence analysis under appropriate conditions. Some test results are performed and compared with relevant methods in the literature to show the efficiency and advantages given by our proposed methods."}],"_id":"7577","date_published":"2022-01-01T00:00:00Z"},{"year":"2022","oa_version":"Published Version","has_accepted_license":"1","article_type":"original","publication_identifier":{"issn":["1098-3600"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-25T08:57:07Z","article_processing_charge":"No","issue":"10","_id":"14355","date_published":"2022-10-01T00:00:00Z","abstract":[{"lang":"eng","text":"Purpose: The mediator (MED) multisubunit-complex modulates the activity of the transcriptional machinery, and genetic defects in different MED subunits (17, 20, 27) have been implicated in neurologic diseases. In this study, we identified a recurrent homozygous variant in MED11 (c.325C>T; p.Arg109Ter) in 7 affected individuals from 5 unrelated families. Methods: To investigate the genetic cause of the disease, exome or genome sequencing were performed in 5 unrelated families identified via different research networks and Matchmaker Exchange. Deep clinical and brain imaging evaluations were performed by clinical pediatric neurologists and neuroradiologists. The functional effect of the candidate variant on both MED11 RNA and protein was assessed using reverse transcriptase polymerase chain reaction and western blotting using fibroblast cell lines derived from 1 affected individual and controls and through computational approaches. Knockouts in zebrafish were generated using clustered regularly interspaced short palindromic repeats/Cas9. Results: The disease was characterized by microcephaly, profound neurodevelopmental impairment, exaggerated startle response, myoclonic seizures, progressive widespread neurodegeneration, and premature death. Functional studies on patient-derived fibroblasts did not show a loss of protein function but rather disruption of the C-terminal of MED11, likely impairing binding to other MED subunits. A zebrafish knockout model recapitulates key clinical phenotypes. Conclusion: Loss of the C-terminal of MED subunit 11 may affect its binding efficiency to other MED subunits, thus implicating the MED-complex stability in brain development and neurodegeneration. (C) 2022 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics."}],"file":[{"checksum":"8117175a89129eb5022d81ffe7625f9f","access_level":"open_access","date_updated":"2023-09-25T08:56:06Z","file_size":1434037,"creator":"dernst","file_name":"2022_GeneticsMedicine_Calin.pdf","date_created":"2023-09-25T08:56:06Z","success":1,"relation":"main_file","file_id":"14371","content_type":"application/pdf"}],"oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":24,"file_date_updated":"2023-09-25T08:56:06Z","title":"A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease","citation":{"mla":"Cali, Elisa, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” <i>Genetics in Medicine</i>, vol. 24, no. 10, Elsevier, 2022, pp. 2194–203, doi:<a href=\"https://doi.org/10.1016/j.gim.2022.07.013\">10.1016/j.gim.2022.07.013</a>.","ista":"Cali E, Lin S-J, Rocca C, Sahin Y, Al Shamsi A, El Chehadeh S, Chaabouni M, Mankad K, Galanaki E, Efthymiou S, Sudhakar S, Athanasiou-Fragkouli A, Celik T, Narli N, Bianca S, Murphy D, Moreira FMDC, Accogli A, Petree C, Huang K, Monastiri K, Edizadeh M, Nardello R, Ognibene M, De Marco P, Ruggieri M, Zara F, Striano P, Sahin Y, Al-Gazali L, Warde MTA, Gerard B, Zifarelli G, Beetz C, Fortuna S, Soler M, Valente EM, Varshney G, Maroofian R, Salpietro V, Houlden H, Grp SynS. 2022. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. 24(10), 2194–2203.","ieee":"E. Cali <i>et al.</i>, “A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease,” <i>Genetics in Medicine</i>, vol. 24, no. 10. Elsevier, pp. 2194–2203, 2022.","chicago":"Cali, Elisa, Sheng-Jia Lin, Clarissa Rocca, Yavuz Sahin, Aisha Al Shamsi, Salima El Chehadeh, Myriam Chaabouni, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” <i>Genetics in Medicine</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.gim.2022.07.013\">https://doi.org/10.1016/j.gim.2022.07.013</a>.","apa":"Cali, E., Lin, S.-J., Rocca, C., Sahin, Y., Al Shamsi, A., El Chehadeh, S., … Grp, Syn. S. (2022). A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. <i>Genetics in Medicine</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gim.2022.07.013\">https://doi.org/10.1016/j.gim.2022.07.013</a>","ama":"Cali E, Lin S-J, Rocca C, et al. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. <i>Genetics in Medicine</i>. 2022;24(10):2194-2203. doi:<a href=\"https://doi.org/10.1016/j.gim.2022.07.013\">10.1016/j.gim.2022.07.013</a>","short":"E. Cali, S.-J. Lin, C. Rocca, Y. Sahin, A. Al Shamsi, S. El Chehadeh, M. Chaabouni, K. Mankad, E. Galanaki, S. Efthymiou, S. Sudhakar, A. Athanasiou-Fragkouli, T. Celik, N. Narli, S. Bianca, D. Murphy, F.M.D.C. Moreira, A. Accogli, C. Petree, K. Huang, K. Monastiri, M. Edizadeh, R. Nardello, M. Ognibene, P. De Marco, M. Ruggieri, F. Zara, P. Striano, Y. Sahin, L. Al-Gazali, M.T.A. Warde, B. Gerard, G. Zifarelli, C. Beetz, S. Fortuna, M. Soler, E.M. Valente, G. Varshney, R. Maroofian, V. Salpietro, H. Houlden, Syn.S. Grp, Genetics in Medicine 24 (2022) 2194–2203."},"type":"journal_article","author":[{"last_name":"Cali","full_name":"Cali, Elisa","first_name":"Elisa"},{"last_name":"Lin","first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia"},{"full_name":"Rocca, Clarissa","first_name":"Clarissa","last_name":"Rocca"},{"full_name":"Sahin, Yavuz","first_name":"Yavuz","last_name":"Sahin"},{"full_name":"Al Shamsi, Aisha","first_name":"Aisha","last_name":"Al Shamsi"},{"first_name":"Salima","full_name":"El Chehadeh, Salima","last_name":"El Chehadeh"},{"last_name":"Chaabouni","first_name":"Myriam","full_name":"Chaabouni, Myriam"},{"last_name":"Mankad","full_name":"Mankad, Kshitij","first_name":"Kshitij"},{"full_name":"Galanaki, Evangelia","first_name":"Evangelia","last_name":"Galanaki"},{"last_name":"Efthymiou","full_name":"Efthymiou, Stephanie","first_name":"Stephanie"},{"full_name":"Sudhakar, Sniya","first_name":"Sniya","last_name":"Sudhakar"},{"full_name":"Athanasiou-Fragkouli, Alkyoni","first_name":"Alkyoni","last_name":"Athanasiou-Fragkouli"},{"first_name":"Tamer","full_name":"Celik, Tamer","last_name":"Celik"},{"last_name":"Narli","full_name":"Narli, Nejat","first_name":"Nejat"},{"full_name":"Bianca, Sebastiano","first_name":"Sebastiano","last_name":"Bianca"},{"full_name":"Murphy, David","first_name":"David","last_name":"Murphy"},{"last_name":"Moreira","first_name":"Francisco Martins De Carvalho","full_name":"Moreira, Francisco Martins De Carvalho"},{"last_name":"Accogli","first_name":"Andrea","full_name":"Accogli, Andrea"},{"full_name":"Petree, Cassidy","first_name":"Cassidy","last_name":"Petree"},{"orcid":"0000-0002-2512-7812","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","full_name":"Huang, Kevin","first_name":"Kevin","last_name":"Huang"},{"first_name":"Kamel","full_name":"Monastiri, Kamel","last_name":"Monastiri"},{"first_name":"Masoud","full_name":"Edizadeh, Masoud","last_name":"Edizadeh"},{"last_name":"Nardello","first_name":"Rosaria","full_name":"Nardello, Rosaria"},{"full_name":"Ognibene, Marzia","first_name":"Marzia","last_name":"Ognibene"},{"full_name":"De Marco, Patrizia","first_name":"Patrizia","last_name":"De Marco"},{"full_name":"Ruggieri, Martino","first_name":"Martino","last_name":"Ruggieri"},{"last_name":"Zara","full_name":"Zara, Federico","first_name":"Federico"},{"last_name":"Striano","first_name":"Pasquale","full_name":"Striano, Pasquale"},{"first_name":"Yavuz","full_name":"Sahin, Yavuz","last_name":"Sahin"},{"full_name":"Al-Gazali, Lihadh","first_name":"Lihadh","last_name":"Al-Gazali"},{"full_name":"Warde, Marie Therese Abi","first_name":"Marie Therese Abi","last_name":"Warde"},{"last_name":"Gerard","full_name":"Gerard, Benedicte","first_name":"Benedicte"},{"first_name":"Giovanni","full_name":"Zifarelli, Giovanni","last_name":"Zifarelli"},{"full_name":"Beetz, Christian","first_name":"Christian","last_name":"Beetz"},{"last_name":"Fortuna","full_name":"Fortuna, Sara","first_name":"Sara"},{"last_name":"Soler","first_name":"Miguel","full_name":"Soler, Miguel"},{"full_name":"Valente, Enza Maria","first_name":"Enza Maria","last_name":"Valente"},{"first_name":"Gaurav","full_name":"Varshney, Gaurav","last_name":"Varshney"},{"full_name":"Maroofian, Reza","first_name":"Reza","last_name":"Maroofian"},{"last_name":"Salpietro","first_name":"Vincenzo","full_name":"Salpietro, Vincenzo"},{"full_name":"Houlden, Henry","first_name":"Henry","last_name":"Houlden"},{"last_name":"Grp","first_name":"SYNaPS Study","full_name":"Grp, SYNaPS Study"}],"day":"01","ddc":["570"],"doi":"10.1016/j.gim.2022.07.013","keyword":["Human mediator complex","MED11","MEDopathies"],"language":[{"iso":"eng"}],"page":"2194-2203","date_created":"2023-09-20T20:57:18Z","month":"10","extern":"1","publisher":"Elsevier","intvolume":"        24","status":"public","publication":"Genetics in Medicine","quality_controlled":"1","department":[{"_id":"GradSch"}]},{"article_processing_charge":"No","issue":"10","file":[{"access_level":"open_access","date_updated":"2023-09-25T08:52:54Z","checksum":"74b01d4e4084b2f64c30ed32b18ee928","creator":"dernst","file_size":12131312,"file_name":"2022_HumanMutation_Lin.pdf","success":1,"date_created":"2023-09-25T08:52:54Z","relation":"main_file","file_id":"14370","content_type":"application/pdf"}],"_id":"14356","abstract":[{"lang":"eng","text":"Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for faithful assignment of amino acids to their cognate tRNA. Variants in ARS genes are frequently associated with clinically heterogeneous phenotypes in humans and follow both autosomal dominant or recessive inheritance patterns in many instances. Variants in tryptophanyl-tRNA synthetase 1 (WARS1) cause autosomal dominantly inherited distal hereditary motor neuropathy and Charcot-Marie-Tooth disease. Presently, only one family with biallelic WARS1 variants has been described. We present three affected individuals from two families with biallelic variants (p.Met1? and p.(Asp419Asn)) in WARS1, showing varying severities of developmental delay and intellectual disability. Hearing impairment and microcephaly, as well as abnormalities of the brain, skeletal system, movement/gait, and behavior were variable features. Phenotyping of knocked down wars-1 in a Caenorhabditis elegans model showed depletion is associated with defects in germ cell development. A wars1 knockout vertebrate model recapitulates the human clinical phenotypes, confirms variant pathogenicity, and uncovers evidence implicating the p.Met1? variant as potentially impacting an exon critical for normal hearing. Together, our findings provide consolidating evidence for biallelic disruption of WARS1 as causal for an autosomal recessive neurodevelopmental syndrome and present a vertebrate model that recapitulates key phenotypes observed in patients."}],"date_published":"2022-10-01T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2023-09-25T08:52:54Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":43,"article_type":"original","year":"2022","oa_version":"Published Version","has_accepted_license":"1","scopus_import":"1","date_updated":"2023-09-25T08:54:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1059-7794"]},"page":"1472-1489","month":"10","extern":"1","date_created":"2023-09-20T20:58:24Z","publisher":"Wiley","publication":"Human Mutation","quality_controlled":"1","intvolume":"        43","status":"public","citation":{"short":"S.-J. Lin, B. Vona, H.M. Porter, M. Izadi, K. Huang, Y. Lacassie, J.A. Rosenfeld, S. Khan, C. Petree, T.A. Ali, N. Muhammad, S.A. Khan, N. Muhammad, P. Liu, M.-L. Haymon, F. Rueschendorf, I.-K. Kong, L. Schnapp, N. Shur, L. Chorich, L. Layman, T. Haaf, E. Pourkarimi, H.-G. Kim, G.K. Varshney, Human Mutation 43 (2022) 1472–1489.","ama":"Lin S-J, Vona B, Porter HM, et al. Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. <i>Human Mutation</i>. 2022;43(10):1472-1489. doi:<a href=\"https://doi.org/10.1002/humu.24435\">10.1002/humu.24435</a>","apa":"Lin, S.-J., Vona, B., Porter, H. M., Izadi, M., Huang, K., Lacassie, Y., … Varshney, G. K. (2022). Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. <i>Human Mutation</i>. Wiley. <a href=\"https://doi.org/10.1002/humu.24435\">https://doi.org/10.1002/humu.24435</a>","chicago":"Lin, Sheng-Jia, Barbara Vona, Hillary M. Porter, Mahmoud Izadi, Kevin Huang, Yves Lacassie, Jill A. Rosenfeld, et al. “Biallelic Variants in WARS1 Cause a Highly Variable Neurodevelopmental Syndrome and Implicate a Critical Exon for Normal Auditory Function.” <i>Human Mutation</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/humu.24435\">https://doi.org/10.1002/humu.24435</a>.","ieee":"S.-J. Lin <i>et al.</i>, “Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function,” <i>Human Mutation</i>, vol. 43, no. 10. Wiley, pp. 1472–1489, 2022.","ista":"Lin S-J, Vona B, Porter HM, Izadi M, Huang K, Lacassie Y, Rosenfeld JA, Khan S, Petree C, Ali TA, Muhammad N, Khan SA, Muhammad N, Liu P, Haymon M-L, Rueschendorf F, Kong I-K, Schnapp L, Shur N, Chorich L, Layman L, Haaf T, Pourkarimi E, Kim H-G, Varshney GK. 2022. Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. Human Mutation. 43(10), 1472–1489.","mla":"Lin, Sheng-Jia, et al. “Biallelic Variants in WARS1 Cause a Highly Variable Neurodevelopmental Syndrome and Implicate a Critical Exon for Normal Auditory Function.” <i>Human Mutation</i>, vol. 43, no. 10, Wiley, 2022, pp. 1472–89, doi:<a href=\"https://doi.org/10.1002/humu.24435\">10.1002/humu.24435</a>."},"title":"Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function","day":"01","type":"journal_article","author":[{"full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia","last_name":"Lin"},{"last_name":"Vona","full_name":"Vona, Barbara","first_name":"Barbara"},{"full_name":"Porter, Hillary M.","first_name":"Hillary M.","last_name":"Porter"},{"first_name":"Mahmoud","full_name":"Izadi, Mahmoud","last_name":"Izadi"},{"id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","orcid":"0000-0002-2512-7812","last_name":"Huang","first_name":"Kevin","full_name":"Huang, Kevin"},{"last_name":"Lacassie","first_name":"Yves","full_name":"Lacassie, Yves"},{"last_name":"Rosenfeld","full_name":"Rosenfeld, Jill A.","first_name":"Jill A."},{"first_name":"Saadullah","full_name":"Khan, Saadullah","last_name":"Khan"},{"first_name":"Cassidy","full_name":"Petree, Cassidy","last_name":"Petree"},{"last_name":"Ali","full_name":"Ali, Tayyiba A.","first_name":"Tayyiba A."},{"first_name":"Nazif","full_name":"Muhammad, Nazif","last_name":"Muhammad"},{"full_name":"Khan, Sher A.","first_name":"Sher A.","last_name":"Khan"},{"last_name":"Muhammad","first_name":"Noor","full_name":"Muhammad, Noor"},{"full_name":"Liu, Pengfei","first_name":"Pengfei","last_name":"Liu"},{"first_name":"Marie-Louise","full_name":"Haymon, Marie-Louise","last_name":"Haymon"},{"last_name":"Rueschendorf","first_name":"Franz","full_name":"Rueschendorf, Franz"},{"first_name":"Il-Keun","full_name":"Kong, Il-Keun","last_name":"Kong"},{"last_name":"Schnapp","full_name":"Schnapp, Linda","first_name":"Linda"},{"full_name":"Shur, Natasha","first_name":"Natasha","last_name":"Shur"},{"first_name":"Lynn","full_name":"Chorich, Lynn","last_name":"Chorich"},{"last_name":"Layman","full_name":"Layman, Lawrence","first_name":"Lawrence"},{"last_name":"Haaf","full_name":"Haaf, Thomas","first_name":"Thomas"},{"last_name":"Pourkarimi","full_name":"Pourkarimi, Ehsan","first_name":"Ehsan"},{"full_name":"Kim, Hyung-Goo","first_name":"Hyung-Goo","last_name":"Kim"},{"first_name":"Gaurav K.","full_name":"Varshney, Gaurav K.","last_name":"Varshney"}],"keyword":["autosomal recessive","biallelic variants","C","elegans","translation initiation sites","tryptophanyl-tRNA synthetase 1 (WARS1)","WHEP domain","zebrafish"],"language":[{"iso":"eng"}],"doi":"10.1002/humu.24435","ddc":["570"]},{"doi":"10.1002/humu.24430","ddc":["570"],"keyword":["aminoacylation","aminoacyl-tRNA synthetase","ARS","CRISPR","Cas9","intellectual disability","microcephaly","SARS1","tRNA","WARS1","zebrafish"],"language":[{"iso":"eng"}],"pmid":1,"author":[{"first_name":"Nina","full_name":"Boegershausen, Nina","last_name":"Boegershausen"},{"first_name":"Hannah E.","full_name":"Krawczyk, Hannah E.","last_name":"Krawczyk"},{"last_name":"Jamra","first_name":"Rami A.","full_name":"Jamra, Rami A."},{"full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia","last_name":"Lin"},{"last_name":"Yigit","full_name":"Yigit, Goekhan","first_name":"Goekhan"},{"last_name":"Huening","full_name":"Huening, Irina","first_name":"Irina"},{"full_name":"Polo, Anna M.","first_name":"Anna M.","last_name":"Polo"},{"full_name":"Vona, Barbara","first_name":"Barbara","last_name":"Vona"},{"id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","orcid":"0000-0002-2512-7812","first_name":"Kevin","full_name":"Huang, Kevin","last_name":"Huang"},{"last_name":"Schmidt","first_name":"Julia","full_name":"Schmidt, Julia"},{"full_name":"Altmueller, Janine","first_name":"Janine","last_name":"Altmueller"},{"first_name":"Johannes","full_name":"Luppe, Johannes","last_name":"Luppe"},{"last_name":"Platzer","full_name":"Platzer, Konrad","first_name":"Konrad"},{"first_name":"Beate B.","full_name":"Doergeloh, Beate B.","last_name":"Doergeloh"},{"first_name":"Andreas","full_name":"Busche, Andreas","last_name":"Busche"},{"full_name":"Biskup, Saskia","first_name":"Saskia","last_name":"Biskup"},{"last_name":"Mendes, I","first_name":"Marisa","full_name":"Mendes, I, Marisa"},{"full_name":"Smith, Desiree E. C.","first_name":"Desiree E. C.","last_name":"Smith"},{"last_name":"Salomons","first_name":"Gajja S.","full_name":"Salomons, Gajja S."},{"last_name":"Zibat","full_name":"Zibat, Arne","first_name":"Arne"},{"first_name":"Eva","full_name":"Bueltmann, Eva","last_name":"Bueltmann"},{"full_name":"Nuernberg, Peter","first_name":"Peter","last_name":"Nuernberg"},{"first_name":"Malte","full_name":"Spielmann, Malte","last_name":"Spielmann"},{"last_name":"Lemke","full_name":"Lemke, Johannes R.","first_name":"Johannes R."},{"first_name":"Yun","full_name":"Li, Yun","last_name":"Li"},{"last_name":"Zenker","first_name":"Martin","full_name":"Zenker, Martin"},{"full_name":"Varshney, Gaurav K.","first_name":"Gaurav K.","last_name":"Varshney"},{"last_name":"Hillen","full_name":"Hillen, Hauke S.","first_name":"Hauke S."},{"last_name":"Kratz","first_name":"Christian P.","full_name":"Kratz, Christian P."},{"last_name":"Wollnik","full_name":"Wollnik, Bernd","first_name":"Bernd"}],"type":"journal_article","day":"01","title":"WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly","citation":{"apa":"Boegershausen, N., Krawczyk, H. E., Jamra, R. A., Lin, S.-J., Yigit, G., Huening, I., … Wollnik, B. (2022). WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. <i>Human Mutation</i>. Wiley. <a href=\"https://doi.org/10.1002/humu.24430\">https://doi.org/10.1002/humu.24430</a>","ama":"Boegershausen N, Krawczyk HE, Jamra RA, et al. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. <i>Human Mutation</i>. 2022;43(10):1454-1471. doi:<a href=\"https://doi.org/10.1002/humu.24430\">10.1002/humu.24430</a>","short":"N. Boegershausen, H.E. Krawczyk, R.A. Jamra, S.-J. Lin, G. Yigit, I. Huening, A.M. Polo, B. Vona, K. Huang, J. Schmidt, J. Altmueller, J. Luppe, K. Platzer, B.B. Doergeloh, A. Busche, S. Biskup, M. Mendes, I, D.E.C. Smith, G.S. Salomons, A. Zibat, E. Bueltmann, P. Nuernberg, M. Spielmann, J.R. Lemke, Y. Li, M. Zenker, G.K. Varshney, H.S. Hillen, C.P. Kratz, B. Wollnik, Human Mutation 43 (2022) 1454–1471.","mla":"Boegershausen, Nina, et al. “WARS1 and SARS1: Two TRNA Synthetases Implicated in Autosomal Recessive Microcephaly.” <i>Human Mutation</i>, vol. 43, no. 10, Wiley, 2022, pp. 1454–71, doi:<a href=\"https://doi.org/10.1002/humu.24430\">10.1002/humu.24430</a>.","ista":"Boegershausen N, Krawczyk HE, Jamra RA, Lin S-J, Yigit G, Huening I, Polo AM, Vona B, Huang K, Schmidt J, Altmueller J, Luppe J, Platzer K, Doergeloh BB, Busche A, Biskup S, Mendes, I M, Smith DEC, Salomons GS, Zibat A, Bueltmann E, Nuernberg P, Spielmann M, Lemke JR, Li Y, Zenker M, Varshney GK, Hillen HS, Kratz CP, Wollnik B. 2022. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Human Mutation. 43(10), 1454–1471.","ieee":"N. Boegershausen <i>et al.</i>, “WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly,” <i>Human Mutation</i>, vol. 43, no. 10. Wiley, pp. 1454–1471, 2022.","chicago":"Boegershausen, Nina, Hannah E. Krawczyk, Rami A. Jamra, Sheng-Jia Lin, Goekhan Yigit, Irina Huening, Anna M. Polo, et al. “WARS1 and SARS1: Two TRNA Synthetases Implicated in Autosomal Recessive Microcephaly.” <i>Human Mutation</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/humu.24430\">https://doi.org/10.1002/humu.24430</a>."},"status":"public","intvolume":"        43","publication":"Human Mutation","quality_controlled":"1","publisher":"Wiley","date_created":"2023-09-20T20:59:33Z","month":"10","extern":"1","page":"1454-1471","publication_identifier":{"issn":["1059-7794"]},"scopus_import":"1","external_id":{"pmid":["35790048"]},"date_updated":"2023-09-25T08:43:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","year":"2022","has_accepted_license":"1","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":43,"file_date_updated":"2023-09-25T08:41:23Z","oa":1,"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"14357","date_published":"2022-10-01T00:00:00Z","abstract":[{"lang":"eng","text":"Aminoacylation of transfer RNA (tRNA) is a key step in protein biosynthesis, carried out by highly specific aminoacyl-tRNA synthetases (ARSs). ARSs have been implicated in autosomal dominant and autosomal recessive human disorders. Autosomal dominant variants in tryptophanyl-tRNA synthetase 1 (WARS1) are known to cause distal hereditary motor neuropathy and Charcot-Marie-Tooth disease, but a recessively inherited phenotype is yet to be clearly defined. Seryl-tRNA synthetase 1 (SARS1) has rarely been implicated in an autosomal recessive developmental disorder. Here, we report five individuals with biallelic missense variants in WARS1 or SARS1, who presented with an overlapping phenotype of microcephaly, developmental delay, intellectual disability, and brain anomalies. Structural mapping showed that the SARS1 variant is located directly within the enzyme’s active site, most likely diminishing activity, while the WARS1 variant is located in the N-terminal domain. We further characterize the identified WARS1 variant by showing that it negatively impacts protein abundance and is unable to rescue the phenotype of a CRISPR/Cas9 wars1 knockout zebrafish model. In summary, we describe two overlapping autosomal recessive syndromes caused by variants in WARS1 and SARS1, present functional insights into the pathogenesis of the WARS1-related syndrome and define an emerging disease spectrum: ARS-related developmental disorders with or without microcephaly."}],"file":[{"date_created":"2023-09-25T08:41:23Z","success":1,"relation":"main_file","file_id":"14367","content_type":"application/pdf","checksum":"c31fc91e0445c35b9da83eb911a9b552","access_level":"open_access","date_updated":"2023-09-25T08:41:23Z","creator":"dernst","file_size":4863605,"file_name":"2022_HumanMutation_Boegershausen.pdf"}],"article_processing_charge":"No","issue":"10"},{"volume":438,"intvolume":"       438","status":"public","quality_controlled":"1","department":[{"_id":"UlWa"}],"publication":"Bulletin de la Societe Mathematique de France","publication_status":"published","publisher":"Societe Mathematique de France","_id":"14381","abstract":[{"text":"Expander graphs (sparse but highly connected graphs) have, since their inception, been the source of deep links between Mathematics and Computer Science as well as applications to other areas. In recent years, a fascinating theory of high-dimensional expanders has begun to emerge, which is still in a formative stage but has nonetheless already lead to a number of striking results. Unlike for graphs, in higher dimensions there is a rich array of non-equivalent notions of expansion (coboundary expansion, cosystolic expansion, topological expansion, spectral expansion, etc.), with differents strengths and applications. In this talk, we will survey this landscape of high-dimensional expansion, with a focus on two main results. First, we will present Gromov’s Topological Overlap Theorem, which asserts that coboundary expansion (a quantitative version of vanishing mod 2 cohomology) implies topological expansion (roughly, the property that for every map from a simplicial complex to a manifold of the same dimension, the images of a positive fraction of the simplices have a point in common). Second, we will outline a construction of bounded degree 2-dimensional topological expanders, due to Kaufman, Kazhdan, and Lubotzky.","lang":"eng"}],"date_published":"2022-01-01T00:00:00Z","date_created":"2023-10-01T22:01:14Z","month":"01","article_processing_charge":"No","page":"281-294","doi":"10.24033/ast.1188","publication_identifier":{"eissn":["2102-622X"],"issn":["0037-9484"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-03T08:04:03Z","language":[{"iso":"eng"}],"scopus_import":"1","year":"2022","oa_version":"None","author":[{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli","last_name":"Wagner"}],"type":"journal_article","day":"01","article_type":"original","title":"High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others)","citation":{"ama":"Wagner U. High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). <i>Bulletin de la Societe Mathematique de France</i>. 2022;438:281-294. doi:<a href=\"https://doi.org/10.24033/ast.1188\">10.24033/ast.1188</a>","apa":"Wagner, U. (2022). High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). <i>Bulletin de La Societe Mathematique de France</i>. Societe Mathematique de France. <a href=\"https://doi.org/10.24033/ast.1188\">https://doi.org/10.24033/ast.1188</a>","short":"U. Wagner, Bulletin de La Societe Mathematique de France 438 (2022) 281–294.","mla":"Wagner, Uli. “High-Dimensional Expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and Others).” <i>Bulletin de La Societe Mathematique de France</i>, vol. 438, Societe Mathematique de France, 2022, pp. 281–94, doi:<a href=\"https://doi.org/10.24033/ast.1188\">10.24033/ast.1188</a>.","chicago":"Wagner, Uli. “High-Dimensional Expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and Others).” <i>Bulletin de La Societe Mathematique de France</i>. Societe Mathematique de France, 2022. <a href=\"https://doi.org/10.24033/ast.1188\">https://doi.org/10.24033/ast.1188</a>.","ieee":"U. Wagner, “High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others),” <i>Bulletin de la Societe Mathematique de France</i>, vol. 438. Societe Mathematique de France, pp. 281–294, 2022.","ista":"Wagner U. 2022. High-dimensional expanders (after Gromov, Kaufman, Kazhdan, Lubotzky, and others). Bulletin de la Societe Mathematique de France. 438, 281–294."}},{"article_type":"letter_note","year":"2022","oa_version":"None","date_updated":"2023-10-18T06:26:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["36543947"]},"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"issue":"7941","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Future LEDs could be based on lead halide perovskites. A breakthrough in preparing device-compatible solids composed of nanoscale perovskite crystals overcomes a long-standing hurdle in making blue perovskite LEDs."}],"_id":"14437","date_published":"2022-12-21T00:00:00Z","publication_status":"published","volume":612,"citation":{"ama":"Utzat H, Ibáñez M. Molecular engineering enables bright blue LEDs. <i>Nature</i>. 2022;612(7941):638-639. doi:<a href=\"https://doi.org/10.1038/d41586-022-04447-0\">10.1038/d41586-022-04447-0</a>","apa":"Utzat, H., &#38; Ibáñez, M. (2022). Molecular engineering enables bright blue LEDs. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/d41586-022-04447-0\">https://doi.org/10.1038/d41586-022-04447-0</a>","short":"H. Utzat, M. Ibáñez, Nature 612 (2022) 638–639.","mla":"Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” <i>Nature</i>, vol. 612, no. 7941, Springer Nature, 2022, pp. 638–39, doi:<a href=\"https://doi.org/10.1038/d41586-022-04447-0\">10.1038/d41586-022-04447-0</a>.","chicago":"Utzat, Hendrik, and Maria Ibáñez. “Molecular Engineering Enables Bright Blue LEDs.” <i>Nature</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/d41586-022-04447-0\">https://doi.org/10.1038/d41586-022-04447-0</a>.","ieee":"H. Utzat and M. Ibáñez, “Molecular engineering enables bright blue LEDs,” <i>Nature</i>, vol. 612, no. 7941. Springer Nature, pp. 638–639, 2022.","ista":"Utzat H, Ibáñez M. 2022. Molecular engineering enables bright blue LEDs. Nature. 612(7941), 638–639."},"title":"Molecular engineering enables bright blue LEDs","day":"21","author":[{"first_name":"Hendrik","full_name":"Utzat, Hendrik","last_name":"Utzat"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"}],"type":"journal_article","pmid":1,"language":[{"iso":"eng"}],"keyword":["Multidisciplinary"],"doi":"10.1038/d41586-022-04447-0","page":"638-639","month":"12","date_created":"2023-10-17T11:14:43Z","publisher":"Springer Nature","quality_controlled":"1","department":[{"_id":"MaIb"}],"publication":"Nature","status":"public","intvolume":"       612"},{"month":"06","_id":"14520","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses\" at arxiv.org/abs/2206.14104. Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"date_published":"2022-06-28T00:00:00Z","date_created":"2023-11-13T08:09:10Z","article_processing_charge":"No","department":[{"_id":"JoFi"}],"status":"public","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"license":"https://creativecommons.org/publicdomain/zero/1.0/","publisher":"Zenodo","main_file_link":[{"url":"https://doi.org/10.5281/ZENODO.8408897","open_access":"1"}],"oa":1,"day":"28","author":[{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin","full_name":"Zemlicka, Martin"},{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matilda","full_name":"Peruzzo, Matilda","last_name":"Peruzzo","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","last_name":"Hassani","full_name":"Hassani, Farid","first_name":"Farid"},{"last_name":"Trioni","first_name":"Andrea","full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh"},{"last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"type":"research_data_reference","has_accepted_license":"1","year":"2022","oa_version":"Published Version","citation":{"chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.8408897\">https://doi.org/10.5281/ZENODO.8408897</a>.","ieee":"M. Zemlicka <i>et al.</i>, “Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses.” Zenodo, 2022.","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2022. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>.","mla":"Zemlicka, Martin, et al. <i>Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>.","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, (2022).","ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.8408897\">10.5281/ZENODO.8408897</a>","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., &#38; Fink, J. M. (2022). Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8408897\">https://doi.org/10.5281/ZENODO.8408897</a>"},"title":"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-09-10T12:23:57Z","ddc":["530"],"doi":"10.5281/ZENODO.8408897","related_material":{"record":[{"id":"14517","relation":"used_in_publication","status":"public"}]}},{"publication_status":"submitted","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2203.17143"}],"department":[{"_id":"JuFi"}],"publication":"arXiv","status":"public","arxiv":1,"article_processing_charge":"No","month":"03","abstract":[{"lang":"eng","text":"Phase-field models such as the Allen-Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen-Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow.\r\nIn the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: As long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen-Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε1/2).\r\nOur approach is based on the gradient flow structure of the Allen-Cahn equation and its limiting motion: Building on the recent concept of \"gradient flow calibrations\" for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen-Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen-Cahn operator or additional convergence hypotheses for the energy at positive times."}],"_id":"14597","date_published":"2022-03-31T00:00:00Z","date_created":"2023-11-23T09:30:02Z","related_material":{"record":[{"id":"14587","relation":"dissertation_contains","status":"public"}]},"project":[{"name":"Bridging Scales in Random Materials","grant_number":"948819","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"language":[{"iso":"eng"}],"date_updated":"2023-11-30T13:25:02Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["2203.17143"]},"doi":"10.48550/ARXIV.2203.17143","ec_funded":1,"citation":{"ista":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv, <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>.","ieee":"J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow,” <i>arXiv</i>. .","chicago":"Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">https://doi.org/10.48550/ARXIV.2203.17143</a>.","mla":"Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>.","short":"J.L. Fischer, A. Marveggio, ArXiv (n.d.).","apa":"Fischer, J. L., &#38; Marveggio, A. (n.d.). Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">https://doi.org/10.48550/ARXIV.2203.17143</a>","ama":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2203.17143\">10.48550/ARXIV.2203.17143</a>"},"title":"Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow","day":"31","oa_version":"Preprint","year":"2022","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","last_name":"Fischer","full_name":"Fischer, Julian L","first_name":"Julian L"},{"id":"25647992-AA84-11E9-9D75-8427E6697425","last_name":"Marveggio","full_name":"Marveggio, Alice","first_name":"Alice"}],"type":"preprint"},{"title":"Learning control policies for stochastic systems with reach-avoid guarantees","citation":{"apa":"Zikelic, D., Lechner, M., Henzinger, T. A., &#38; Chatterjee, K. (n.d.). Learning control policies for stochastic systems with reach-avoid guarantees. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">https://doi.org/10.48550/ARXIV.2210.05308</a>","ama":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">10.48550/ARXIV.2210.05308</a>","short":"D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, ArXiv (n.d.).","mla":"Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">10.48550/ARXIV.2210.05308</a>.","ista":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. arXiv, <a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">10.48550/ARXIV.2210.05308</a>.","ieee":"D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control policies for stochastic systems with reach-avoid guarantees,” <i>arXiv</i>. .","chicago":"Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2210.05308\">https://doi.org/10.48550/ARXIV.2210.05308</a>."},"ec_funded":1,"type":"preprint","author":[{"last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"oa_version":"Preprint","year":"2022","day":"29","related_material":{"record":[{"id":"14539","relation":"dissertation_contains","status":"public"},{"id":"14830","relation":"later_version","status":"public"}]},"project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"doi":"10.48550/ARXIV.2210.05308","external_id":{"arxiv":["2210.05308"]},"date_updated":"2025-07-14T09:10:02Z","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","arxiv":1,"_id":"14600","abstract":[{"lang":"eng","text":"We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold $p\\in[0,1]$ over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on $3$ stochastic non-linear reinforcement learning tasks."}],"date_published":"2022-11-29T00:00:00Z","date_created":"2023-11-24T13:10:09Z","month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2210.05308"}],"publication_status":"submitted","license":"https://creativecommons.org/licenses/by-sa/4.0/","status":"public","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"publication":"arXiv","department":[{"_id":"KrCh"},{"_id":"ToHe"}]},{"article_processing_charge":"No","arxiv":1,"_id":"14601","date_published":"2022-05-24T00:00:00Z","date_created":"2023-11-24T13:22:30Z","abstract":[{"text":"In this work, we address the problem of learning provably stable neural\r\nnetwork policies for stochastic control systems. While recent work has\r\ndemonstrated the feasibility of certifying given policies using martingale\r\ntheory, the problem of how to learn such policies is little explored. Here, we\r\nstudy the effectiveness of jointly learning a policy together with a martingale\r\ncertificate that proves its stability using a single learning algorithm. We\r\nobserve that the joint optimization problem becomes easily stuck in local\r\nminima when starting from a randomly initialized policy. Our results suggest\r\nthat some form of pre-training of the policy is required for the joint\r\noptimization to repair and verify the policy successfully.","lang":"eng"}],"month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2205.11991"}],"oa":1,"publication_status":"submitted","status":"public","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication":"arXiv","title":"Learning stabilizing policies in stochastic control systems","ec_funded":1,"citation":{"short":"D. Zikelic, M. Lechner, K. Chatterjee, T.A. Henzinger, ArXiv (n.d.).","ama":"Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2205.11991\">10.48550/arXiv.2205.11991</a>","apa":"Zikelic, D., Lechner, M., Chatterjee, K., &#38; Henzinger, T. A. (n.d.). Learning stabilizing policies in stochastic control systems. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2205.11991\">https://doi.org/10.48550/arXiv.2205.11991</a>","chicago":"Zikelic, Dorde, Mathias Lechner, Krishnendu Chatterjee, and Thomas A Henzinger. “Learning Stabilizing Policies in Stochastic Control Systems.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2205.11991\">https://doi.org/10.48550/arXiv.2205.11991</a>.","ieee":"D. Zikelic, M. Lechner, K. Chatterjee, and T. A. Henzinger, “Learning stabilizing policies in stochastic control systems,” <i>arXiv</i>. .","ista":"Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. arXiv, <a href=\"https://doi.org/10.48550/arXiv.2205.11991\">10.48550/arXiv.2205.11991</a>.","mla":"Zikelic, Dorde, et al. “Learning Stabilizing Policies in Stochastic Control Systems.” <i>ArXiv</i>, doi:<a href=\"https://doi.org/10.48550/arXiv.2205.11991\">10.48550/arXiv.2205.11991</a>."},"oa_version":"Preprint","year":"2022","author":[{"last_name":"Zikelic","full_name":"Zikelic, Dorde","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","full_name":"Lechner, Mathias","last_name":"Lechner"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"type":"preprint","day":"24","project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14539"}]},"doi":"10.48550/arXiv.2205.11991","date_updated":"2025-07-14T09:10:00Z","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["2205.11991"]}},{"date_updated":"2023-08-03T12:40:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"doi":"10.5061/DRYAD.GTHT76HMZ","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11733"}]},"day":"02","author":[{"last_name":"Orliac","first_name":"Etienne","full_name":"Orliac, Etienne"},{"first_name":"Daniel","full_name":"Trejo Banos, Daniel","last_name":"Trejo Banos"},{"last_name":"Ojavee","full_name":"Ojavee, Sven","first_name":"Sven"},{"full_name":"Läll, Kristi","first_name":"Kristi","last_name":"Läll"},{"last_name":"Mägi","full_name":"Mägi, Reedik","first_name":"Reedik"},{"last_name":"Visscher","full_name":"Visscher, Peter","first_name":"Peter"},{"last_name":"Robinson","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"type":"research_data_reference","year":"2022","oa_version":"Published Version","citation":{"chicago":"Orliac, Etienne, Daniel Trejo Banos, Sven Ojavee, Kristi Läll, Reedik Mägi, Peter Visscher, and Matthew Richard Robinson. “Improving Genome-Wide Association Discovery and Genomic Prediction Accuracy in Biobank Data.” Dryad, 2022. <a href=\"https://doi.org/10.5061/DRYAD.GTHT76HMZ\">https://doi.org/10.5061/DRYAD.GTHT76HMZ</a>.","ista":"Orliac E, Trejo Banos D, Ojavee S, Läll K, Mägi R, Visscher P, Robinson MR. 2022. Improving genome-wide association discovery and genomic prediction accuracy in biobank data, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.GTHT76HMZ\">10.5061/DRYAD.GTHT76HMZ</a>.","ieee":"E. Orliac <i>et al.</i>, “Improving genome-wide association discovery and genomic prediction accuracy in biobank data.” Dryad, 2022.","mla":"Orliac, Etienne, et al. <i>Improving Genome-Wide Association Discovery and Genomic Prediction Accuracy in Biobank Data</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.5061/DRYAD.GTHT76HMZ\">10.5061/DRYAD.GTHT76HMZ</a>.","short":"E. Orliac, D. Trejo Banos, S. Ojavee, K. Läll, R. Mägi, P. Visscher, M.R. Robinson, (2022).","ama":"Orliac E, Trejo Banos D, Ojavee S, et al. Improving genome-wide association discovery and genomic prediction accuracy in biobank data. 2022. doi:<a href=\"https://doi.org/10.5061/DRYAD.GTHT76HMZ\">10.5061/DRYAD.GTHT76HMZ</a>","apa":"Orliac, E., Trejo Banos, D., Ojavee, S., Läll, K., Mägi, R., Visscher, P., &#38; Robinson, M. R. (2022). Improving genome-wide association discovery and genomic prediction accuracy in biobank data. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.GTHT76HMZ\">https://doi.org/10.5061/DRYAD.GTHT76HMZ</a>"},"title":"Improving genome-wide association discovery and genomic prediction accuracy in biobank data","department":[{"_id":"MaRo"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"status":"public","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.gtht76hmz"}],"oa":1,"month":"09","_id":"13064","abstract":[{"text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R 2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h SNP 2 . We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies.","lang":"eng"}],"date_created":"2023-05-23T16:28:13Z","date_published":"2022-09-02T00:00:00Z","article_processing_charge":"No"},{"month":"07","date_published":"2022-07-28T00:00:00Z","_id":"13066","abstract":[{"text":"Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.","lang":"eng"}],"date_created":"2023-05-23T16:33:12Z","article_processing_charge":"No","department":[{"_id":"NiBa"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"status":"public","publisher":"Dryad","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.m905qfv4b","open_access":"1"}],"day":"28","year":"2022","oa_version":"Published Version","type":"research_data_reference","author":[{"full_name":"Koch, Eva","first_name":"Eva","last_name":"Koch"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"},{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"full_name":"Jonannesson, Kerstin","first_name":"Kerstin","last_name":"Jonannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"citation":{"ama":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. 2022. doi:<a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">10.5061/DRYAD.M905QFV4B</a>","apa":"Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., &#38; Butlin, R. (2022). Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">https://doi.org/10.5061/DRYAD.M905QFV4B</a>","short":"E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022).","mla":"Koch, Eva, et al. <i>Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">10.5061/DRYAD.M905QFV4B</a>.","chicago":"Koch, Eva, Mark Ravinet, Anja M Westram, Kerstin Jonannesson, and Roger Butlin. “Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution.” Dryad, 2022. <a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">https://doi.org/10.5061/DRYAD.M905QFV4B</a>.","ista":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. 2022. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.M905QFV4B\">10.5061/DRYAD.M905QFV4B</a>.","ieee":"E. Koch, M. Ravinet, A. M. Westram, K. Jonannesson, and R. Butlin, “Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution.” Dryad, 2022."},"title":"Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution","date_updated":"2023-08-04T09:42:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"doi":"10.5061/DRYAD.M905QFV4B","related_material":{"record":[{"status":"public","id":"12247","relation":"used_in_publication"}]}}]