[{"publication_status":"published","publisher":"American Mathematical Society","department":[{"_id":"JaMa"}],"acknowledgement":"The second author was supported by the priority program SPP2026 of the German Research Foundation (DFG). The fourth author was supported by the German Academic Scholarship Foundation (Studienstiftung des deutschen Volkes) and by the German Research Foundation (DFG) via RTG 1523/2.","year":"2023","date_updated":"2023-11-14T13:07:09Z","date_created":"2023-07-02T22:00:43Z","volume":151,"author":[{"first_name":"Bobo","last_name":"Hua","full_name":"Hua, Bobo"},{"last_name":"Keller","first_name":"Matthias","full_name":"Keller, Matthias"},{"full_name":"Schwarz, Michael","last_name":"Schwarz","first_name":"Michael"},{"full_name":"Wirth, Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","first_name":"Melchior","last_name":"Wirth"}],"month":"08","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1804.08353"],"isi":["000988204400001"]},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1804.08353"}],"language":[{"iso":"eng"}],"doi":"10.1090/proc/14361","type":"journal_article","abstract":[{"text":"In this note we study the eigenvalue growth of infinite graphs with discrete spectrum. We assume that the corresponding Dirichlet forms satisfy certain Sobolev-type inequalities and that the total measure is finite. In this sense, the associated operators on these graphs display similarities to elliptic operators on bounded domains in the continuum. Specifically, we prove lower bounds on the eigenvalue growth and show by examples that corresponding upper bounds cannot be established.","lang":"eng"}],"issue":"8","status":"public","title":"Sobolev-type inequalities and eigenvalue growth on graphs with finite measure","intvolume":" 151","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13177","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"3401-3414","publication":"Proceedings of the American Mathematical Society","citation":{"chicago":"Hua, Bobo, Matthias Keller, Michael Schwarz, and Melchior Wirth. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings of the American Mathematical Society. American Mathematical Society, 2023. https://doi.org/10.1090/proc/14361.","mla":"Hua, Bobo, et al. “Sobolev-Type Inequalities and Eigenvalue Growth on Graphs with Finite Measure.” Proceedings of the American Mathematical Society, vol. 151, no. 8, American Mathematical Society, 2023, pp. 3401–14, doi:10.1090/proc/14361.","short":"B. Hua, M. Keller, M. Schwarz, M. Wirth, Proceedings of the American Mathematical Society 151 (2023) 3401–3414.","ista":"Hua B, Keller M, Schwarz M, Wirth M. 2023. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. 151(8), 3401–3414.","ieee":"B. Hua, M. Keller, M. Schwarz, and M. Wirth, “Sobolev-type inequalities and eigenvalue growth on graphs with finite measure,” Proceedings of the American Mathematical Society, vol. 151, no. 8. American Mathematical Society, pp. 3401–3414, 2023.","apa":"Hua, B., Keller, M., Schwarz, M., & Wirth, M. (2023). Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/14361","ama":"Hua B, Keller M, Schwarz M, Wirth M. Sobolev-type inequalities and eigenvalue growth on graphs with finite measure. Proceedings of the American Mathematical Society. 2023;151(8):3401-3414. doi:10.1090/proc/14361"},"date_published":"2023-08-01T00:00:00Z"},{"ec_funded":1,"department":[{"_id":"MoHe"}],"publisher":"Society for Industrial and Applied Mathematics","publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grants 715672 and\r\n101019564 ``The Design of Modern Fully Dynamic Data Structures (MoDynStruct)\"\") and from the Engineering and Physical Sciences Research Council, UK (EPSRC) under grant EP/S03353X/1. The second author was also supported by the Austrian Science Fund (FWF) project ``Fast Algorithms for a Reactive Network Layer (ReactNet),\"\" P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020--2024, project ``Static and Dynamic Hierarchical Graph Decompositions,\"\"I 5982-N, and project Z 422-N. The third author was also supported by the Swedish Research Council (Reg. No. 2015-04659). The fourth author was also supported by the Science and Technology Development Fund (FDCT), Macau SAR (file 0014/2022/AFJ, 0085/2022/A, 0143/2020/A3, and SKL-IOTSC-2021-2023).","year":"2023","volume":52,"date_created":"2023-11-19T23:00:56Z","date_updated":"2023-11-20T08:21:07Z","author":[{"first_name":"Sayan","last_name":"Bhattacharya","full_name":"Bhattacharya, Sayan"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Danupon","last_name":"Nanongkai","full_name":"Nanongkai, Danupon"},{"full_name":"Wu, Xiaowei","last_name":"Wu","first_name":"Xiaowei"}],"publication_identifier":{"eissn":["1095-7111"],"issn":["0097-5397"]},"month":"10","project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger"},{"grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1137/21M1428649","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"n the dynamic minimum set cover problem, the challenge is to minimize the update time while guaranteeing a close-to-optimal min{O(log n), f} approximation factor. (Throughout, n, m, f , and C are parameters denoting the maximum number of elements, the number of sets, the frequency, and the cost range.) In the high-frequency range, when f = Ω(log n) , this was achieved by a deterministic O(log n) -approximation algorithm with O(f log n) amortized update time by Gupta et al. [Online and dynamic algorithms for set cover, in Proceedings STOC 2017, ACM, pp. 537–550]. In this paper we consider the low-frequency range, when f = O(log n) , and obtain deterministic algorithms with a (1 + ∈)f -approximation ratio and the following guarantees on the update time. (1) O ((f/∈)-log(Cn)) amortized update time: Prior to our work, the best approximation ratio guaranteed by deterministic algorithms was O(f2) of Bhattacharya, Henzinger, and Italiano [Design of dynamic algorithms via primal-dual method, in Proceedings ICALP 2015, Springer, pp. 206–218]. In contrast, the only result with O(f) -approximation was that of Abboud et al. [Dynamic set cover: Improved algorithms and lower bounds, in Proceedings STOC 2019, ACM, pp. 114–125], who designed a randomized (1+∈)f -approximation algorithm with amortized update time. (2) O(f2/∈3 + (f/∈2).logC) amortized update time: This result improves the above update time bound for most values of f\r\n in the low-frequency range, i.e., f=o(log n) . It is also the first result that is independent of m\r\n and n. It subsumes the constant amortized update time of Bhattacharya and Kulkarni [Deterministically maintaining a (2 + ∈) -approximate minimum vertex cover in O(1/∈2) amortized update time, in Proceedings SODA 2019, SIAM, pp. 1872–1885] for unweighted dynamic vertex cover (i.e., when f = 2 and C = 1). (3) O((f/∈3).log2(Cn)) worst-case update time: No nontrivial worst-case update time was previously known for the dynamic set cover problem. Our bound subsumes and improves by a logarithmic factor the O(log3n/poly (∈)) \r\n worst-case update time for the unweighted dynamic vertex cover problem (i.e., when f = 2\r\n and C =1) of Bhattacharya, Henzinger, and Nanongkai [Fully dynamic approximate maximum matching and minimum vertex cover in O(log3)n worst case update time, in Proceedings SODA 2017, SIAM, pp. 470–489]. We achieve our results via the primal-dual approach, by maintaining a fractional packing solution as a dual certificate. Prior work in dynamic algorithms that employs the primal-dual approach uses a local update scheme that maintains relaxed complementary slackness conditions for every set. For our first result we use instead a global update scheme that does not always maintain complementary slackness conditions. For our second result we combine the global and the local update schema. To achieve our third result we use a hierarchy of background schedulers. It is an interesting open question whether this background scheduler technique can also be used to transform algorithms with amortized running time bounds into algorithms with worst-case running time bounds."}],"intvolume":" 52","title":"Deterministic near-optimal approximation algorithms for dynamic set cover","status":"public","_id":"14558","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"01","page":"1132-1192","article_type":"original","citation":{"ista":"Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. 2023. Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. 52(5), 1132–1192.","apa":"Bhattacharya, S., Henzinger, M. H., Nanongkai, D., & Wu, X. (2023). Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21M1428649","ieee":"S. Bhattacharya, M. H. Henzinger, D. Nanongkai, and X. Wu, “Deterministic near-optimal approximation algorithms for dynamic set cover,” SIAM Journal on Computing, vol. 52, no. 5. Society for Industrial and Applied Mathematics, pp. 1132–1192, 2023.","ama":"Bhattacharya S, Henzinger MH, Nanongkai D, Wu X. Deterministic near-optimal approximation algorithms for dynamic set cover. SIAM Journal on Computing. 2023;52(5):1132-1192. doi:10.1137/21M1428649","chicago":"Bhattacharya, Sayan, Monika H Henzinger, Danupon Nanongkai, and Xiaowei Wu. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/21M1428649.","mla":"Bhattacharya, Sayan, et al. “Deterministic Near-Optimal Approximation Algorithms for Dynamic Set Cover.” SIAM Journal on Computing, vol. 52, no. 5, Society for Industrial and Applied Mathematics, 2023, pp. 1132–92, doi:10.1137/21M1428649.","short":"S. Bhattacharya, M.H. Henzinger, D. Nanongkai, X. Wu, SIAM Journal on Computing 52 (2023) 1132–1192."},"publication":"SIAM Journal on Computing","date_published":"2023-10-01T00:00:00Z"},{"publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Springer Nature","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2023","date_created":"2023-11-19T23:00:56Z","date_updated":"2023-11-20T08:30:20Z","volume":14215,"author":[{"full_name":"Ansaripour, Matin","last_name":"Ansaripour","first_name":"Matin"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias","last_name":"Lechner","full_name":"Lechner, Mathias"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde","last_name":"Zikelic"}],"ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"language":[{"iso":"eng"}],"conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2023-10-27","location":"Singapore, Singapore","start_date":"2023-10-24"},"doi":"10.1007/978-3-031-45329-8_17","month":"10","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031453281"]},"title":"Learning provably stabilizing neural controllers for discrete-time stochastic systems","status":"public","intvolume":" 14215","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14559","oa_version":"None","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice.","lang":"eng"}],"page":"357-379","publication":"21st International Symposium on Automated Technology for Verification and Analysis","citation":{"ama":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. Learning provably stabilizing neural controllers for discrete-time stochastic systems. In: 21st International Symposium on Automated Technology for Verification and Analysis. Vol 14215. Springer Nature; 2023:357-379. doi:10.1007/978-3-031-45329-8_17","ieee":"M. Ansaripour, K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “Learning provably stabilizing neural controllers for discrete-time stochastic systems,” in 21st International Symposium on Automated Technology for Verification and Analysis, Singapore, Singapore, 2023, vol. 14215, pp. 357–379.","apa":"Ansaripour, M., Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). Learning provably stabilizing neural controllers for discrete-time stochastic systems. In 21st International Symposium on Automated Technology for Verification and Analysis (Vol. 14215, pp. 357–379). Singapore, Singapore: Springer Nature. https://doi.org/10.1007/978-3-031-45329-8_17","ista":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. Learning provably stabilizing neural controllers for discrete-time stochastic systems. 21st International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 14215, 357–379.","short":"M. Ansaripour, K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, 21st International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2023, pp. 357–379.","mla":"Ansaripour, Matin, et al. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” 21st International Symposium on Automated Technology for Verification and Analysis, vol. 14215, Springer Nature, 2023, pp. 357–79, doi:10.1007/978-3-031-45329-8_17.","chicago":"Ansaripour, Matin, Krishnendu Chatterjee, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” In 21st International Symposium on Automated Technology for Verification and Analysis, 14215:357–79. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-45329-8_17."},"date_published":"2023-10-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No"},{"article_type":"original","page":"3061-3090","publication":"ESAIM: Mathematical Modelling and Numerical Analysis","citation":{"chicago":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences, 2023. https://doi.org/10.1051/m2an/2023077.","short":"F. Cornalba, T. Shardlow, ESAIM: Mathematical Modelling and Numerical Analysis 57 (2023) 3061–3090.","mla":"Cornalba, Federico, and Tony Shardlow. “The Regularised Inertial Dean’ Kawasaki Equation: Discontinuous Galerkin Approximation and Modelling for Low-Density Regime.” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5, EDP Sciences, 2023, pp. 3061–90, doi:10.1051/m2an/2023077.","ieee":"F. Cornalba and T. Shardlow, “The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime,” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 57, no. 5. EDP Sciences, pp. 3061–3090, 2023.","apa":"Cornalba, F., & Shardlow, T. (2023). The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2023077","ista":"Cornalba F, Shardlow T. 2023. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 57(5), 3061–3090.","ama":"Cornalba F, Shardlow T. The regularised inertial Dean’ Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime. ESAIM: Mathematical Modelling and Numerical Analysis. 2023;57(5):3061-3090. doi:10.1051/m2an/2023077"},"date_published":"2023-09-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","status":"public","ddc":["510"],"title":"The regularised inertial Dean' Kawasaki equation: Discontinuous Galerkin approximation and modelling for low-density regime","intvolume":" 57","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14554","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14560","date_created":"2023-11-20T08:34:57Z","date_updated":"2023-11-20T08:34:57Z","checksum":"3aef1475b1882c8dec112df9a5167c39","success":1,"file_name":"2023_ESAIM_Cornalba.pdf","access_level":"open_access","file_size":1508534,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The Regularised Inertial Dean–Kawasaki model (RIDK) – introduced by the authors and J. Zimmer in earlier works – is a nonlinear stochastic PDE capturing fluctuations around the meanfield limit for large-scale particle systems in both particle density and momentum density. We focus on the following two aspects. Firstly, we set up a Discontinuous Galerkin (DG) discretisation scheme for the RIDK model: we provide suitable definitions of numerical fluxes at the interface of the mesh elements which are consistent with the wave-type nature of the RIDK model and grant stability of the simulations, and we quantify the rate of convergence in mean square to the continuous RIDK model. Secondly, we introduce modifications of the RIDK model in order to preserve positivity of the density (such a feature only holds in a “high-probability sense” for the original RIDK model). By means of numerical simulations, we show that the modifications lead to physically realistic and positive density profiles. In one case, subject to additional regularity constraints, we also prove positivity. Finally, we present an application of our methodology to a system of diffusing and reacting particles. Our Python code is available in open-source format."}],"issue":"5","quality_controlled":"1","project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1051/m2an/2023077","month":"09","publication_identifier":{"eissn":["2804-7214"],"issn":["2822-7840"]},"publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"EDP Sciences","year":"2023","acknowledgement":"The authors thank the anonymous referees for their careful reading of the manuscript and their\r\nvaluable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement No. 754411 (the latter funding source covered the first part of this project).","date_updated":"2023-11-20T08:38:47Z","date_created":"2023-11-19T23:00:55Z","volume":57,"author":[{"full_name":"Cornalba, Federico","orcid":"0000-0002-6269-5149","id":"2CEB641C-A400-11E9-A717-D712E6697425","last_name":"Cornalba","first_name":"Federico"},{"last_name":"Shardlow","first_name":"Tony","full_name":"Shardlow, Tony"}],"related_material":{"link":[{"url":"https://github.com/tonyshardlow/RIDK-FD","relation":"software"}]},"file_date_updated":"2023-11-20T08:34:57Z","ec_funded":1},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","article_number":"14242","author":[{"last_name":"Berdan","first_name":"Emma L.","full_name":"Berdan, Emma L."},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"last_name":"Fragata","first_name":"Inês","full_name":"Fragata, Inês"},{"full_name":"Gilbert, Kimberly J.","first_name":"Kimberly J.","last_name":"Gilbert"},{"full_name":"Jay, Paul","first_name":"Paul","last_name":"Jay"},{"first_name":"Martin","last_name":"Kapun","full_name":"Kapun, Martin"},{"full_name":"Lotterhos, Katie E.","first_name":"Katie E.","last_name":"Lotterhos"},{"full_name":"Mérot, Claire","last_name":"Mérot","first_name":"Claire"},{"full_name":"Durmaz Mitchell, Esra","last_name":"Durmaz Mitchell","first_name":"Esra"},{"full_name":"Pascual, Marta","first_name":"Marta","last_name":"Pascual"},{"first_name":"Catherine L.","last_name":"Peichel","full_name":"Peichel, Catherine L."},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Schaeffer, Stephen W.","last_name":"Schaeffer","first_name":"Stephen W."},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Flatt, Thomas","first_name":"Thomas","last_name":"Flatt"}],"date_updated":"2023-11-20T08:51:09Z","date_created":"2023-11-19T23:00:55Z","year":"2023","acknowledgement":"We are grateful to two referees and Luke Holman for valuable comments on a previous version of our manuscript. This paper was conceived at the ESEB Progress Meeting ‘Disentangling neutral versus adaptive evolution in chromosomal inversions’, organized by ELB, KJ and TF and held at Tjärnö Marine Laboratory (Sweden) between 28 February and 3 March 2022. We are indebted to ESEB for sponsoring our workshop and to the following funding bodies for supporting our research: ERC AdG 101055327 to NHB; Swedish Research Council (VR) 2018-03695 and Leverhulme Trust RPG-2021-141 to RKB; Fundação para a Ciência e a Tecnologia (FCT) contract 2020.00275.CEECIND and research project PTDC/BIA-1232 EVL/1614/2021 to RF; Fundação para a Ciência e a Tecnologia (FCT) junior researcher contract CEECIND/02616/2018 to IF; Swiss National Science Foundation (SNSF) Ambizione #PZ00P3_185952 to KJG; National Science Foundation NSF-OCE 2043905 and NSF-DEB 1655701 to KEL; Swiss National Science Foundation (SNSF) 310030_204681 to CLP; Swedish Research Council (VR) 2021-05243 to MR; Norwegian Research Council grant 315287 to AMW; Swiss National Science Foundation (SNSF) 31003A-182262 and FZEB-0-214654 to TF. We also thank Luca Ferretti for the discussion and Eliane Zinn (Flatt lab) for help with reference formatting.","publication_status":"epub_ahead","department":[{"_id":"NiBa"}],"publisher":"Wiley","month":"11","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"doi":"10.1111/jeb.14242","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.14242"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","abstract":[{"text":"Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","_id":"14556","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"How chromosomal inversions reorient the evolutionary process","day":"08","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-11-08T00:00:00Z","publication":"Journal of Evolutionary Biology","citation":{"chicago":"Berdan, Emma L., Nicholas H Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Inês Fragata, Kimberly J. Gilbert, et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology. Wiley, 2023. https://doi.org/10.1111/jeb.14242.","short":"E.L. Berdan, N.H. Barton, R. Butlin, B. Charlesworth, R. Faria, I. Fragata, K.J. Gilbert, P. Jay, M. Kapun, K.E. Lotterhos, C. Mérot, E. Durmaz Mitchell, M. Pascual, C.L. Peichel, M. Rafajlović, A.M. Westram, S.W. Schaeffer, K. Johannesson, T. Flatt, Journal of Evolutionary Biology (2023).","mla":"Berdan, Emma L., et al. “How Chromosomal Inversions Reorient the Evolutionary Process.” Journal of Evolutionary Biology, 14242, Wiley, 2023, doi:10.1111/jeb.14242.","ieee":"E. L. Berdan et al., “How chromosomal inversions reorient the evolutionary process,” Journal of Evolutionary Biology. Wiley, 2023.","apa":"Berdan, E. L., Barton, N. H., Butlin, R., Charlesworth, B., Faria, R., Fragata, I., … Flatt, T. (2023). How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14242","ista":"Berdan EL, Barton NH, Butlin R, Charlesworth B, Faria R, Fragata I, Gilbert KJ, Jay P, Kapun M, Lotterhos KE, Mérot C, Durmaz Mitchell E, Pascual M, Peichel CL, Rafajlović M, Westram AM, Schaeffer SW, Johannesson K, Flatt T. 2023. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology., 14242.","ama":"Berdan EL, Barton NH, Butlin R, et al. How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology. 2023. doi:10.1111/jeb.14242"},"article_type":"review"},{"language":[{"iso":"eng"}],"doi":"10.3389/fcell.2023.1287420","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["2296-634X"]},"month":"10","volume":11,"date_updated":"2023-11-20T08:44:17Z","date_created":"2023-11-19T23:00:55Z","author":[{"last_name":"Riedl","first_name":"Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"publisher":"Frontiers","department":[{"_id":"MiSi"}],"publication_status":"published","year":"2023","acknowledgement":"The author(s) declare that no financial support was received for the research, authorship, and/or publication of this article.","file_date_updated":"2023-11-20T08:41:15Z","article_number":"1287420","date_published":"2023-10-31T00:00:00Z","article_type":"original","citation":{"chicago":"Riedl, Michael, and Michael K Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental Biology. Frontiers, 2023. https://doi.org/10.3389/fcell.2023.1287420.","short":"M. Riedl, M.K. Sixt, Frontiers in Cell and Developmental Biology 11 (2023).","mla":"Riedl, Michael, and Michael K. Sixt. “The Excitable Nature of Polymerizing Actin and the Belousov-Zhabotinsky Reaction.” Frontiers in Cell and Developmental Biology, vol. 11, 1287420, Frontiers, 2023, doi:10.3389/fcell.2023.1287420.","ieee":"M. Riedl and M. K. Sixt, “The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction,” Frontiers in Cell and Developmental Biology, vol. 11. Frontiers, 2023.","apa":"Riedl, M., & Sixt, M. K. (2023). The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2023.1287420","ista":"Riedl M, Sixt MK. 2023. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 11, 1287420.","ama":"Riedl M, Sixt MK. The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction. Frontiers in Cell and Developmental Biology. 2023;11. doi:10.3389/fcell.2023.1287420"},"publication":"Frontiers in Cell and Developmental Biology","article_processing_charge":"Yes","has_accepted_license":"1","day":"31","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2023_FrontiersCellDevBio_Riedl.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2047622,"file_id":"14561","relation":"main_file","date_created":"2023-11-20T08:41:15Z","date_updated":"2023-11-20T08:41:15Z","success":1,"checksum":"61857fc3ebf019354932e7ee684658ce"}],"intvolume":" 11","status":"public","ddc":["570"],"title":"The excitable nature of polymerizing actin and the Belousov-Zhabotinsky reaction","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14555","abstract":[{"lang":"eng","text":"The intricate regulatory processes behind actin polymerization play a crucial role in cellular biology, including essential mechanisms such as cell migration or cell division. However, the self-organizing principles governing actin polymerization are still poorly understood. In this perspective article, we compare the Belousov-Zhabotinsky (BZ) reaction, a classic and well understood chemical oscillator known for its self-organizing spatiotemporal dynamics, with the excitable dynamics of polymerizing actin. While the BZ reaction originates from the domain of inorganic chemistry, it shares remarkable similarities with actin polymerization, including the characteristic propagating waves, which are influenced by geometry and external fields, and the emergent collective behavior. Starting with a general description of emerging patterns, we elaborate on single droplets or cell-level dynamics, the influence of geometric confinements and conclude with collective interactions. Comparing these two systems sheds light on the universal nature of self-organization principles in both living and inanimate systems."}],"type":"journal_article"},{"year":"2023","publisher":"Oxford University Press","department":[{"_id":"GradSch"}],"publication_status":"epub_ahead","author":[{"last_name":"Kaiyrzhanov","first_name":"Rauan","full_name":"Kaiyrzhanov, Rauan"},{"first_name":"Aboulfazl","last_name":"Rad","full_name":"Rad, Aboulfazl"},{"last_name":"Lin","first_name":"Sheng-Jia","full_name":"Lin, Sheng-Jia"},{"full_name":"Bertoli-Avella, Aida","last_name":"Bertoli-Avella","first_name":"Aida"},{"first_name":"Wouter W","last_name":"Kallemeijn","full_name":"Kallemeijn, Wouter W"},{"first_name":"Annie","last_name":"Godwin","full_name":"Godwin, Annie"},{"first_name":"Maha S","last_name":"Zaki","full_name":"Zaki, Maha S"},{"id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","orcid":"0000-0002-2512-7812","first_name":"Kevin","last_name":"Huang","full_name":"Huang, Kevin"},{"full_name":"Lau, Tracy","last_name":"Lau","first_name":"Tracy"},{"full_name":"Petree, Cassidy","first_name":"Cassidy","last_name":"Petree"},{"full_name":"Efthymiou, Stephanie","first_name":"Stephanie","last_name":"Efthymiou"},{"first_name":"Ehsan","last_name":"Ghayoor Karimiani","full_name":"Ghayoor Karimiani, Ehsan"},{"full_name":"Hempel, Maja","last_name":"Hempel","first_name":"Maja"},{"first_name":"Elizabeth A","last_name":"Normand","full_name":"Normand, Elizabeth A"},{"full_name":"Rudnik-Schöneborn, Sabine","last_name":"Rudnik-Schöneborn","first_name":"Sabine"},{"full_name":"Schatz, Ulrich A","first_name":"Ulrich A","last_name":"Schatz"},{"full_name":"Baggelaar, Marc P","first_name":"Marc P","last_name":"Baggelaar"},{"first_name":"Muhammad","last_name":"Ilyas","full_name":"Ilyas, Muhammad"},{"full_name":"Sultan, Tipu","first_name":"Tipu","last_name":"Sultan"},{"first_name":"Javeria Raza","last_name":"Alvi","full_name":"Alvi, Javeria Raza"},{"first_name":"Manizha","last_name":"Ganieva","full_name":"Ganieva, Manizha"},{"full_name":"Fowler, Ben","first_name":"Ben","last_name":"Fowler"},{"full_name":"Aanicai, Ruxandra","last_name":"Aanicai","first_name":"Ruxandra"},{"full_name":"Akay Tayfun, Gulsen","first_name":"Gulsen","last_name":"Akay Tayfun"},{"full_name":"Al Saman, Abdulaziz","last_name":"Al Saman","first_name":"Abdulaziz"},{"full_name":"Alswaid, Abdulrahman","first_name":"Abdulrahman","last_name":"Alswaid"},{"last_name":"Amiri","first_name":"Nafise","full_name":"Amiri, Nafise"},{"first_name":"Nilufar","last_name":"Asilova","full_name":"Asilova, Nilufar"},{"last_name":"Shotelersuk","first_name":"Vorasuk","full_name":"Shotelersuk, Vorasuk"},{"full_name":"Yeetong, Patra","last_name":"Yeetong","first_name":"Patra"},{"last_name":"Azam","first_name":"Matloob","full_name":"Azam, Matloob"},{"first_name":"Meisam","last_name":"Babaei","full_name":"Babaei, Meisam"},{"last_name":"Bahrami Monajemi","first_name":"Gholamreza","full_name":"Bahrami Monajemi, Gholamreza"},{"first_name":"Pouria","last_name":"Mohammadi","full_name":"Mohammadi, Pouria"},{"full_name":"Samie, Saeed","last_name":"Samie","first_name":"Saeed"},{"full_name":"Banu, Selina Husna","first_name":"Selina Husna","last_name":"Banu"},{"first_name":"Jorge Pinto","last_name":"Basto","full_name":"Basto, Jorge Pinto"},{"full_name":"Kortüm, Fanny","first_name":"Fanny","last_name":"Kortüm"},{"full_name":"Bauer, Mislen","last_name":"Bauer","first_name":"Mislen"},{"full_name":"Bauer, Peter","first_name":"Peter","last_name":"Bauer"},{"last_name":"Beetz","first_name":"Christian","full_name":"Beetz, Christian"},{"full_name":"Garshasbi, Masoud","first_name":"Masoud","last_name":"Garshasbi"},{"first_name":"Awatif","last_name":"Hameed Issa","full_name":"Hameed Issa, Awatif"},{"full_name":"Eyaid, Wafaa","last_name":"Eyaid","first_name":"Wafaa"},{"full_name":"Ahmed, Hind","last_name":"Ahmed","first_name":"Hind"},{"first_name":"Narges","last_name":"Hashemi","full_name":"Hashemi, Narges"},{"full_name":"Hassanpour, Kazem","last_name":"Hassanpour","first_name":"Kazem"},{"full_name":"Herman, Isabella","last_name":"Herman","first_name":"Isabella"},{"last_name":"Ibrohimov","first_name":"Sherozjon","full_name":"Ibrohimov, Sherozjon"},{"full_name":"Abdul-Majeed, Ban A","first_name":"Ban A","last_name":"Abdul-Majeed"},{"first_name":"Maria","last_name":"Imdad","full_name":"Imdad, Maria"},{"full_name":"Isrofilov, Maksudjon","last_name":"Isrofilov","first_name":"Maksudjon"},{"last_name":"Kaiyal","first_name":"Qassem","full_name":"Kaiyal, Qassem"},{"full_name":"Khan, Suliman","last_name":"Khan","first_name":"Suliman"},{"full_name":"Kirmse, Brian","last_name":"Kirmse","first_name":"Brian"},{"full_name":"Koster, Janet","last_name":"Koster","first_name":"Janet"},{"last_name":"Lourenço","first_name":"Charles Marques","full_name":"Lourenço, Charles Marques"},{"full_name":"Mitani, Tadahiro","last_name":"Mitani","first_name":"Tadahiro"},{"full_name":"Moldovan, Oana","first_name":"Oana","last_name":"Moldovan"},{"full_name":"Murphy, David","first_name":"David","last_name":"Murphy"},{"full_name":"Najafi, Maryam","first_name":"Maryam","last_name":"Najafi"},{"full_name":"Pehlivan, Davut","first_name":"Davut","last_name":"Pehlivan"},{"first_name":"Maria Eugenia","last_name":"Rocha","full_name":"Rocha, Maria Eugenia"},{"first_name":"Vincenzo","last_name":"Salpietro","full_name":"Salpietro, Vincenzo"},{"last_name":"Schmidts","first_name":"Miriam","full_name":"Schmidts, Miriam"},{"last_name":"Shalata","first_name":"Adel","full_name":"Shalata, Adel"},{"full_name":"Mahroum, Mohammad","last_name":"Mahroum","first_name":"Mohammad"},{"full_name":"Talbeya, Jawabreh Kassem","last_name":"Talbeya","first_name":"Jawabreh Kassem"},{"full_name":"Taylor, Robert W","last_name":"Taylor","first_name":"Robert W"},{"full_name":"Vazquez, Dayana","last_name":"Vazquez","first_name":"Dayana"},{"full_name":"Vetro, Annalisa","first_name":"Annalisa","last_name":"Vetro"},{"full_name":"Waterham, Hans R","first_name":"Hans R","last_name":"Waterham"},{"full_name":"Zaman, Mashaya","last_name":"Zaman","first_name":"Mashaya"},{"full_name":"Schrader, Tina A","first_name":"Tina A","last_name":"Schrader"},{"first_name":"Wendy K","last_name":"Chung","full_name":"Chung, Wendy K"},{"first_name":"Renzo","last_name":"Guerrini","full_name":"Guerrini, Renzo"},{"full_name":"Lupski, James R","first_name":"James R","last_name":"Lupski"},{"full_name":"Gleeson, Joseph","first_name":"Joseph","last_name":"Gleeson"},{"full_name":"Suri, Mohnish","first_name":"Mohnish","last_name":"Suri"},{"full_name":"Jamshidi, Yalda","first_name":"Yalda","last_name":"Jamshidi"},{"last_name":"Bhatia","first_name":"Kailash P","full_name":"Bhatia, Kailash P"},{"full_name":"Vona, Barbara","first_name":"Barbara","last_name":"Vona"},{"full_name":"Schrader, Michael","first_name":"Michael","last_name":"Schrader"},{"full_name":"Severino, Mariasavina","last_name":"Severino","first_name":"Mariasavina"},{"first_name":"Matthew","last_name":"Guille","full_name":"Guille, Matthew"},{"first_name":"Edward W","last_name":"Tate","full_name":"Tate, Edward W"},{"full_name":"Varshney, Gaurav K","first_name":"Gaurav K","last_name":"Varshney"},{"last_name":"Houlden","first_name":"Henry","full_name":"Houlden, Henry"},{"full_name":"Maroofian, Reza","first_name":"Reza","last_name":"Maroofian"}],"date_created":"2023-11-16T12:36:51Z","date_updated":"2023-11-20T10:17:32Z","article_number":"awad380","extern":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/brain/awad380"}],"quality_controlled":"1","doi":"10.1093/brain/awad380","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0006-8950"],"eissn":["1460-2156"]},"month":"11","_id":"14543","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders.","lang":"eng"}],"citation":{"ama":"Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2023. doi:10.1093/brain/awad380","apa":"Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2023). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. Oxford University Press. https://doi.org/10.1093/brain/awad380","ieee":"R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” Brain. Oxford University Press, 2023.","ista":"Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2023. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain., awad380.","short":"R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain (2023).","mla":"Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain, awad380, Oxford University Press, 2023, doi:10.1093/brain/awad380.","chicago":"Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain. Oxford University Press, 2023. https://doi.org/10.1093/brain/awad380."},"publication":"Brain","article_type":"original","date_published":"2023-11-10T00:00:00Z","scopus_import":"1","keyword":["Neurology (clinical)"],"article_processing_charge":"No","day":"10"},{"type":"journal_article","abstract":[{"lang":"eng","text":"It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit."}],"title":"Universality in low-dimensional BCS theory","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14542","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"31","article_type":"original","citation":{"ama":"Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. 2023. doi:10.1142/s0129055x2360005x","apa":"Henheik, S. J., Lauritsen, A. B., & Roos, B. (2023). Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/s0129055x2360005x","ieee":"S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” Reviews in Mathematical Physics. World Scientific Publishing, 2023.","ista":"Henheik SJ, Lauritsen AB, Roos B. 2023. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics., 2360005.","short":"S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics (2023).","mla":"Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics, 2360005, World Scientific Publishing, 2023, doi:10.1142/s0129055x2360005x.","chicago":"Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World Scientific Publishing, 2023. https://doi.org/10.1142/s0129055x2360005x."},"publication":"Reviews in Mathematical Physics","date_published":"2023-10-31T00:00:00Z","article_number":"2360005 ","ec_funded":1,"publisher":"World Scientific Publishing","department":[{"_id":"GradSch"},{"_id":"LaEr"},{"_id":"RoSe"}],"publication_status":"epub_ahead","acknowledgement":"We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427.","year":"2023","date_updated":"2023-11-20T10:04:38Z","date_created":"2023-11-15T23:48:14Z","author":[{"first_name":"Sven Joscha","last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha"},{"id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","orcid":"0000-0003-4476-2288","first_name":"Asbjørn Bækgaard","last_name":"Lauritsen","full_name":"Lauritsen, Asbjørn Bækgaard"},{"last_name":"Roos","first_name":"Barbara","orcid":"0000-0002-9071-5880","id":"5DA90512-D80F-11E9-8994-2E2EE6697425","full_name":"Roos, Barbara"}],"publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"month":"10","project":[{"grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta"},{"_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b","grant_number":"I06427","name":"Mathematical Challenges in BCS Theory of Superconductivity"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1142/S0129055X2360005X"}],"external_id":{"arxiv":["2301.05621"]},"language":[{"iso":"eng"}],"doi":"10.1142/s0129055x2360005x"},{"author":[{"orcid":"0000-0001-7242-015X","id":"c1bea5e1-878e-11ee-9dff-d7404e4422ab","last_name":"Fedotova","first_name":"Ekaterina","full_name":"Fedotova, Ekaterina"},{"last_name":"Kuznetsov","first_name":"Nikolai","full_name":"Kuznetsov, Nikolai"},{"first_name":"Egor","last_name":"Tiunov","full_name":"Tiunov, Egor"},{"last_name":"Ulanov","first_name":"A. E.","full_name":"Ulanov, A. E."},{"first_name":"A. I.","last_name":"Lvovsky","full_name":"Lvovsky, A. I."}],"date_created":"2023-11-19T23:00:54Z","date_updated":"2023-11-20T10:26:51Z","volume":108,"year":"2023","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","article_number":"042430","doi":"10.1103/PhysRevA.108.042430","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2212.07406","open_access":"1"}],"external_id":{"arxiv":["2212.07406"]},"oa":1,"quality_controlled":"1","month":"10","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14553","title":"Continuous-variable quantum tomography of high-amplitude states","status":"public","intvolume":" 108","abstract":[{"text":"Quantum state tomography is an essential component of modern quantum technology. In application to continuous-variable harmonic-oscillator systems, such as the electromagnetic field, existing tomography methods typically reconstruct the state in discrete bases, and are hence limited to states with relatively low amplitudes and energies. Here, we overcome this limitation by utilizing a feed-forward neural network to obtain the density matrix directly in the continuous position basis. An important benefit of our approach is the ability to choose specific regions in the phase space for detailed reconstruction. This results in a relatively slow scaling of the amount of resources required for the reconstruction with the state amplitude, and hence allows us to dramatically increase the range of amplitudes accessible with our method.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2023-10-30T00:00:00Z","publication":"Physical Review A","citation":{"ama":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 2023;108(4). doi:10.1103/PhysRevA.108.042430","ieee":"E. Fedotova, N. Kuznetsov, E. Tiunov, A. E. Ulanov, and A. I. Lvovsky, “Continuous-variable quantum tomography of high-amplitude states,” Physical Review A, vol. 108, no. 4. American Physical Society, 2023.","apa":"Fedotova, E., Kuznetsov, N., Tiunov, E., Ulanov, A. E., & Lvovsky, A. I. (2023). Continuous-variable quantum tomography of high-amplitude states. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.108.042430","ista":"Fedotova E, Kuznetsov N, Tiunov E, Ulanov AE, Lvovsky AI. 2023. Continuous-variable quantum tomography of high-amplitude states. Physical Review A. 108(4), 042430.","short":"E. Fedotova, N. Kuznetsov, E. Tiunov, A.E. Ulanov, A.I. Lvovsky, Physical Review A 108 (2023).","mla":"Fedotova, Ekaterina, et al. “Continuous-Variable Quantum Tomography of High-Amplitude States.” Physical Review A, vol. 108, no. 4, 042430, American Physical Society, 2023, doi:10.1103/PhysRevA.108.042430.","chicago":"Fedotova, Ekaterina, Nikolai Kuznetsov, Egor Tiunov, A. E. Ulanov, and A. I. Lvovsky. “Continuous-Variable Quantum Tomography of High-Amplitude States.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.108.042430."},"article_type":"original","day":"30","article_processing_charge":"No","scopus_import":"1"},{"date_updated":"2023-11-20T09:24:48Z","date_created":"2023-11-19T23:00:55Z","volume":46,"author":[{"first_name":"D.","last_name":"Dikranjan","full_name":"Dikranjan, D."},{"full_name":"Giordano Bruno, A.","first_name":"A.","last_name":"Giordano Bruno"},{"first_name":"Nicolò","last_name":"Zava","id":"c8b3499c-7a77-11eb-b046-aa368cbbf2ad","orcid":"0000-0001-8686-1888","full_name":"Zava, Nicolò"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Taylor & Francis","year":"2023","acknowledgement":"The first and second named authors are members of GNSAGA – INdAM.\r\nThe third named author was supported by the FWF Grant, Project number I4245–N35","month":"11","publication_identifier":{"issn":["1607-3606"],"eissn":["1727-933X"]},"language":[{"iso":"eng"}],"doi":"10.2989/16073606.2023.2247731","quality_controlled":"1","project":[{"_id":"26AD5D90-B435-11E9-9278-68D0E5697425","grant_number":"I04245","call_identifier":"FWF","name":"Algebraic Footprints of Geometric Features in Homology"}],"abstract":[{"lang":"eng","text":"Motivated by a problem posed in [10], we investigate the closure operators of the category SLatt of join semilattices and its subcategory SLattO of join semilattices with bottom element. In particular, we show that there are only finitely many closure operators of both categories, and provide a complete classification. We use this result to deduce the known fact that epimorphisms of SLatt and SLattO are surjective. We complement the paper with two different proofs of this result using either generators or Isbell’s zigzag theorem."}],"issue":"S1","type":"journal_article","oa_version":"None","title":"Epimorphisms and closure operators of categories of semilattices","status":"public","intvolume":" 46","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14557","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-11-01T00:00:00Z","article_type":"original","page":"191-221","publication":"Quaestiones Mathematicae","citation":{"short":"D. Dikranjan, A. Giordano Bruno, N. Zava, Quaestiones Mathematicae 46 (2023) 191–221.","mla":"Dikranjan, D., et al. “Epimorphisms and Closure Operators of Categories of Semilattices.” Quaestiones Mathematicae, vol. 46, no. S1, Taylor & Francis, 2023, pp. 191–221, doi:10.2989/16073606.2023.2247731.","chicago":"Dikranjan, D., A. Giordano Bruno, and Nicolò Zava. “Epimorphisms and Closure Operators of Categories of Semilattices.” Quaestiones Mathematicae. Taylor & Francis, 2023. https://doi.org/10.2989/16073606.2023.2247731.","ama":"Dikranjan D, Giordano Bruno A, Zava N. Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. 2023;46(S1):191-221. doi:10.2989/16073606.2023.2247731","ieee":"D. Dikranjan, A. Giordano Bruno, and N. Zava, “Epimorphisms and closure operators of categories of semilattices,” Quaestiones Mathematicae, vol. 46, no. S1. Taylor & Francis, pp. 191–221, 2023.","apa":"Dikranjan, D., Giordano Bruno, A., & Zava, N. (2023). Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. Taylor & Francis. https://doi.org/10.2989/16073606.2023.2247731","ista":"Dikranjan D, Giordano Bruno A, Zava N. 2023. Epimorphisms and closure operators of categories of semilattices. Quaestiones Mathematicae. 46(S1), 191–221."}},{"citation":{"chicago":"Robinson, M. L., P. G. Hahn, B. D. Inouye, N. Underwood, S. R. Whitehead, K. C. Abbott, E. M. Bruna, et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science. AAAS, 2023. https://doi.org/10.1126/science.adh8830.","mla":"Robinson, M. L., et al. “Plant Size, Latitude, and Phylogeny Explain within-Population Variability in Herbivory.” Science, vol. 382, no. 6671, AAAS, 2023, pp. 679–83, doi:10.1126/science.adh8830.","short":"M.L. Robinson, P.G. Hahn, B.D. Inouye, N. Underwood, S.R. Whitehead, K.C. Abbott, E.M. Bruna, N.I. Cacho, L.A. Dyer, L. Abdala-Roberts, W.J. Allen, J.F. Andrade, D.F. Angulo, D. Anjos, D.N. Anstett, R. Bagchi, S. Bagchi, M. Barbosa, S. Barrett, C. Baskett, E. Ben-Simchon, K.J. Bloodworth, J.L. Bronstein, Y.M. Buckley, K.T. Burghardt, C. Bustos-Segura, E.S. Calixto, R.L. Carvalho, B. Castagneyrol, M.C. Chiuffo, D. Cinoğlu, E. Cinto Mejía, M.C. Cock, R. Cogni, O.L. Cope, T. Cornelissen, D.R. Cortez, D.W. Crowder, C. Dallstream, W. Dáttilo, J.K. Davis, R.D. Dimarco, H.E. Dole, I.N. Egbon, M. Eisenring, A. Ejomah, B.D. Elderd, M.J. Endara, M.D. Eubanks, S.E. Everingham, K.N. Farah, R.P. Farias, A.P. Fernandes, G.W. Fernandes, M. Ferrante, A. Finn, G.A. Florjancic, M.L. Forister, Q.N. Fox, E. Frago, F.M. França, A.S. Getman-Pickering, Z. Getman-Pickering, E. Gianoli, B. Gooden, M.M. Gossner, K.A. Greig, S. Gripenberg, R. Groenteman, P. Grof-Tisza, N. Haack, L. Hahn, S.M. Haq, A.M. Helms, J. Hennecke, S.L. Hermann, L.M. Holeski, S. Holm, M.C. Hutchinson, E.E. Jackson, S. Kagiya, A. Kalske, M. Kalwajtys, R. Karban, R. Kariyat, T. Keasar, M.F. Kersch-Becker, H.M. Kharouba, T.N. Kim, D.M. Kimuyu, J. Kluse, S.E. Koerner, K.J. Komatsu, S. Krishnan, M. Laihonen, L. Lamelas-López, M.C. Lascaleia, N. Lecomte, C.R. Lehn, X. Li, R.L. Lindroth, E.F. Lopresti, M. Losada, A.M. Louthan, V.J. Luizzi, S.C. Lynch, J.S. Lynn, N.J. Lyon, L.F. Maia, R.A. Maia, T.L. Mannall, B.S. Martin, T.J. Massad, A.C. Mccall, K. Mcgurrin, A.C. Merwin, Z. Mijango-Ramos, C.H. Mills, A.T. Moles, C.M. Moore, X. Moreira, C.R. Morrison, M.C. Moshobane, A. Muola, R. Nakadai, K. Nakajima, S. Novais, C.O. Ogbebor, H. Ohsaki, V.S. Pan, N.A. Pardikes, M. Pareja, N. Parthasarathy, R.R. Pawar, Q. Paynter, I.S. Pearse, R.M. Penczykowski, A.A. Pepi, C.C. Pereira, S.S. Phartyal, F.I. Piper, K. Poveda, E.G. Pringle, J. Puy, T. Quijano, C. Quintero, S. Rasmann, C. Rosche, L.Y. Rosenheim, J.A. Rosenheim, J.B. Runyon, A. Sadeh, Y. Sakata, D.M. Salcido, C. Salgado-Luarte, B.A. Santos, Y. Sapir, Y. Sasal, Y. Sato, M. Sawant, H. Schroeder, I. Schumann, M. Segoli, H. Segre, O. Shelef, N. Shinohara, R.P. Singh, D.S. Smith, M. Sobral, G.C. Stotz, A.J.M. Tack, M. Tayal, J.F. Tooker, D. Torrico-Bazoberry, K. Tougeron, A.M. Trowbridge, S. Utsumi, O. Uyi, J.L. Vaca-Uribe, A. Valtonen, L.J.A. Van Dijk, V. Vandvik, J. Villellas, L.P. Waller, M.G. Weber, A. Yamawo, S. Yim, P.L. Zarnetske, L.N. Zehr, Z. Zhong, W.C. Wetzel, Science 382 (2023) 679–683.","ista":"Robinson ML et al. 2023. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 382(6671), 679–683.","ieee":"M. L. Robinson et al., “Plant size, latitude, and phylogeny explain within-population variability in herbivory,” Science, vol. 382, no. 6671. AAAS, pp. 679–683, 2023.","apa":"Robinson, M. L., Hahn, P. G., Inouye, B. D., Underwood, N., Whitehead, S. R., Abbott, K. C., … Wetzel, W. C. (2023). Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. AAAS. https://doi.org/10.1126/science.adh8830","ama":"Robinson ML, Hahn PG, Inouye BD, et al. Plant size, latitude, and phylogeny explain within-population variability in herbivory. Science. 2023;382(6671):679-683. doi:10.1126/science.adh8830"},"publication":"Science","page":"679-683","article_type":"original","date_published":"2023-11-09T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14552","intvolume":" 382","title":"Plant size, latitude, and phylogeny explain within-population variability in herbivory","status":"public","oa_version":"None","type":"journal_article","issue":"6671","abstract":[{"lang":"eng","text":"Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth."}],"external_id":{"pmid":["37943897"]},"quality_controlled":"1","doi":"10.1126/science.adh8830","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"]},"month":"11","pmid":1,"year":"2023","acknowledgement":"The authors acknowledge funding for central project coordination from NSF Research Coordination Network grant DEB-2203582; the Ecology, Evolution, and Behavior Program at Michigan State University; and AgBioResearch at Michigan State University. Site-specific funding is listed in the supplementary materials.","publisher":"AAAS","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"14579"}]},"author":[{"last_name":"Robinson","first_name":"M. L.","full_name":"Robinson, M. L."},{"full_name":"Hahn, P. G.","first_name":"P. G.","last_name":"Hahn"},{"last_name":"Inouye","first_name":"B. D.","full_name":"Inouye, B. D."},{"full_name":"Underwood, N.","first_name":"N.","last_name":"Underwood"},{"first_name":"S. R.","last_name":"Whitehead","full_name":"Whitehead, S. R."},{"last_name":"Abbott","first_name":"K. C.","full_name":"Abbott, K. C."},{"full_name":"Bruna, E. M.","first_name":"E. M.","last_name":"Bruna"},{"first_name":"N. I.","last_name":"Cacho","full_name":"Cacho, N. I."},{"first_name":"L. A.","last_name":"Dyer","full_name":"Dyer, L. A."},{"last_name":"Abdala-Roberts","first_name":"L.","full_name":"Abdala-Roberts, L."},{"full_name":"Allen, W. J.","first_name":"W. J.","last_name":"Allen"},{"first_name":"J. F.","last_name":"Andrade","full_name":"Andrade, J. F."},{"full_name":"Angulo, D. F.","first_name":"D. F.","last_name":"Angulo"},{"full_name":"Anjos, D.","first_name":"D.","last_name":"Anjos"},{"first_name":"D. N.","last_name":"Anstett","full_name":"Anstett, D. N."},{"full_name":"Bagchi, R.","last_name":"Bagchi","first_name":"R."},{"first_name":"S.","last_name":"Bagchi","full_name":"Bagchi, S."},{"first_name":"M.","last_name":"Barbosa","full_name":"Barbosa, M."},{"full_name":"Barrett, S.","first_name":"S.","last_name":"Barrett"},{"orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","first_name":"Carina","full_name":"Baskett, Carina"},{"last_name":"Ben-Simchon","first_name":"E.","full_name":"Ben-Simchon, E."},{"last_name":"Bloodworth","first_name":"K. J.","full_name":"Bloodworth, K. J."},{"full_name":"Bronstein, J. L.","first_name":"J. L.","last_name":"Bronstein"},{"full_name":"Buckley, Y. M.","last_name":"Buckley","first_name":"Y. M."},{"full_name":"Burghardt, K. T.","last_name":"Burghardt","first_name":"K. T."},{"full_name":"Bustos-Segura, C.","last_name":"Bustos-Segura","first_name":"C."},{"full_name":"Calixto, E. S.","first_name":"E. S.","last_name":"Calixto"},{"full_name":"Carvalho, R. L.","last_name":"Carvalho","first_name":"R. L."},{"full_name":"Castagneyrol, B.","last_name":"Castagneyrol","first_name":"B."},{"last_name":"Chiuffo","first_name":"M. C.","full_name":"Chiuffo, M. C."},{"first_name":"D.","last_name":"Cinoğlu","full_name":"Cinoğlu, D."},{"last_name":"Cinto Mejía","first_name":"E.","full_name":"Cinto Mejía, E."},{"full_name":"Cock, M. C.","last_name":"Cock","first_name":"M. C."},{"last_name":"Cogni","first_name":"R.","full_name":"Cogni, R."},{"first_name":"O. L.","last_name":"Cope","full_name":"Cope, O. L."},{"full_name":"Cornelissen, T.","first_name":"T.","last_name":"Cornelissen"},{"last_name":"Cortez","first_name":"D. R.","full_name":"Cortez, D. R."},{"first_name":"D. W.","last_name":"Crowder","full_name":"Crowder, D. W."},{"full_name":"Dallstream, C.","first_name":"C.","last_name":"Dallstream"},{"last_name":"Dáttilo","first_name":"W.","full_name":"Dáttilo, W."},{"full_name":"Davis, J. K.","first_name":"J. K.","last_name":"Davis"},{"last_name":"Dimarco","first_name":"R. D.","full_name":"Dimarco, R. D."},{"full_name":"Dole, H. E.","first_name":"H. E.","last_name":"Dole"},{"last_name":"Egbon","first_name":"I. N.","full_name":"Egbon, I. N."},{"full_name":"Eisenring, M.","first_name":"M.","last_name":"Eisenring"},{"full_name":"Ejomah, A.","first_name":"A.","last_name":"Ejomah"},{"full_name":"Elderd, B. D.","first_name":"B. D.","last_name":"Elderd"},{"first_name":"M. J.","last_name":"Endara","full_name":"Endara, M. J."},{"full_name":"Eubanks, M. D.","last_name":"Eubanks","first_name":"M. D."},{"first_name":"S. E.","last_name":"Everingham","full_name":"Everingham, S. E."},{"full_name":"Farah, K. N.","last_name":"Farah","first_name":"K. N."},{"full_name":"Farias, R. P.","first_name":"R. P.","last_name":"Farias"},{"first_name":"A. P.","last_name":"Fernandes","full_name":"Fernandes, A. P."},{"full_name":"Fernandes, G. W.","first_name":"G. W.","last_name":"Fernandes"},{"full_name":"Ferrante, M.","first_name":"M.","last_name":"Ferrante"},{"full_name":"Finn, A.","first_name":"A.","last_name":"Finn"},{"first_name":"G. A.","last_name":"Florjancic","full_name":"Florjancic, G. A."},{"full_name":"Forister, M. L.","last_name":"Forister","first_name":"M. L."},{"full_name":"Fox, Q. N.","last_name":"Fox","first_name":"Q. N."},{"first_name":"E.","last_name":"Frago","full_name":"Frago, E."},{"full_name":"França, F. M.","first_name":"F. M.","last_name":"França"},{"first_name":"A. S.","last_name":"Getman-Pickering","full_name":"Getman-Pickering, A. S."},{"last_name":"Getman-Pickering","first_name":"Z.","full_name":"Getman-Pickering, Z."},{"last_name":"Gianoli","first_name":"E.","full_name":"Gianoli, E."},{"full_name":"Gooden, B.","last_name":"Gooden","first_name":"B."},{"first_name":"M. M.","last_name":"Gossner","full_name":"Gossner, M. M."},{"full_name":"Greig, K. A.","last_name":"Greig","first_name":"K. A."},{"last_name":"Gripenberg","first_name":"S.","full_name":"Gripenberg, S."},{"full_name":"Groenteman, R.","first_name":"R.","last_name":"Groenteman"},{"first_name":"P.","last_name":"Grof-Tisza","full_name":"Grof-Tisza, P."},{"last_name":"Haack","first_name":"N.","full_name":"Haack, N."},{"full_name":"Hahn, L.","last_name":"Hahn","first_name":"L."},{"full_name":"Haq, S. M.","first_name":"S. M.","last_name":"Haq"},{"last_name":"Helms","first_name":"A. M.","full_name":"Helms, A. M."},{"first_name":"J.","last_name":"Hennecke","full_name":"Hennecke, J."},{"first_name":"S. L.","last_name":"Hermann","full_name":"Hermann, S. L."},{"last_name":"Holeski","first_name":"L. M.","full_name":"Holeski, L. M."},{"full_name":"Holm, S.","last_name":"Holm","first_name":"S."},{"full_name":"Hutchinson, M. C.","last_name":"Hutchinson","first_name":"M. C."},{"last_name":"Jackson","first_name":"E. E.","full_name":"Jackson, E. E."},{"full_name":"Kagiya, S.","first_name":"S.","last_name":"Kagiya"},{"last_name":"Kalske","first_name":"A.","full_name":"Kalske, A."},{"first_name":"M.","last_name":"Kalwajtys","full_name":"Kalwajtys, M."},{"full_name":"Karban, R.","first_name":"R.","last_name":"Karban"},{"full_name":"Kariyat, R.","first_name":"R.","last_name":"Kariyat"},{"first_name":"T.","last_name":"Keasar","full_name":"Keasar, T."},{"full_name":"Kersch-Becker, M. F.","first_name":"M. F.","last_name":"Kersch-Becker"},{"full_name":"Kharouba, H. M.","first_name":"H. M.","last_name":"Kharouba"},{"full_name":"Kim, T. N.","last_name":"Kim","first_name":"T. N."},{"first_name":"D. M.","last_name":"Kimuyu","full_name":"Kimuyu, D. M."},{"full_name":"Kluse, J.","last_name":"Kluse","first_name":"J."},{"full_name":"Koerner, S. E.","last_name":"Koerner","first_name":"S. E."},{"last_name":"Komatsu","first_name":"K. J.","full_name":"Komatsu, K. 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M."},{"full_name":"Moreira, X.","first_name":"X.","last_name":"Moreira"},{"last_name":"Morrison","first_name":"C. R.","full_name":"Morrison, C. R."},{"full_name":"Moshobane, M. C.","first_name":"M. C.","last_name":"Moshobane"},{"full_name":"Muola, A.","first_name":"A.","last_name":"Muola"},{"first_name":"R.","last_name":"Nakadai","full_name":"Nakadai, R."},{"first_name":"K.","last_name":"Nakajima","full_name":"Nakajima, K."},{"full_name":"Novais, S.","first_name":"S.","last_name":"Novais"},{"last_name":"Ogbebor","first_name":"C. O.","full_name":"Ogbebor, C. O."},{"full_name":"Ohsaki, H.","first_name":"H.","last_name":"Ohsaki"},{"full_name":"Pan, V. S.","first_name":"V. S.","last_name":"Pan"},{"last_name":"Pardikes","first_name":"N. A.","full_name":"Pardikes, N. A."},{"first_name":"M.","last_name":"Pareja","full_name":"Pareja, M."},{"full_name":"Parthasarathy, N.","last_name":"Parthasarathy","first_name":"N."},{"first_name":"R. R.","last_name":"Pawar","full_name":"Pawar, R. R."},{"first_name":"Q.","last_name":"Paynter","full_name":"Paynter, Q."},{"full_name":"Pearse, I. S.","first_name":"I. S.","last_name":"Pearse"},{"full_name":"Penczykowski, R. M.","first_name":"R. M.","last_name":"Penczykowski"},{"first_name":"A. A.","last_name":"Pepi","full_name":"Pepi, A. A."},{"first_name":"C. C.","last_name":"Pereira","full_name":"Pereira, C. C."},{"last_name":"Phartyal","first_name":"S. S.","full_name":"Phartyal, S. S."},{"first_name":"F. I.","last_name":"Piper","full_name":"Piper, F. I."},{"first_name":"K.","last_name":"Poveda","full_name":"Poveda, K."},{"full_name":"Pringle, E. G.","last_name":"Pringle","first_name":"E. G."},{"first_name":"J.","last_name":"Puy","full_name":"Puy, J."},{"first_name":"T.","last_name":"Quijano","full_name":"Quijano, T."},{"last_name":"Quintero","first_name":"C.","full_name":"Quintero, C."},{"first_name":"S.","last_name":"Rasmann","full_name":"Rasmann, S."},{"last_name":"Rosche","first_name":"C.","full_name":"Rosche, C."},{"first_name":"L. Y.","last_name":"Rosenheim","full_name":"Rosenheim, L. Y."},{"first_name":"J. A.","last_name":"Rosenheim","full_name":"Rosenheim, J. A."},{"full_name":"Runyon, J. B.","last_name":"Runyon","first_name":"J. B."},{"last_name":"Sadeh","first_name":"A.","full_name":"Sadeh, A."},{"full_name":"Sakata, Y.","last_name":"Sakata","first_name":"Y."},{"last_name":"Salcido","first_name":"D. M.","full_name":"Salcido, D. M."},{"last_name":"Salgado-Luarte","first_name":"C.","full_name":"Salgado-Luarte, C."},{"first_name":"B. A.","last_name":"Santos","full_name":"Santos, B. 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J.M.","full_name":"Tack, A. J.M."},{"last_name":"Tayal","first_name":"M.","full_name":"Tayal, M."},{"first_name":"J. F.","last_name":"Tooker","full_name":"Tooker, J. F."},{"first_name":"D.","last_name":"Torrico-Bazoberry","full_name":"Torrico-Bazoberry, D."},{"last_name":"Tougeron","first_name":"K.","full_name":"Tougeron, K."},{"full_name":"Trowbridge, A. M.","first_name":"A. M.","last_name":"Trowbridge"},{"full_name":"Utsumi, S.","last_name":"Utsumi","first_name":"S."},{"full_name":"Uyi, O.","last_name":"Uyi","first_name":"O."},{"full_name":"Vaca-Uribe, J. L.","first_name":"J. L.","last_name":"Vaca-Uribe"},{"last_name":"Valtonen","first_name":"A.","full_name":"Valtonen, A."},{"first_name":"L. J.A.","last_name":"Van Dijk","full_name":"Van Dijk, L. J.A."},{"first_name":"V.","last_name":"Vandvik","full_name":"Vandvik, V."},{"first_name":"J.","last_name":"Villellas","full_name":"Villellas, J."},{"full_name":"Waller, L. P.","last_name":"Waller","first_name":"L. P."},{"first_name":"M. G.","last_name":"Weber","full_name":"Weber, M. G."},{"full_name":"Yamawo, A.","first_name":"A.","last_name":"Yamawo"},{"full_name":"Yim, S.","last_name":"Yim","first_name":"S."},{"full_name":"Zarnetske, P. L.","first_name":"P. L.","last_name":"Zarnetske"},{"full_name":"Zehr, L. N.","last_name":"Zehr","first_name":"L. N."},{"last_name":"Zhong","first_name":"Z.","full_name":"Zhong, Z."},{"last_name":"Wetzel","first_name":"W. C.","full_name":"Wetzel, W. C."}],"volume":382,"date_created":"2023-11-19T23:00:54Z","date_updated":"2023-11-20T11:17:34Z"},{"issue":"11","abstract":[{"text":"Methylation of CG dinucleotides (mCGs), which regulates eukaryotic genome functions, is epigenetically propagated by Dnmt1/MET1 methyltransferases. How mCG is established and transmitted across generations despite imperfect enzyme fidelity is unclear. Whether mCG variation in natural populations is governed by genetic or epigenetic inheritance also remains mysterious. Here, we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is restricted by active demethylation and suppressed by histone variant H2A.Z, producing localized mCG patterns. Based on these observations, we develop a stochastic mathematical model that precisely recapitulates mCG inheritance dynamics and predicts intragenic mCG patterns and their population-scale variation given only CG site spacing. Our results demonstrate that intragenic mCG establishment, inheritance, and variance constitute a unified epigenetic process, revealing that intragenic mCG undergoes large, millennia-long epigenetic fluctuations and can therefore mediate evolution on this timescale.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":5587897,"creator":"dernst","file_name":"2023_CellSystems_Briffa.pdf","access_level":"open_access","date_updated":"2023-11-20T11:22:52Z","date_created":"2023-11-20T11:22:52Z","checksum":"101fdac59e6f1102d68ef91f2b5bd51a","success":1,"relation":"main_file","file_id":"14580"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14551","intvolume":" 14","title":"Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations","status":"public","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"15","scopus_import":"1","date_published":"2023-11-15T00:00:00Z","citation":{"chicago":"Briffa, Amy, Elizabeth Hollwey, Zaigham Shahzad, Jonathan D. Moore, David B. Lyons, Martin Howard, and Daniel Zilberman. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems. Elsevier, 2023. https://doi.org/10.1016/j.cels.2023.10.007.","mla":"Briffa, Amy, et al. “Millennia-Long Epigenetic Fluctuations Generate Intragenic DNA Methylation Variance in Arabidopsis Populations.” Cell Systems, vol. 14, no. 11, Elsevier, 2023, pp. 953–67, doi:10.1016/j.cels.2023.10.007.","short":"A. Briffa, E. Hollwey, Z. Shahzad, J.D. Moore, D.B. Lyons, M. Howard, D. Zilberman, Cell Systems 14 (2023) 953–967.","ista":"Briffa A, Hollwey E, Shahzad Z, Moore JD, Lyons DB, Howard M, Zilberman D. 2023. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 14(11), 953–967.","apa":"Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., & Zilberman, D. (2023). Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. Elsevier. https://doi.org/10.1016/j.cels.2023.10.007","ieee":"A. Briffa et al., “Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations,” Cell Systems, vol. 14, no. 11. Elsevier, pp. 953–967, 2023.","ama":"Briffa A, Hollwey E, Shahzad Z, et al. Millennia-long epigenetic fluctuations generate intragenic DNA methylation variance in Arabidopsis populations. Cell Systems. 2023;14(11):953-967. doi:10.1016/j.cels.2023.10.007"},"publication":"Cell Systems","page":"953-967","article_type":"original","ec_funded":1,"file_date_updated":"2023-11-20T11:22:52Z","author":[{"first_name":"Amy","last_name":"Briffa","full_name":"Briffa, Amy"},{"first_name":"Elizabeth","last_name":"Hollwey","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","full_name":"Hollwey, Elizabeth"},{"last_name":"Shahzad","first_name":"Zaigham","full_name":"Shahzad, Zaigham"},{"first_name":"Jonathan D.","last_name":"Moore","full_name":"Moore, Jonathan D."},{"full_name":"Lyons, David B.","last_name":"Lyons","first_name":"David B."},{"last_name":"Howard","first_name":"Martin","full_name":"Howard, Martin"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel"}],"volume":14,"date_created":"2023-11-19T23:00:54Z","date_updated":"2023-11-20T11:24:34Z","pmid":1,"acknowledgement":"We would like to thank Xiaoqi Feng, Ander Movilla Miangolarra, and Suzanne de Bruijn for discussions. This work was supported by BBSRC Institute Strategic Programme GEN (BB/P013511/1) to M.H. and D.Z. and by a European Research Council grant MaintainMeth (725746) to D.Z.","year":"2023","publisher":"Elsevier","department":[{"_id":"DaZi"}],"publication_status":"published","publication_identifier":{"issn":["2405-4712"],"eissn":["2405-4720"]},"month":"11","doi":"10.1016/j.cels.2023.10.007","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37944515"]},"project":[{"call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin","_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746"}],"quality_controlled":"1"},{"citation":{"ista":"Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, 10.5281/ZENODO.8133117.","ieee":"W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.","apa":"Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. https://doi.org/10.5281/ZENODO.8133117","ama":"Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117","chicago":"Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.","mla":"Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0. Zenodo, 2023, doi:10.5281/ZENODO.8133117.","short":"W. Wetzel, (2023)."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8133118"}],"doi":"10.5281/ZENODO.8133117","date_published":"2023-07-11T00:00:00Z","day":"11","month":"07","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14579","year":"2023","status":"public","title":"HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0","ddc":["570"],"publisher":"Zenodo","department":[{"_id":"NiBa"}],"author":[{"last_name":"Wetzel","first_name":"William","full_name":"Wetzel, William"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14552"}]},"date_created":"2023-11-20T11:07:45Z","date_updated":"2023-11-20T11:17:33Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n","lang":"eng"}]},{"month":"01","publication_identifier":{"issn":["2375-2548"]},"isi":1,"quality_controlled":"1","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"}],"external_id":{"isi":["000964550100015"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.add6495","article_number":"add6495","file_date_updated":"2023-01-23T07:45:54Z","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nThis research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","year":"2023","date_updated":"2023-11-21T08:05:35Z","date_created":"2023-01-23T07:26:42Z","volume":9,"author":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian"},{"full_name":"Javoor, Manjunath","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2","last_name":"Javoor","first_name":"Manjunath"},{"full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","first_name":"Julia","last_name":"Datler"},{"first_name":"Hermann","last_name":"Döring","full_name":"Döring, Hermann"},{"id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","last_name":"Hofer","first_name":"Florian","full_name":"Hofer, Florian"},{"full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","first_name":"Georgi A","last_name":"Dimchev"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"14562"}]},"keyword":["Multidisciplinary"],"scopus_import":"1","day":"20","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Science Advances","citation":{"short":"F. Fäßler, M. Javoor, J. Datler, H. Döring, F. Hofer, G.A. Dimchev, V.-V. Hodirnau, J. Faix, K. Rottner, F.K. Schur, Science Advances 9 (2023).","mla":"Fäßler, Florian, et al. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances, vol. 9, no. 3, add6495, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.add6495.","chicago":"Fäßler, Florian, Manjunath Javoor, Julia Datler, Hermann Döring, Florian Hofer, Georgi A Dimchev, Victor-Valentin Hodirnau, Jan Faix, Klemens Rottner, and Florian KM Schur. “ArpC5 Isoforms Regulate Arp2/3 Complex–Dependent Protrusion through Differential Ena/VASP Positioning.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.add6495.","ama":"Fäßler F, Javoor M, Datler J, et al. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 2023;9(3). doi:10.1126/sciadv.add6495","ieee":"F. Fäßler et al., “ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning,” Science Advances, vol. 9, no. 3. American Association for the Advancement of Science, 2023.","apa":"Fäßler, F., Javoor, M., Datler, J., Döring, H., Hofer, F., Dimchev, G. A., … Schur, F. K. (2023). ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.add6495","ista":"Fäßler F, Javoor M, Datler J, Döring H, Hofer F, Dimchev GA, Hodirnau V-V, Faix J, Rottner K, Schur FK. 2023. ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning. Science Advances. 9(3), add6495."},"date_published":"2023-01-20T00:00:00Z","type":"journal_article","abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.","lang":"eng"}],"issue":"3","ddc":["570"],"title":"ArpC5 isoforms regulate Arp2/3 complex–dependent protrusion through differential Ena/VASP positioning","status":"public","intvolume":" 9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12334","oa_version":"Published Version","file":[{"success":1,"checksum":"ce81a6d0b84170e5e8c62f6acfa15d9e","date_updated":"2023-01-23T07:45:54Z","date_created":"2023-01-23T07:45:54Z","file_id":"12335","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1756234,"access_level":"open_access","file_name":"2023_ScienceAdvances_Faessler.pdf"}]},{"doi":"10.15479/AT:ISTA:14562","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"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"},"oa":1,"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"month":"11","author":[{"first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"contributor":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","first_name":"Florian","last_name":"Fäßler","contributor_type":"researcher"},{"first_name":"Manjunath","contributor_type":"researcher","last_name":"Javoor","id":"305ab18b-dc7d-11ea-9b2f-b58195228ea2"},{"id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580","first_name":"Julia","contributor_type":"researcher","last_name":"Datler"},{"first_name":"Hermann","last_name":"Döring","contributor_type":"researcher"},{"id":"b9d234ba-9e33-11ed-95b6-cd561df280e6","last_name":"Hofer","contributor_type":"researcher","first_name":"Florian"},{"orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Dimchev","first_name":"Georgi A"},{"contributor_type":"researcher","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Faix","contributor_type":"researcher"},{"first_name":"Klemens","contributor_type":"researcher","last_name":"Rottner"},{"first_name":"Florian KM","last_name":"Schur","contributor_type":"researcher","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"related_material":{"record":[{"id":"12334","status":"public","relation":"used_in_publication"}]},"date_created":"2023-11-20T09:22:33Z","date_updated":"2023-11-21T08:05:34Z","year":"2023","acknowledgement":"We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R.","publisher":"Institute of Science and Technology Austria","department":[{"_id":"FlSc"}],"file_date_updated":"2023-11-20T11:49:58Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","date_published":"2023-11-21T00:00:00Z","citation":{"short":"F.K. Schur, (2023).","mla":"Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562.","chicago":"Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562.","ama":"Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:10.15479/AT:ISTA:14562","ieee":"F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023.","apa":"Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562","ista":"Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562."},"day":"21","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14570","date_updated":"2023-11-20T10:27:17Z","date_created":"2023-11-20T10:27:17Z","checksum":"e9bab797b44614f144a5b02d9636f8c3","success":1,"file_name":"Figure2.zip","access_level":"open_access","file_size":1581687449,"content_type":"application/zip","creator":"fschur"},{"creator":"fschur","file_size":116088565,"content_type":"application/zip","access_level":"open_access","file_name":"SupplementaryFigure3.zip","success":1,"checksum":"4efd388cccd03c549fc90f6e46d37006","date_created":"2023-11-20T10:29:18Z","date_updated":"2023-11-20T10:29:18Z","file_id":"14571","relation":"main_file"},{"creator":"fschur","file_size":5154614201,"content_type":"application/zip","access_level":"open_access","file_name":"Figure5.zip","success":1,"checksum":"bdeb232dc94d0c22a3f7e0d18189ce89","date_created":"2023-11-20T10:44:39Z","date_updated":"2023-11-20T10:44:39Z","file_id":"14572","relation":"main_file"},{"file_size":1277893286,"content_type":"application/zip","creator":"fschur","file_name":"SupplementaryFigure7.zip","access_level":"open_access","date_updated":"2023-11-20T10:46:00Z","date_created":"2023-11-20T10:46:00Z","checksum":"83aee17d621a05d865f68f39c8892d27","success":1,"relation":"main_file","file_id":"14573"},{"date_created":"2023-11-20T10:46:08Z","date_updated":"2023-11-20T10:46:08Z","checksum":"fb9beb6fe15c8dac6679dd02044d2ea6","success":1,"relation":"main_file","file_id":"14574","file_size":228485124,"content_type":"application/zip","creator":"fschur","file_name":"SupplementaryFigure9.zip","access_level":"open_access"},{"success":1,"checksum":"4f3644e5feabe4824486d56885bb79fe","date_updated":"2023-11-20T10:46:32Z","date_created":"2023-11-20T10:46:32Z","file_id":"14575","relation":"main_file","creator":"fschur","file_size":1226788198,"content_type":"application/zip","access_level":"open_access","file_name":"SupplementaryFigure10.zip"},{"creator":"fschur","content_type":"application/zip","file_size":277577131,"access_level":"open_access","file_name":"SupplementaryFigure11.zip","success":1,"checksum":"96167f722ed0ca78e30681cd1573b9d7","date_created":"2023-11-20T10:46:17Z","date_updated":"2023-11-20T10:46:17Z","file_id":"14576","relation":"main_file"},{"file_name":"SupplementaryFigure15.zip","access_level":"open_access","content_type":"application/zip","file_size":591483468,"creator":"fschur","relation":"main_file","file_id":"14577","date_created":"2023-11-20T10:46:29Z","date_updated":"2023-11-20T10:46:29Z","checksum":"d1e03c9805c18cfbc2e9fdf38a9f556f","success":1},{"relation":"main_file","file_id":"14578","checksum":"4d437c04fdb3c1e699618063c4bd21c3","success":1,"date_updated":"2023-11-20T10:47:00Z","date_created":"2023-11-20T10:47:00Z","access_level":"open_access","file_name":"SupplementaryFigure17.zip","content_type":"application/zip","file_size":1709528579,"creator":"fschur"},{"date_updated":"2023-11-20T11:26:36Z","date_created":"2023-11-20T11:26:36Z","checksum":"967b5378a4f16c43f490eae328afe50e","success":1,"relation":"main_file","file_id":"14581","file_size":1920765280,"content_type":"application/zip","creator":"fschur","file_name":"SupplementaryFigure4.zip","access_level":"open_access"},{"file_id":"14583","relation":"main_file","success":1,"checksum":"11899986cf0b471d258fe168ee33a3ea","date_updated":"2023-11-20T11:38:12Z","date_created":"2023-11-20T11:38:12Z","access_level":"open_access","file_name":"Figure1_partA.zip","creator":"fschur","file_size":3013566196,"content_type":"application/zip"},{"file_name":"Figure1_partB.zip","access_level":"open_access","content_type":"application/zip","file_size":3250260203,"creator":"fschur","relation":"main_file","file_id":"14584","date_created":"2023-11-20T11:43:23Z","date_updated":"2023-11-20T11:43:23Z","checksum":"c452afe1ab506d58d32e601d5b3878bb","success":1},{"file_id":"14585","relation":"main_file","date_updated":"2023-11-20T11:49:58Z","date_created":"2023-11-20T11:49:58Z","success":1,"checksum":"223c98eceecbe65dd268f4f363a620d8","file_name":"ReadMe.rtf","access_level":"open_access","creator":"fschur","content_type":"text/rtf","file_size":1460}],"_id":"14562","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Research data of the publication \"ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning\"","status":"public","abstract":[{"text":"Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n","lang":"eng"}],"type":"research_data"},{"type":"software","license":"https://choosealicense.com/licenses/agpl-3.0/","abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"file_date_updated":"2023-11-21T08:20:23Z","department":[{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"status":"public","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14502","year":"2023","file":[{"file_size":347641117,"content_type":"application/zip","creator":"fschur","access_level":"open_access","file_name":"Computational_Toolbox_v1.2.zip","checksum":"a8b9adeb53a4109dea4d5e39fa1acccf","success":1,"date_updated":"2023-11-08T20:23:07Z","date_created":"2023-11-08T20:23:07Z","relation":"main_file","file_id":"14503"},{"access_level":"open_access","file_name":"Readme.txt","creator":"dernst","file_size":1522,"content_type":"text/plain","file_id":"14586","relation":"main_file","success":1,"checksum":"14db2addbfca61a085ba301ed6f2900b","date_updated":"2023-11-21T08:20:23Z","date_created":"2023-11-21T08:20:23Z"}],"date_updated":"2023-11-21T08:36:02Z","date_created":"2023-11-08T19:40:54Z","related_material":{"record":[{"id":"10290","relation":"used_for_analysis_in","status":"public"}]},"author":[{"full_name":"Dimchev, Georgi A","first_name":"Georgi A","last_name":"Dimchev","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161"},{"last_name":"Amiri","first_name":"Behnam","full_name":"Amiri, Behnam"},{"first_name":"Florian","last_name":"Fäßler","id":"404F5528-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7149-769X","full_name":"Fäßler, Florian"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"},{"last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"has_accepted_license":"1","day":"21","month":"11","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"citation":{"ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:10.15479/AT:ISTA:14502","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14502.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14502","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023.","mla":"Dimchev, Georgi A., et al. Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14502.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14502."},"tmp":{"short":"GNU AGPLv3 ","legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html","name":"GNU Affero General Public License v3.0"},"oa":1,"date_published":"2023-11-21T00:00:00Z","doi":"10.15479/AT:ISTA:14502"},{"publication_identifier":{"eissn":["1460-2075"],"issn":["0261-4189"]},"month":"11","language":[{"iso":"eng"}],"doi":"10.15252/embj.2023114557","quality_controlled":"1","external_id":{"pmid":["37987147"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2023-11-27T08:45:56Z","article_number":"e114557","date_created":"2023-08-01T08:59:06Z","date_updated":"2023-11-27T08:47:45Z","author":[{"first_name":"Janina","last_name":"Kroll","full_name":"Kroll, Janina"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"first_name":"Arthur","last_name":"Kuznetcov","full_name":"Kuznetcov, Arthur"},{"full_name":"Stefanowski, Kasia","last_name":"Stefanowski","first_name":"Kasia"},{"last_name":"Hermann","first_name":"Monika D.","full_name":"Hermann, Monika D."},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack"},{"last_name":"Shafeek","first_name":"Lubuna B","orcid":"0000-0001-7180-6050","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","full_name":"Shafeek, Lubuna B"},{"first_name":"Annette","last_name":"Müller-Taubenberger","full_name":"Müller-Taubenberger, Annette"},{"last_name":"Renkawitz","first_name":"Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg"}],"department":[{"_id":"NanoFab"},{"_id":"Bio"}],"publisher":"Embo Press","publication_status":"published","pmid":1,"acknowledgement":"We thank Christoph Mayr and Bingzhi Wang for initial experiments on amoeboid nucleokinesis, Ana-Maria Lennon-Duménil and Aline Yatim for bone marrow from MyoIIA-Flox*CD11c-Cre mice, Michael Sixt and Aglaja Kopf for EMTB-mCherry, EB3-mCherry, Lifeact-GFP, Lfc knockout, and Myh9-GFP expressing HoxB8 cells, Malte Benjamin Braun, Mauricio Ruiz, and Madeleine T. Schmitt for critical reading of the manuscript, and the Core Facility Bioimaging, the Core Facility Flow Cytometry, and the Animal Core Facility of the Biomedical Center (BMC) for excellent support. This study was supported by the Peter Hans Hofschneider Professorship of the foundation “Stiftung Experimentelle Biomedizin” (to JR), the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to JR), and the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation; SFB914 project A12, to JR), and the CZI grant DAF2020-225401 (https://doi.org/10.37921/120055ratwvi) from the Chan Zuckerberg Initiative DAF (to RH; an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989)). Open Access funding enabled and organized by Projekt DEAL.","year":"2023","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"21","scopus_import":"1","date_published":"2023-11-21T00:00:00Z","article_type":"original","citation":{"chicago":"Kroll, Janina, Robert Hauschild, Arthur Kuznetcov, Kasia Stefanowski, Monika D. Hermann, Jack Merrin, Lubuna B Shafeek, Annette Müller-Taubenberger, and Jörg Renkawitz. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal. Embo Press, 2023. https://doi.org/10.15252/embj.2023114557.","mla":"Kroll, Janina, et al. “Adaptive Pathfinding by Nucleokinesis during Amoeboid Migration.” EMBO Journal, e114557, Embo Press, 2023, doi:10.15252/embj.2023114557.","short":"J. Kroll, R. Hauschild, A. Kuznetcov, K. Stefanowski, M.D. Hermann, J. Merrin, L.B. Shafeek, A. Müller-Taubenberger, J. Renkawitz, EMBO Journal (2023).","ista":"Kroll J, Hauschild R, Kuznetcov A, Stefanowski K, Hermann MD, Merrin J, Shafeek LB, Müller-Taubenberger A, Renkawitz J. 2023. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal., e114557.","ieee":"J. Kroll et al., “Adaptive pathfinding by nucleokinesis during amoeboid migration,” EMBO Journal. Embo Press, 2023.","apa":"Kroll, J., Hauschild, R., Kuznetcov, A., Stefanowski, K., Hermann, M. D., Merrin, J., … Renkawitz, J. (2023). Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2023114557","ama":"Kroll J, Hauschild R, Kuznetcov A, et al. Adaptive pathfinding by nucleokinesis during amoeboid migration. EMBO Journal. 2023. doi:10.15252/embj.2023114557"},"publication":"EMBO Journal","abstract":[{"lang":"eng","text":"Motile cells moving in multicellular organisms encounter microenvironments of locally heterogeneous mechanochemical composition. Individual compositional parameters like chemotactic signals, adhesiveness, and pore sizes are well known to be sensed by motile cells, providing individual guidance cues for cellular pathfinding. However, motile cells encounter diverse mechanochemical signals at the same time, raising the question of how cells respond to locally diverse and potentially competing signals on their migration routes. Here, we reveal that motile amoeboid cells require nuclear repositioning, termed nucleokinesis, for adaptive pathfinding in heterogeneous mechanochemical microenvironments. Using mammalian immune cells and the amoebaDictyostelium discoideum, we discover that frequent, rapid and long-distance nucleokinesis is a basic component of amoeboid pathfinding, enabling cells to reorientate quickly between locally competing cues. Amoeboid nucleokinesis comprises a two-step cell polarity switch and is driven by myosin II-forces, sliding the nucleus from a ‘losing’ to the ‘winning’ leading edge to re-adjust the nuclear to the cellular path. Impaired nucleokinesis distorts fast path adaptions and causes cellular arrest in the microenvironment. Our findings establish that nucleokinesis is required for amoeboid cell navigation. Given that motile single-cell amoebae, many immune cells, and some cancer cells utilize an amoeboid migration strategy, these results suggest that amoeboid nucleokinesis underlies cellular navigation during unicellular biology, immunity, and disease."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2023-11-27T08:45:56Z","date_created":"2023-11-27T08:45:56Z","checksum":"6261d0041c7e8d284c39712c40079730","success":1,"relation":"main_file","file_id":"14611","content_type":"application/pdf","file_size":4862497,"creator":"dernst","file_name":"2023_EmboJournal_Kroll.pdf","access_level":"open_access"}],"ddc":["570"],"status":"public","title":"Adaptive pathfinding by nucleokinesis during amoeboid migration","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13342"},{"oa_version":"Published Version","title":"Stress granules plug and stabilize damaged endolysosomal membranes","status":"public","_id":"14610","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host."}],"type":"journal_article","date_published":"2023-11-15T00:00:00Z","article_type":"original","citation":{"ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. 2023. doi:10.1038/s41586-023-06726-w","apa":"Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06726-w","ieee":"C. Bussi et al., “Stress granules plug and stabilize damaged endolysosomal membranes,” Nature. Springer Nature, 2023.","ista":"Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature.","short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature (2023).","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature, Springer Nature, 2023, doi:10.1038/s41586-023-06726-w.","chicago":"Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06726-w."},"publication":"Nature","article_processing_charge":"Yes (via OA deal)","day":"15","keyword":["Multidisciplinary"],"date_created":"2023-11-27T07:56:37Z","date_updated":"2023-11-27T09:05:08Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"14472"}],"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-023-06882-z"}]},"author":[{"first_name":"Claudio","last_name":"Bussi","full_name":"Bussi, Claudio"},{"last_name":"Mangiarotti","first_name":"Agustín","full_name":"Mangiarotti, Agustín"},{"first_name":"Christian Eduardo","last_name":"Vanhille-Campos","id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo"},{"last_name":"Aylan","first_name":"Beren","full_name":"Aylan, Beren"},{"full_name":"Pellegrino, Enrica","first_name":"Enrica","last_name":"Pellegrino"},{"full_name":"Athanasiadi, Natalia","first_name":"Natalia","last_name":"Athanasiadi"},{"full_name":"Fearns, Antony","last_name":"Fearns","first_name":"Antony"},{"first_name":"Angela","last_name":"Rodgers","full_name":"Rodgers, Angela"},{"full_name":"Franzmann, Titus M.","first_name":"Titus M.","last_name":"Franzmann"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"last_name":"Dimova","first_name":"Rumiana","full_name":"Dimova, Rumiana"},{"full_name":"Gutierrez, Maximiliano G.","last_name":"Gutierrez","first_name":"Maximiliano G."}],"department":[{"_id":"AnSa"}],"publisher":"Springer Nature","publication_status":"epub_ahead","pmid":1,"acknowledgement":"We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute.","year":"2023","language":[{"iso":"eng"}],"doi":"10.1038/s41586-023-06726-w","quality_controlled":"1","oa":1,"external_id":{"pmid":["37968398"]},"main_file_link":[{"url":"https://doi.org/10.1038/s41586-023-06726-w","open_access":"1"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"month":"11"},{"file":[{"file_id":"14473","relation":"main_file","date_created":"2023-10-30T16:31:08Z","date_updated":"2023-10-30T16:31:08Z","success":1,"checksum":"a18706e952e8660c51ede52a167270b7","file_name":"SGporecondensation-main.zip","access_level":"open_access","creator":"ipalaia","file_size":62821432,"content_type":"application/zip"},{"file_id":"14474","relation":"main_file","date_created":"2023-10-31T08:57:50Z","date_updated":"2023-10-31T08:57:50Z","success":1,"checksum":"389eab31c6509dbc05795017fb618758","file_name":"README.txt","access_level":"open_access","creator":"dernst","content_type":"text/plain","file_size":1697}],"oa_version":"Published Version","date_created":"2023-10-30T16:38:32Z","date_updated":"2023-11-27T09:05:07Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14610"}]},"author":[{"full_name":"Vanhille-Campos, Christian Eduardo","first_name":"Christian Eduardo","last_name":"Vanhille-Campos","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"AnSa"}],"status":"public","ddc":["570"],"title":"Stress granules plug and stabilize damaged endolysosomal membranes","_id":"14472","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"text":"Data related to the following paper:\r\n\"Stress granules plug and stabilize damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract: \r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in \"Stress granules plug and stabilize damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.","lang":"eng"}],"file_date_updated":"2023-10-31T08:57:50Z","type":"research_data","doi":"10.15479/AT:ISTA:14472","date_published":"2023-10-31T00:00:00Z","citation":{"mla":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14472.","short":"C.E. Vanhille-Campos, A. Šarić, (2023).","chicago":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472.","ama":"Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:10.15479/AT:ISTA:14472","ista":"Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.","ieee":"C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023.","apa":"Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14472"},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"article_processing_charge":"No","has_accepted_license":"1","month":"10","day":"31"},{"department":[{"_id":"Bio"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"The authors thank the participants and their families for participating in the study. We thank all members of our laboratories for helpful discussions. We are grateful to Vienna BioCenter Core Facilities: Mouse Phenotyping Unit, Histopathology Unit, Bioinformatics Unit, BioOptics Unit, Electron Microscopy Unit and Comparative Medicine Unit. We are grateful to the Lipidomics Facility, and K. Klavins and T. Hannich at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences for assistance with lipidomics analysis. We also thank T. Huan and A. Hui (UBC Vancouver) for mouse tissue and mitochondria lipidomics analysis. We thank A. Klymchenko (Laboratoire de Bioimagerie et Pathologies Université de Strasbourg, Strasbourg, France) for providing the NR12S probe. We are thankful to the Sen. Paul D. Wellstone Muscular Dystrophy Cooperative Specialized Research Center Viral Vector Core Facility for AAV6 production. We also thank K. P. Campbell and M. E. Anderson (University of Iowa, Carver College of Medicine) for advice on muscle tissue handling. We thank A. Al-Qassabi from the Sultan Qaboos University for the clinical assessment of the participants. D.C. and J.M.P. are supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, and the City of Vienna, and grants from the Austrian Science Fund (FWF) Wittgenstein award (Z 271-B19), the T. von Zastrow Foundation, and a Canada 150 Research Chairs Program (F18-01336). J.S.C. is supported by grants RO1AR44533 and P50AR065139 from the US National Institutes of Health. C.K. is supported by a grant from the Agence Nationale de la Recherche (ANR-18-CE14-0007-01). A.V.K. is supported by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 67544, and an Austrian Science Fund (FWF; no P-33799). A.W. is supported by Austrian Research Promotion Agency (FFG) project no 867674. E.S. is supported by a SciLifeLab fellowship and Karolinska Institutet Foundation Grants. Work in the laboratory of G.S.-F. is supported by the Austrian Academy of Sciences, the European Research Council (ERC AdG 695214 GameofGates) and the Innovative Medicines Initiative 2 Joint Undertaking (grant agreement no. 777372, ReSOLUTE). S.B., M.L. and R.Y. acknowledge the support of the Spastic Paraplegia Foundation.","year":"2023","volume":5,"date_updated":"2023-11-28T07:31:33Z","date_created":"2023-03-23T12:58:43Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s42255-023-00791-1"}]},"author":[{"first_name":"Domagoj","last_name":"Cikes","full_name":"Cikes, Domagoj"},{"last_name":"Elsayad","first_name":"Kareem","full_name":"Elsayad, Kareem"},{"full_name":"Sezgin, Erdinc","first_name":"Erdinc","last_name":"Sezgin"},{"last_name":"Koitai","first_name":"Erika","full_name":"Koitai, Erika"},{"last_name":"Ferenc","first_name":"Torma","full_name":"Ferenc, Torma"},{"full_name":"Orthofer, Michael","first_name":"Michael","last_name":"Orthofer"},{"full_name":"Yarwood, Rebecca","first_name":"Rebecca","last_name":"Yarwood"},{"first_name":"Leonhard X.","last_name":"Heinz","full_name":"Heinz, Leonhard X."},{"last_name":"Sedlyarov","first_name":"Vitaly","full_name":"Sedlyarov, Vitaly"},{"id":"39CD9926-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8821-8236","first_name":"Nasser","last_name":"Darwish-Miranda","full_name":"Darwish-Miranda, Nasser"},{"full_name":"Taylor, Adrian","last_name":"Taylor","first_name":"Adrian"},{"full_name":"Grapentine, Sophie","first_name":"Sophie","last_name":"Grapentine"},{"full_name":"al-Murshedi, Fathiya","last_name":"al-Murshedi","first_name":"Fathiya"},{"full_name":"Abot, Anne","first_name":"Anne","last_name":"Abot"},{"full_name":"Weidinger, Adelheid","last_name":"Weidinger","first_name":"Adelheid"},{"full_name":"Kutchukian, Candice","first_name":"Candice","last_name":"Kutchukian"},{"full_name":"Sanchez, Colline","first_name":"Colline","last_name":"Sanchez"},{"last_name":"Cronin","first_name":"Shane J. F.","full_name":"Cronin, Shane J. F."},{"last_name":"Novatchkova","first_name":"Maria","full_name":"Novatchkova, Maria"},{"full_name":"Kavirayani, Anoop","first_name":"Anoop","last_name":"Kavirayani"},{"first_name":"Thomas","last_name":"Schuetz","full_name":"Schuetz, Thomas"},{"last_name":"Haubner","first_name":"Bernhard","full_name":"Haubner, Bernhard"},{"full_name":"Haas, Lisa","last_name":"Haas","first_name":"Lisa"},{"full_name":"Hagelkruys, Astrid","last_name":"Hagelkruys","first_name":"Astrid"},{"full_name":"Jackowski, Suzanne","last_name":"Jackowski","first_name":"Suzanne"},{"last_name":"Kozlov","first_name":"Andrey","full_name":"Kozlov, Andrey"},{"first_name":"Vincent","last_name":"Jacquemond","full_name":"Jacquemond, Vincent"},{"last_name":"Knauf","first_name":"Claude","full_name":"Knauf, Claude"},{"first_name":"Giulio","last_name":"Superti-Furga","full_name":"Superti-Furga, Giulio"},{"last_name":"Rullman","first_name":"Eric","full_name":"Rullman, Eric"},{"full_name":"Gustafsson, Thomas","last_name":"Gustafsson","first_name":"Thomas"},{"last_name":"McDermot","first_name":"John","full_name":"McDermot, John"},{"full_name":"Lowe, Martin","first_name":"Martin","last_name":"Lowe"},{"last_name":"Radak","first_name":"Zsolt","full_name":"Radak, Zsolt"},{"first_name":"Jeffrey S.","last_name":"Chamberlain","full_name":"Chamberlain, Jeffrey S."},{"full_name":"Bakovic, Marica","last_name":"Bakovic","first_name":"Marica"},{"first_name":"Siddharth","last_name":"Banka","full_name":"Banka, Siddharth"},{"full_name":"Penninger, Josef M.","first_name":"Josef M.","last_name":"Penninger"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000992064000002"],"pmid":["36941451"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.02.482658"}],"language":[{"iso":"eng"}],"doi":"10.1038/s42255-023-00766-2","publication_identifier":{"issn":["2522-5812"]},"month":"03","intvolume":" 5","title":"PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing","status":"public","_id":"12747","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases, represents an important goal in improving human health. Here, we show that the lipid synthesis enzyme phosphatidylethanolamine cytidyltransferase (PCYT2/ECT) is critical to muscle health. Human deficiency in PCYT2 causes a severe disease with failure to thrive and progressive weakness. pcyt2-mutant zebrafish and muscle-specific Pcyt2-knockout mice recapitulate the participant phenotypes, with failure to thrive, progressive muscle weakness and accelerated ageing. Mechanistically, muscle Pcyt2 deficiency affects cellular bioenergetics and membrane lipid bilayer structure and stability. PCYT2 activity declines in ageing muscles of mice and humans, and adeno-associated virus-based delivery of PCYT2 ameliorates muscle weakness in Pcyt2-knockout and old mice, offering a therapy for individuals with a rare disease and muscle ageing. Thus, PCYT2 plays a fundamental and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2-synthesized lipids to severe muscle dystrophy and ageing.","lang":"eng"}],"page":"495-515","article_type":"original","citation":{"ista":"Cikes D, Elsayad K, Sezgin E, Koitai E, Ferenc T, Orthofer M, Yarwood R, Heinz LX, Sedlyarov V, Darwish-Miranda N, Taylor A, Grapentine S, al-Murshedi F, Abot A, Weidinger A, Kutchukian C, Sanchez C, Cronin SJF, Novatchkova M, Kavirayani A, Schuetz T, Haubner B, Haas L, Hagelkruys A, Jackowski S, Kozlov A, Jacquemond V, Knauf C, Superti-Furga G, Rullman E, Gustafsson T, McDermot J, Lowe M, Radak Z, Chamberlain JS, Bakovic M, Banka S, Penninger JM. 2023. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 5, 495–515.","ieee":"D. Cikes et al., “PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing,” Nature Metabolism, vol. 5. Springer Nature, pp. 495–515, 2023.","apa":"Cikes, D., Elsayad, K., Sezgin, E., Koitai, E., Ferenc, T., Orthofer, M., … Penninger, J. M. (2023). PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-023-00766-2","ama":"Cikes D, Elsayad K, Sezgin E, et al. PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing. Nature Metabolism. 2023;5:495-515. doi:10.1038/s42255-023-00766-2","chicago":"Cikes, Domagoj, Kareem Elsayad, Erdinc Sezgin, Erika Koitai, Torma Ferenc, Michael Orthofer, Rebecca Yarwood, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism. Springer Nature, 2023. https://doi.org/10.1038/s42255-023-00766-2.","mla":"Cikes, Domagoj, et al. “PCYT2-Regulated Lipid Biosynthesis Is Critical to Muscle Health and Ageing.” Nature Metabolism, vol. 5, Springer Nature, 2023, pp. 495–515, doi:10.1038/s42255-023-00766-2.","short":"D. Cikes, K. Elsayad, E. Sezgin, E. Koitai, T. Ferenc, M. Orthofer, R. Yarwood, L.X. Heinz, V. Sedlyarov, N. Darwish-Miranda, A. Taylor, S. Grapentine, F. al-Murshedi, A. Abot, A. Weidinger, C. Kutchukian, C. Sanchez, S.J.F. Cronin, M. Novatchkova, A. Kavirayani, T. Schuetz, B. Haubner, L. Haas, A. Hagelkruys, S. Jackowski, A. Kozlov, V. Jacquemond, C. Knauf, G. Superti-Furga, E. Rullman, T. Gustafsson, J. McDermot, M. Lowe, Z. Radak, J.S. Chamberlain, M. Bakovic, S. Banka, J.M. Penninger, Nature Metabolism 5 (2023) 495–515."},"publication":"Nature Metabolism","date_published":"2023-03-20T00:00:00Z","keyword":["Cell Biology","Physiology (medical)","Endocrinology","Diabetes and Metabolism","Internal Medicine"],"scopus_import":"1","article_processing_charge":"No","day":"20"},{"abstract":[{"text":"The phonon transport mechanisms and ultralow lattice thermal conductivities (κL) in silver halide AgX (X=Cl,Br,I) compounds are not yet well understood. Herein, we study the lattice dynamics and thermal property of AgX under the framework of perturbation theory and the two-channel Wigner thermal transport model based on accurate machine learning potentials. We find that an accurate extraction of the third-order atomic force constants from largely displaced configurations is significant for the calculation of the κL of AgX, and the coherence thermal transport is also non-negligible. In AgI, however, the calculated κL still considerably overestimates the experimental values even including four-phonon scatterings. Molecular dynamics (MD) simulations using machine learning potential suggest an important role of the higher-than-fourth-order lattice anharmonicity in the low-frequency phonon linewidths of AgI at room temperature, which can be related to the simultaneous restrictions of the three- and four-phonon phase spaces. The κL of AgI calculated using MD phonon lifetimes including full-order lattice anharmonicity shows a better agreement with experiments.","lang":"eng"}],"issue":"17","type":"journal_article","oa_version":"None","status":"public","title":"Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I)","intvolume":" 108","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14605","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-11-01T00:00:00Z","article_type":"original","publication":"Physical Review B","citation":{"chicago":"Ouyang, Niuchang, Zezhu Zeng, Chen Wang, Qi Wang, and Yue Chen. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.174302.","mla":"Ouyang, Niuchang, et al. “Role of High-Order Lattice Anharmonicity in the Phonon Thermal Transport of Silver Halide AgX (X=Cl,Br, I).” Physical Review B, vol. 108, no. 17, 174302, American Physical Society, 2023, doi:10.1103/PhysRevB.108.174302.","short":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, Y. Chen, Physical Review B 108 (2023).","ista":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. 2023. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. 108(17), 174302.","ieee":"N. Ouyang, Z. Zeng, C. Wang, Q. Wang, and Y. Chen, “Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I),” Physical Review B, vol. 108, no. 17. American Physical Society, 2023.","apa":"Ouyang, N., Zeng, Z., Wang, C., Wang, Q., & Chen, Y. (2023). Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.174302","ama":"Ouyang N, Zeng Z, Wang C, Wang Q, Chen Y. Role of high-order lattice anharmonicity in the phonon thermal transport of silver halide AgX (X=Cl,Br, I). Physical Review B. 2023;108(17). doi:10.1103/PhysRevB.108.174302"},"ec_funded":1,"article_number":"174302","date_created":"2023-11-26T23:00:54Z","date_updated":"2023-11-28T07:48:55Z","volume":108,"author":[{"full_name":"Ouyang, Niuchang","last_name":"Ouyang","first_name":"Niuchang"},{"last_name":"Zeng","first_name":"Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","full_name":"Zeng, Zezhu"},{"last_name":"Wang","first_name":"Chen","full_name":"Wang, Chen"},{"last_name":"Wang","first_name":"Qi","full_name":"Wang, Qi"},{"first_name":"Yue","last_name":"Chen","full_name":"Chen, Yue"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"BiCh"}],"year":"2023","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (Grants No. 17318122 and No. 17306721). The authors are grateful for the research computing facilities offered by ITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","month":"11","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.108.174302","quality_controlled":"1","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}]},{"abstract":[{"text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art.","lang":"eng"}],"type":"conference","file":[{"success":1,"checksum":"1a730765930138e23c6efd2575872641","date_updated":"2023-11-28T09:14:34Z","date_created":"2023-11-28T09:14:34Z","file_id":"14621","relation":"main_file","creator":"dernst","file_size":704331,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_USENIX_Das.pdf"}],"oa_version":"Published Version","_id":"14609","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling","ddc":["000"],"status":"public","intvolume":" 8","day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-08-15T00:00:00Z","publication":"32nd USENIX Security Symposium","citation":{"mla":"Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” 32nd USENIX Security Symposium, vol. 8, Usenix, 2023, pp. 5359–76.","short":"S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix, 2023, pp. 5359–5376.","chicago":"Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” In 32nd USENIX Security Symposium, 8:5359–76. Usenix, 2023.","ama":"Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In: 32nd USENIX Security Symposium. Vol 8. Usenix; 2023:5359-5376.","ista":"Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. 32nd USENIX Security Symposium. USENIX Security Symposium vol. 8, 5359–5376.","apa":"Das, S., Xiang, Z., Kokoris Kogias, E., & Ren, L. (2023). Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In 32nd USENIX Security Symposium (Vol. 8, pp. 5359–5376). Anaheim, CA, United States: Usenix.","ieee":"S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling,” in 32nd USENIX Security Symposium, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376."},"page":"5359-5376","file_date_updated":"2023-11-28T09:14:34Z","author":[{"full_name":"Das, Sourav","last_name":"Das","first_name":"Sourav"},{"full_name":"Xiang, Zhuolun","last_name":"Xiang","first_name":"Zhuolun"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Ren, Ling","last_name":"Ren","first_name":"Ling"}],"date_updated":"2023-11-28T09:17:38Z","date_created":"2023-11-26T23:00:55Z","volume":8,"acknowledgement":"The authors would like to thank Amit Agarwal, Andrew Miller, and Tom Yurek for the helpful discussions related to the paper. This work is funded in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship, the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.","year":"2023","publication_status":"published","department":[{"_id":"ElKo"}],"publisher":"Usenix","month":"08","publication_identifier":{"isbn":["9781713879497"]},"conference":{"start_date":"2023-08-09","location":"Anaheim, CA, United States","end_date":"2023-08-11","name":"USENIX Security Symposium"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/1389"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"F8512","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","name":"Secure Network and Hardware for Efficient Blockchains"}]},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"14","article_type":"original","citation":{"chicago":"Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0173341.","short":"A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).","mla":"Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics, vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:10.1063/5.0173341.","apa":"Reinhardt, A., Chew, P. Y., & Cheng, B. (2023). A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0173341","ieee":"A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals,” Journal of Chemical Physics, vol. 159, no. 18. AIP Publishing, 2023.","ista":"Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 159(18), 184110.","ama":"Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals. Journal of Chemical Physics. 2023;159(18). doi:10.1063/5.0173341"},"publication":"Journal of Chemical Physics","date_published":"2023-11-14T00:00:00Z","type":"journal_article","issue":"18","abstract":[{"text":"Computing the solubility of crystals in a solvent using atomistic simulations is notoriously challenging due to the complexities and convergence issues associated with free-energy methods, as well as the slow equilibration in direct-coexistence simulations. This paper introduces a molecular-dynamics workflow that simplifies and robustly computes the solubility of molecular or ionic crystals. This method is considerably more straightforward than the state-of-the-art, as we have streamlined and optimised each step of the process. Specifically, we calculate the chemical potential of the crystal using the gas-phase molecule as a reference state, and employ the S0 method to determine the concentration dependence of the chemical potential of the solute. We use this workflow to predict the solubilities of sodium chloride in water, urea polymorphs in water, and paracetamol polymorphs in both water and ethanol. Our findings indicate that the predicted solubility is sensitive to the chosen potential energy surface. Furthermore, we note that the harmonic approximation often fails for both molecular crystals and gas molecules at or above room temperature, and that the assumption of an ideal solution becomes less valid for highly soluble substances.","lang":"eng"}],"intvolume":" 159","title":"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals","ddc":["530","540"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14603","file":[{"file_size":6276059,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_JourChemicalPhysics_Reinhardt.pdf","checksum":"f668ee0d07096eef81159d05bc27aabc","success":1,"date_created":"2023-11-28T08:39:06Z","date_updated":"2023-11-28T08:39:06Z","relation":"main_file","file_id":"14620"}],"oa_version":"Published Version","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"month":"11","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2308.10886"]},"language":[{"iso":"eng"}],"doi":"10.1063/5.0173341","article_number":"184110","file_date_updated":"2023-11-28T08:39:06Z","publisher":"AIP Publishing","department":[{"_id":"BiCh"}],"publication_status":"published","acknowledgement":"A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.","year":"2023","volume":159,"date_updated":"2023-11-28T08:39:23Z","date_created":"2023-11-26T23:00:54Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"14619"}]},"author":[{"first_name":"Aleks","last_name":"Reinhardt","full_name":"Reinhardt, Aleks"},{"last_name":"Chew","first_name":"Pin Yu","full_name":"Chew, Pin Yu"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing"}]},{"article_type":"original","page":"2504-2511","publication":"Evolution","citation":{"ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 2023;77(11):2504-2511. doi:10.1093/evolut/qpad169","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of class Insecta,” Evolution, vol. 77, no. 11. Oxford University Press, pp. 2504–2511, 2023.","apa":"Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpad169","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.","mla":"Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Evolution, vol. 77, no. 11, Oxford University Press, 2023, pp. 2504–11, doi:10.1093/evolut/qpad169.","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpad169."},"date_published":"2023-11-02T00:00:00Z","scopus_import":"1","day":"02","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","title":"The X chromosome of insects likely predates the origin of class Insecta","status":"public","ddc":["570"],"intvolume":" 77","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14604","file":[{"creator":"dernst","file_size":1399102,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_Evolution_Toups.pdf","success":1,"checksum":"b66dc10edae92d38918d534e64dda77c","date_updated":"2023-11-28T08:12:15Z","date_created":"2023-11-28T08:12:15Z","file_id":"14618","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"issue":"11","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37738212"]},"language":[{"iso":"eng"}],"doi":"10.1093/evolut/qpad169","month":"11","publication_identifier":{"eissn":["1558-5646"]},"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","year":"2023","acknowledgement":"All computational analyses were performed on the server at Institute of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for analytical advice, and Tanja Schwander and Vincent Merel for useful discussions. We also thank Matthew Hahn for comments on an earlier version of the manuscript.","pmid":1,"date_updated":"2023-11-28T08:25:28Z","date_created":"2023-11-26T23:00:54Z","volume":77,"author":[{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"related_material":{"link":[{"url":"https://git.ista.ac.at/bvicoso/veryoldx","relation":"software"}],"record":[{"status":"public","relation":"research_data","id":"14616"},{"relation":"research_data","status":"public","id":"14617"}]},"file_date_updated":"2023-11-28T08:12:15Z"},{"publisher":"Dryad","department":[{"_id":"BeVi"}],"title":"The X chromosome of insects likely predates the origin of Class Insecta","ddc":["570"],"status":"public","_id":"14616","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","oa_version":"Published Version","date_created":"2023-11-28T08:01:53Z","date_updated":"2023-11-28T08:17:31Z","related_material":{"record":[{"id":"14604","relation":"used_in_publication","status":"public"}]},"author":[{"orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A","full_name":"Toups, Melissa A"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.hx3ffbgkt"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Dryad, 10.5061/DRYAD.HX3FFBGKT.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","apa":"Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Dryad. https://doi.org/10.5061/DRYAD.HX3FFBGKT","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:10.5061/DRYAD.HX3FFBGKT","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Dryad, 2023. https://doi.org/10.5061/DRYAD.HX3FFBGKT.","mla":"Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely Predates the Origin of Class Insecta. Dryad, 2023, doi:10.5061/DRYAD.HX3FFBGKT.","short":"M.A. Toups, B. Vicoso, (2023)."},"oa":1,"doi":"10.5061/DRYAD.HX3FFBGKT","date_published":"2023-09-15T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","month":"09","day":"15"},{"oa_version":"Published Version","date_created":"2023-11-28T08:04:03Z","date_updated":"2023-11-28T08:25:28Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14604"}]},"author":[{"last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"publisher":"Zenodo","department":[{"_id":"BeVi"}],"title":"The X chromosome of insects likely predates the origin of Class Insecta","ddc":["570"],"status":"public","_id":"14617","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","abstract":[{"text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"type":"research_data_reference","date_published":"2023-09-15T00:00:00Z","doi":"10.5281/ZENODO.8138705","citation":{"apa":"Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Zenodo. https://doi.org/10.5281/ZENODO.8138705","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, 10.5281/ZENODO.8138705.","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:10.5281/ZENODO.8138705","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8138705.","short":"M.A. Toups, B. Vicoso, (2023).","mla":"Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely Predates the Origin of Class Insecta. Zenodo, 2023, doi:10.5281/ZENODO.8138705."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8138705","open_access":"1"}],"has_accepted_license":"1","article_processing_charge":"No","month":"09","day":"15","other_data_license":"MIT License"},{"article_processing_charge":"No","has_accepted_license":"1","month":"10","day":"02","doi":"10.5281/ZENODO.8398094","date_published":"2023-10-02T00:00:00Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8398094","open_access":"1"}],"citation":{"mla":"Cheng, Bingqing. BingqingCheng/Solubility: V1.0. Zenodo, 2023, doi:10.5281/ZENODO.8398094.","short":"B. Cheng, (2023).","chicago":"Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8398094.","ama":"Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:10.5281/ZENODO.8398094","ista":"Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, 10.5281/ZENODO.8398094.","ieee":"B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.","apa":"Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. https://doi.org/10.5281/ZENODO.8398094"},"abstract":[{"text":"Data underlying the publication \"A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals\" (DOI https://doi.org/10.1063/5.0173341).","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-11-28T08:39:22Z","date_created":"2023-11-28T08:32:18Z","related_material":{"record":[{"id":"14603","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"}],"department":[{"_id":"BiCh"}],"publisher":"Zenodo","title":"BingqingCheng/solubility: V1.0","ddc":["530"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14619","year":"2023"},{"oa_version":"Published Version","file":[{"creator":"dernst","file_size":6435697,"content_type":"application/pdf","file_name":"2023_JAMES_Khoulder.pdf","access_level":"open_access","date_updated":"2023-11-20T11:29:16Z","date_created":"2023-11-20T11:29:16Z","success":1,"checksum":"e30329dd985559de0ddc7021ca7382b4","file_id":"14582","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14564","status":"public","title":"A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model","ddc":["550"],"intvolume":" 15","abstract":[{"lang":"eng","text":"Cumulus parameterization (CP) in state‐of‐the‐art global climate models is based on the quasi‐equilibrium assumption (QEA), which views convection as the action of an ensemble of cumulus clouds, in a state of equilibrium with respect to a slowly varying atmospheric state. This view is not compatible with the organization and dynamical interactions across multiple scales of cloud systems in the tropics and progress in this research area was slow over decades despite the widely recognized major shortcomings. Novel ideas on how to represent key physical processes of moist convection‐large‐scale interaction to overcome the QEA have surged recently. The stochastic multicloud model (SMCM) CP in particular mimics the dynamical interactions of multiple cloud types that characterize organized tropical convection. Here, the SMCM is used to modify the Zhang‐McFarlane (ZM) CP by changing the way in which the bulk mass flux and bulk entrainment and detrainment rates are calculated. This is done by introducing a stochastic ensemble of plumes characterized by randomly varying detrainment level distributions based on the cloud area fraction of the SMCM. The SMCM is here extended to include shallow cumulus clouds resulting in a unified shallow‐deep CP. The new stochastic multicloud plume CP is validated against the control ZM scheme in the context of the single column Community Climate Model of the National Center for Atmospheric Research using data from both tropical ocean and midlatitude land convection. Some key features of the SMCM CP such as it capability to represent the tri‐modal nature of organized convection are emphasized."}],"issue":"11","type":"journal_article","date_published":"2023-11-01T00:00:00Z","publication":"Journal of Advances in Modeling Earth Systems","citation":{"chicago":"Khouider, B., BIDYUT B GOSWAMI, R. Phani, and A. J. Majda. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” Journal of Advances in Modeling Earth Systems. American Geophysical Union, 2023. https://doi.org/10.1029/2022ms003391.","short":"B. Khouider, B.B. GOSWAMI, R. Phani, A.J. Majda, Journal of Advances in Modeling Earth Systems 15 (2023).","mla":"Khouider, B., et al. “A Shallow‐deep Unified Stochastic Mass Flux Cumulus Parameterization in the Single Column Community Climate Model.” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11, e2022MS003391, American Geophysical Union, 2023, doi:10.1029/2022ms003391.","ieee":"B. Khouider, B. B. GOSWAMI, R. Phani, and A. J. Majda, “A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 11. American Geophysical Union, 2023.","apa":"Khouider, B., GOSWAMI, B. B., Phani, R., & Majda, A. J. (2023). A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. American Geophysical Union. https://doi.org/10.1029/2022ms003391","ista":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. 2023. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 15(11), e2022MS003391.","ama":"Khouider B, GOSWAMI BB, Phani R, Majda AJ. A shallow‐deep unified stochastic mass flux cumulus parameterization in the single column community climate model. Journal of Advances in Modeling Earth Systems. 2023;15(11). doi:10.1029/2022ms003391"},"article_type":"original","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","keyword":["General Earth and Planetary Sciences","Environmental Chemistry","Global and Planetary Change"],"author":[{"first_name":"B.","last_name":"Khouider","full_name":"Khouider, B."},{"full_name":"GOSWAMI, BIDYUT B","orcid":"0000-0001-8602-3083","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","last_name":"GOSWAMI","first_name":"BIDYUT B"},{"first_name":"R.","last_name":"Phani","full_name":"Phani, R."},{"full_name":"Majda, A. J.","last_name":"Majda","first_name":"A. J."}],"date_updated":"2023-11-28T12:04:42Z","date_created":"2023-11-20T09:18:21Z","volume":15,"acknowledgement":"The research of B.K. is supported in part by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (RGPIN-04246-2020). This research was conducted during the visits of P.M. Krishna to the Center for Prototype Climate Models at NYU Abu Dhabi and University of Victoria from November 2018 to June 2019 and July 2019 and October 2019, respectively. The authors are very grateful to the three anonymous reviewers who provided very thoughtful and constructive comments during the review process that helped greatly improve and shape the final version of the manuscript.","year":"2023","publication_status":"published","publisher":"American Geophysical Union","department":[{"_id":"CaMu"}],"file_date_updated":"2023-11-20T11:29:16Z","article_number":"e2022MS003391","doi":"10.1029/2022ms003391","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","month":"11","publication_identifier":{"eissn":["1942-2466"]}},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Physical Review E","citation":{"ama":"Mujica N, Waitukaitis SR. Accurate determination of the shapes of granular charge distributions. Physical Review E. 2023;107(3). doi:10.1103/PhysRevE.107.034901","apa":"Mujica, N., & Waitukaitis, S. R. (2023). Accurate determination of the shapes of granular charge distributions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.034901","ieee":"N. Mujica and S. R. Waitukaitis, “Accurate determination of the shapes of granular charge distributions,” Physical Review E, vol. 107, no. 3. American Physical Society, 2023.","ista":"Mujica N, Waitukaitis SR. 2023. Accurate determination of the shapes of granular charge distributions. Physical Review E. 107(3), 034901.","short":"N. Mujica, S.R. Waitukaitis, Physical Review E 107 (2023).","mla":"Mujica, Nicolás, and Scott R. Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E, vol. 107, no. 3, 034901, American Physical Society, 2023, doi:10.1103/PhysRevE.107.034901.","chicago":"Mujica, Nicolás, and Scott R Waitukaitis. “Accurate Determination of the Shapes of Granular Charge Distributions.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.034901."},"date_published":"2023-03-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Experiments have shown that charge distributions of granular materials are non-Gaussian, with broad tails that indicate many particles with high charge. This observation has consequences for the behavior of granular materials in many settings, and may bear relevance to the underlying charge transfer mechanism. However, there is the unaddressed possibility that broad tails arise due to experimental uncertainties, as determining the shapes of tails is nontrivial. Here we show that measurement uncertainties can indeed account for most of the tail broadening previously observed. The clue that reveals this is that distributions are sensitive to the electric field at which they are measured; ones measured at low (high) fields have larger (smaller) tails. Accounting for sources of uncertainty, we reproduce this broadening in silico. Finally, we use our results to back out the true charge distribution without broadening, which we find is still non-Guassian, though with substantially different behavior at the tails and indicating significantly fewer highly charged particles. These results have implications in many natural settings where electrostatic interactions, especially among highly charged particles, strongly affect granular behavior.","lang":"eng"}],"issue":"3","ddc":["530"],"status":"public","title":"Accurate determination of the shapes of granular charge distributions","intvolume":" 107","_id":"12789","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"14612","checksum":"48f5dfe4e5f1c46c3c86805cd8f84bea","success":1,"date_created":"2023-11-27T09:51:48Z","date_updated":"2023-11-27T09:51:48Z","access_level":"open_access","file_name":"PhysRevE.107.034901 (1).pdf","file_size":1428631,"content_type":"application/pdf","creator":"swaituka"}],"oa_version":"Published Version","month":"03","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"}],"oa":1,"external_id":{"isi":["000992142700001"]},"acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.107.034901","article_number":"034901","file_date_updated":"2023-11-27T09:51:48Z","ec_funded":1,"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"ScWa"}],"year":"2023","acknowledgement":"This research was supported by Grants QUIMAL 160001 and Fondecyt 1221597. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 949120). This research was supported by the Scientific Service Units of The Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine Shop. We thank the machine shop technical assistance of Ricardo Silva and Andrés Espinosa at Departamento de Física, Universidad de Chile.","date_created":"2023-04-02T22:01:10Z","date_updated":"2023-11-28T09:22:25Z","volume":107,"author":[{"full_name":"Mujica, Nicolás","last_name":"Mujica","first_name":"Nicolás"},{"full_name":"Waitukaitis, Scott R","first_name":"Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}]},{"ec_funded":1,"related_material":{"record":[{"id":"14506","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Schmid, Stefan","last_name":"Schmid","first_name":"Stefan"},{"full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","first_name":"Jakub"},{"full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","last_name":"Yeo"}],"volume":13892,"date_updated":"2023-11-30T10:54:51Z","date_created":"2023-07-16T22:01:12Z","acknowledgement":"We thank Mahsa Bastankhah and Mohammad Ali Maddah-Ali for fruitful discussions about different variants of the problem. This work is supported by the European Research Council (ERC) Consolidator Project 864228 (AdjustNet), 2020-2025, the ERC CoG 863818 (ForM-SMArt), and the German Research Foundation (DFG) grant 470029389 (FlexNets), 2021–2024.","year":"2023","publisher":"Springer Nature","department":[{"_id":"KrPi"},{"_id":"KrCh"}],"publication_status":"published","publication_identifier":{"isbn":["9783031327322"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"05","doi":"10.1007/978-3-031-32733-9_26","conference":{"name":"SIROCCO: Structural Information and Communication Complexity","end_date":"2023-06-09","location":"Alcala de Henares, Spain","start_date":"2023-06-06"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.13459","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2204.13459"]},"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider a natural problem dealing with weighted packet selection across a rechargeable link, which e.g., finds applications in cryptocurrency networks. The capacity of a link (u, v) is determined by how much nodes u and v allocate for this link. Specifically, the input is a finite ordered sequence of packets that arrive in both directions along a link. Given (u, v) and a packet of weight x going from u to v, node u can either accept or reject the packet. If u accepts the packet, the capacity on link (u, v) decreases by x. Correspondingly, v’s capacity on (u, v) increases by x. If a node rejects the packet, this will entail a cost affinely linear in the weight of the packet. A link is “rechargeable” in the sense that the total capacity of the link has to remain constant, but the allocation of capacity at the ends of the link can depend arbitrarily on the nodes’ decisions. The goal is to minimise the sum of the capacity injected into the link and the cost of rejecting packets. We show that the problem is NP-hard, but can be approximated efficiently with a ratio of (1+ε)⋅(1+3–√) for some arbitrary ε>0.\r\n."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13238","intvolume":" 13892","title":"Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation","status":"public","article_processing_charge":"No","day":"25","scopus_import":"1","date_published":"2023-05-25T00:00:00Z","citation":{"chicago":"Schmid, Stefan, Jakub Svoboda, and Michelle X Yeo. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” In SIROCCO 2023: Structural Information and Communication Complexity , 13892:576–94. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_26.","mla":"Schmid, Stefan, et al. “Weighted Packet Selection for Rechargeable Links in Cryptocurrency Networks: Complexity and Approximation.” SIROCCO 2023: Structural Information and Communication Complexity , vol. 13892, Springer Nature, 2023, pp. 576–94, doi:10.1007/978-3-031-32733-9_26.","short":"S. Schmid, J. Svoboda, M.X. Yeo, in:, SIROCCO 2023: Structural Information and Communication Complexity , Springer Nature, 2023, pp. 576–594.","ista":"Schmid S, Svoboda J, Yeo MX. 2023. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. SIROCCO 2023: Structural Information and Communication Complexity . SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 576–594.","ieee":"S. Schmid, J. Svoboda, and M. X. Yeo, “Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation,” in SIROCCO 2023: Structural Information and Communication Complexity , Alcala de Henares, Spain, 2023, vol. 13892, pp. 576–594.","apa":"Schmid, S., Svoboda, J., & Yeo, M. X. (2023). Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In SIROCCO 2023: Structural Information and Communication Complexity (Vol. 13892, pp. 576–594). Alcala de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_26","ama":"Schmid S, Svoboda J, Yeo MX. Weighted packet selection for rechargeable links in cryptocurrency networks: Complexity and approximation. In: SIROCCO 2023: Structural Information and Communication Complexity . Vol 13892. Springer Nature; 2023:576-594. doi:10.1007/978-3-031-32733-9_26"},"publication":"SIROCCO 2023: Structural Information and Communication Complexity ","page":"576-594"},{"date_created":"2023-11-10T08:10:43Z","date_updated":"2023-11-30T10:54:51Z","related_material":{"record":[{"id":"9969","status":"public","relation":"part_of_dissertation"},{"id":"13238","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14490"}]},"author":[{"first_name":"Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"publication_status":"published","year":"2023","ec_funded":1,"file_date_updated":"2023-11-23T10:30:08Z","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"degree_awarded":"PhD","doi":"10.15479/14506","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa":1,"publication_identifier":{"issn":["2663 - 337X"]},"month":"11","oa_version":"Published Version","file":[{"checksum":"521c72818d720a52b377207b2ee87b6a","date_updated":"2023-11-23T10:29:55Z","date_created":"2023-11-23T10:29:55Z","file_id":"14598","relation":"source_file","creator":"cchlebak","file_size":3037720,"content_type":"application/x-zip-compressed","access_level":"closed","file_name":"thesis_yeo.zip"},{"relation":"main_file","file_id":"14599","date_updated":"2023-11-23T10:30:08Z","date_created":"2023-11-23T10:30:08Z","checksum":"0ed5d16899687aecf13d843c9878c9f2","success":1,"file_name":"thesis_yeo.pdf","access_level":"open_access","file_size":2717256,"content_type":"application/pdf","creator":"cchlebak"}],"title":"Advances in efficiency and privacy in payment channel network analysis","status":"public","ddc":["000"],"_id":"14506","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2023-11-10T00:00:00Z","page":"162","citation":{"chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14506.","short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023.","mla":"Yeo, Michelle X. Advances in Efficiency and Privacy in Payment Channel Network Analysis. Institute of Science and Technology Austria, 2023, doi:10.15479/14506.","ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023.","apa":"Yeo, M. X. (2023). Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/14506","ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria.","ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:10.15479/14506"},"article_processing_charge":"No","has_accepted_license":"1","day":"10"},{"volume":2023,"date_updated":"2023-11-30T10:54:51Z","date_created":"2023-11-05T23:00:54Z","related_material":{"record":[{"id":"14506","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Zeta","last_name":"Avarikioti","full_name":"Avarikioti, Zeta"},{"full_name":"Lizurej, Tomasz","first_name":"Tomasz","last_name":"Lizurej"},{"full_name":"Michalak, Tomasz","first_name":"Tomasz","last_name":"Michalak"},{"id":"2D82B818-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle X","last_name":"Yeo","full_name":"Yeo, Michelle X"}],"department":[{"_id":"KrPi"}],"publisher":"IEEE","publication_status":"published","acknowledgement":"The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant 2020388). It was also partially supported by NCN Grant 2019/35/B/ST6/04138 and ERC Grant 885666.","year":"2023","language":[{"iso":"eng"}],"doi":"10.1109/ICDCS57875.2023.00037","conference":{"end_date":"2023-07-21","location":"Hong Kong, China","start_date":"2023-07-18","name":"ICDCS: International Conference on Distributed Computing Systems"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.16006"}],"oa":1,"external_id":{"arxiv":["2306.16006"]},"publication_identifier":{"eissn":["2575-8411"],"isbn":["9798350339864"]},"month":"10","oa_version":"Preprint","intvolume":" 2023","status":"public","title":"Lightning creation games","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14490","abstract":[{"lang":"eng","text":"Payment channel networks (PCNs) are a promising solution to the scalability problem of cryptocurrencies. Any two users connected by a payment channel in the network can theoretically send an unbounded number of instant, costless transactions between them. Users who are not directly connected can also transact with each other in a multi-hop fashion. In this work, we study the incentive structure behind the creation of payment channel networks, particularly from the point of view of a single user that wants to join the network. We define a utility function for a new user in terms of expected revenue, expected fees, and the cost of creating channels, and then provide constant factor approximation algorithms that optimise the utility function given a certain budget. Additionally, we take a step back from a single user to the whole network and examine the parameter spaces under which simple graph topologies form a Nash equilibrium."}],"type":"conference","date_published":"2023-10-11T00:00:00Z","page":"603-613","citation":{"apa":"Avarikioti, Z., Lizurej, T., Michalak, T., & Yeo, M. X. (2023). Lightning creation games. In 43rd International Conference on Distributed Computing Systems (Vol. 2023, pp. 603–613). Hong Kong, China: IEEE. https://doi.org/10.1109/ICDCS57875.2023.00037","ieee":"Z. Avarikioti, T. Lizurej, T. Michalak, and M. X. Yeo, “Lightning creation games,” in 43rd International Conference on Distributed Computing Systems, Hong Kong, China, 2023, vol. 2023, pp. 603–613.","ista":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. 2023. Lightning creation games. 43rd International Conference on Distributed Computing Systems. ICDCS: International Conference on Distributed Computing Systems vol. 2023, 603–613.","ama":"Avarikioti Z, Lizurej T, Michalak T, Yeo MX. Lightning creation games. In: 43rd International Conference on Distributed Computing Systems. Vol 2023. IEEE; 2023:603-613. doi:10.1109/ICDCS57875.2023.00037","chicago":"Avarikioti, Zeta, Tomasz Lizurej, Tomasz Michalak, and Michelle X Yeo. “Lightning Creation Games.” In 43rd International Conference on Distributed Computing Systems, 2023:603–13. IEEE, 2023. https://doi.org/10.1109/ICDCS57875.2023.00037.","short":"Z. Avarikioti, T. Lizurej, T. Michalak, M.X. Yeo, in:, 43rd International Conference on Distributed Computing Systems, IEEE, 2023, pp. 603–613.","mla":"Avarikioti, Zeta, et al. “Lightning Creation Games.” 43rd International Conference on Distributed Computing Systems, vol. 2023, IEEE, 2023, pp. 603–13, doi:10.1109/ICDCS57875.2023.00037."},"publication":"43rd International Conference on Distributed Computing Systems","article_processing_charge":"No","day":"11","scopus_import":"1"},{"year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"author":[{"orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl","first_name":"Michael","full_name":"Riedl, Michael"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10703"},{"id":"10791","relation":"part_of_dissertation","status":"public"},{"id":"7932","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"461"},{"id":"14530","status":"public","relation":"new_edition"}]},"date_created":"2023-03-15T13:22:13Z","date_updated":"2023-11-30T10:55:13Z","file_date_updated":"2023-11-24T11:57:46Z","doi":"10.15479/at:ista:12726","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"_id":"12726","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Synchronization in collectively moving active matter","status":"public","ddc":["530"],"file":[{"content_type":"application/pdf","file_size":63734746,"creator":"cchlebak","description":"the main file is missing the bibliography. See new thesis record 14530 for updated files.","file_name":"Thesis_Riedl_2023.pdf","access_level":"closed","date_updated":"2023-11-24T11:57:46Z","date_created":"2023-03-23T12:49:23Z","checksum":"eba0e19fe57a8c15e7aeab55a845efb7","relation":"main_file","file_id":"12745"},{"access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Riedl_2023_source.rar","content_type":"application/octet-stream","file_size":339473651,"creator":"cchlebak","relation":"source_file","file_id":"12746","checksum":"0eb7b650cc8ae843bcec7c8a6109ae03","date_created":"2023-03-23T12:54:34Z","date_updated":"2023-09-24T22:30:03Z"}],"oa_version":"None","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Most motions of many-body systems at any scale in nature with sufficient degrees\r\nof freedom tend to be chaotic; reaching from the orbital motion of planets, the air\r\ncurrents in our atmosphere, down to the water flowing through our pipelines or\r\nthe movement of a population of bacteria. To the observer it is therefore intriguing\r\nwhen a moving collective exhibits order. Collective motion of flocks of birds, schools\r\nof fish or swarms of self-propelled particles or robots have been studied extensively\r\nover the past decades but the mechanisms involved in the transition from chaos to\r\norder remain unclear. Here, the interactions, that in most systems give rise to chaos,\r\nsustain order. In this thesis we investigate mechanisms that preserve, destabilize\r\nor lead to the ordered state. We show that endothelial cells migrating in circular\r\nconfinements transition to a collective rotating state and concomitantly synchronize\r\nthe frequencies of nucleating actin waves within individual cells. Consequently,\r\nthe frequency dependent cell migration speed uniformizes across the population.\r\nComplementary to the WAVE dependent nucleation of traveling actin waves, we\r\nshow that in leukocytes the actin polymerization depending on WASp generates\r\npushing forces locally at stationary patches. Next, in pipe flows, we study methods\r\nto disrupt the self–sustaining cycle of turbulence and therefore relaminarize the\r\nflow. While we find in pulsating flow conditions that turbulence emerges through a\r\nhelical instability during the decelerating phase. Finally, we show quantitatively in\r\nbrain slices of mice that wild-type control neurons can compensate the migratory\r\ndeficits of a genetically modified neuronal sub–population in the developing cortex.","lang":"eng"}],"citation":{"ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/at:ista:12726","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12726","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12726.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12726."},"page":"260","date_published":"2023-03-23T00:00:00Z","day":"23","article_processing_charge":"No","has_accepted_license":"1"},{"title":"Synchronization in collectively moving active matter","ddc":["530","570"],"status":"public","_id":"14530","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Updated Version","file":[{"success":1,"checksum":"52e1d0ab6c1abe59c82dfe8c9ff5f83a","date_created":"2023-11-15T09:52:54Z","date_updated":"2023-11-15T09:52:54Z","file_id":"14536","relation":"main_file","creator":"mriedl","content_type":"application/pdf","file_size":36743942,"access_level":"open_access","file_name":"Thesis_Riedl_2023_corr.pdf"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Most motions of many-body systems at any scale in nature with sufficient degrees of freedom tend to be chaotic; reaching from the orbital motion of planets, the air currents in our atmosphere, down to the water flowing through our pipelines or the movement of a population of bacteria. To the observer it is therefore intriguing when a moving collective exhibits order. Collective motion of flocks of birds, schools of fish or swarms of self-propelled particles or robots have been studied extensively over the past decades but the mechanisms involved in the transition from chaos to order remain unclear. Here, the interactions, that in most systems give rise to chaos, sustain order. In this thesis we investigate mechanisms that preserve, destabilize or lead to the ordered state. We show that endothelial cells migrating in circular confinements transition to a collective rotating state and concomitantly synchronize the frequencies of nucleating actin waves within individual cells. Consequently, the frequency dependent cell migration speed uniformizes across the population. Complementary to the WAVE dependent nucleation of traveling actin waves, we show that in leukocytes the actin polymerization depending on WASp generates pushing forces locally at stationary patches. Next, in pipe flows, we study methods to disrupt the self--sustaining cycle of turbulence and therefore relaminarize the flow. While we find in pulsating flow conditions that turbulence emerges through a helical instability during the decelerating phase. Finally, we show quantitatively in brain slices of mice that wild-type control neurons can compensate the migratory deficits of a genetically modified neuronal sub--population in the developing cortex. "}],"page":"260","citation":{"chicago":"Riedl, Michael. “Synchronization in Collectively Moving Active Matter.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14530.","mla":"Riedl, Michael. Synchronization in Collectively Moving Active Matter. Institute of Science and Technology Austria, 2023, doi:10.15479/14530.","short":"M. Riedl, Synchronization in Collectively Moving Active Matter, Institute of Science and Technology Austria, 2023.","ista":"Riedl M. 2023. Synchronization in collectively moving active matter. Institute of Science and Technology Austria.","ieee":"M. Riedl, “Synchronization in collectively moving active matter,” Institute of Science and Technology Austria, 2023.","apa":"Riedl, M. (2023). Synchronization in collectively moving active matter. Institute of Science and Technology Austria. https://doi.org/10.15479/14530","ama":"Riedl M. Synchronization in collectively moving active matter. 2023. doi:10.15479/14530"},"date_published":"2023-11-16T00:00:00Z","keyword":["Synchronization","Collective Movement","Active Matter","Cell Migration","Active Colloids"],"day":"16","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","year":"2023","date_created":"2023-11-15T09:59:03Z","date_updated":"2023-11-30T10:55:13Z","author":[{"first_name":"Michael","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10703"},{"relation":"part_of_dissertation","status":"public","id":"10791"},{"id":"7932","relation":"part_of_dissertation","status":"public"},{"id":"461","relation":"part_of_dissertation","status":"public"},{"id":"12726","status":"public","relation":"old_edition"}]},"file_date_updated":"2023-11-15T09:52:54Z","oa":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/14530","month":"11","publication_identifier":{"issn":["2663 - 337X"]}},{"date_published":"2023-11-16T00:00:00Z","citation":{"ieee":"D. T. Phan, “Resonant microwave spectroscopy of Al-InAs,” Institute of Science and Technology Austria, 2023.","apa":"Phan, D. T. (2023). Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria. https://doi.org/10.15479/14547","ista":"Phan DT. 2023. Resonant microwave spectroscopy of Al-InAs. Institute of Science and Technology Austria.","ama":"Phan DT. Resonant microwave spectroscopy of Al-InAs. 2023. doi:10.15479/14547","chicago":"Phan, Duc T. “Resonant Microwave Spectroscopy of Al-InAs.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14547.","short":"D.T. Phan, Resonant Microwave Spectroscopy of Al-InAs, Institute of Science and Technology Austria, 2023.","mla":"Phan, Duc T. Resonant Microwave Spectroscopy of Al-InAs. Institute of Science and Technology Austria, 2023, doi:10.15479/14547."},"page":"80","article_processing_charge":"No","has_accepted_license":"1","day":"16","keyword":["superconductor-semiconductor","superconductivity","Al","InAs","p-wave","superconductivity","JPA","microwave"],"oa_version":"Published Version","file":[{"file_name":"Phan_Thesis_pdfa.pdf","access_level":"open_access","creator":"pduc","content_type":"application/pdf","file_size":34828019,"file_id":"14548","relation":"main_file","date_updated":"2023-11-22T09:46:06Z","date_created":"2023-11-17T13:36:44Z","checksum":"db0c37d213bc002125bd59690e9db246"},{"file_id":"14549","relation":"source_file","checksum":"8d3bd6afa279a0078ffd13e06bb6d56d","date_updated":"2023-11-17T13:47:54Z","date_created":"2023-11-17T13:44:53Z","access_level":"closed","file_name":"dissertation_src.zip","creator":"pduc","file_size":279319709,"content_type":"application/zip"}],"_id":"14547","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Resonant microwave spectroscopy of Al-InAs","ddc":["530"],"abstract":[{"lang":"eng","text":"Superconductor-semiconductor heterostructures currently capture a significant amount of research interest and they serve as the physical platform in many proposals towards topological quantum computation.\r\nDespite being under extensive investigations, historically using transport techniques, the basic properties of the interface between the superconductor and the semiconductor remain to be understood.\r\n\r\nIn this thesis, two separate studies on the Al-InAs heterostructures are reported with the first focusing on the physics of the material motivated by the emergence of a new phase, the Bogoliubov-Fermi surface. \r\nThe second focuses on a technological application, a gate-tunable Josephson parametric amplifier.\r\n\r\nIn the first study, we investigate the hypothesized unconventional nature of the induced superconductivity at the interface between the Al thin film and the InAs quantum well.\r\nWe embed a two-dimensional Al-InAs hybrid system in a resonant microwave circuit allowing measurements of change in inductance.\r\nThe behaviour of the resonance in a range of temperature and in-plane magnetic field has been studied and compared with the theory of conventional s-wave superconductor and a two-component theory that includes both contribution of the $s$-wave pairing in Al and the intraband $p \\pm ip$ pairing in InAs.\r\nMeasuring the temperature dependence of resonant frequency, no discrepancy is found between data and the conventional theory.\r\nWe observe the breakdown of superconductivity due to an applied magnetic field which contradicts the conventional theory.\r\nIn contrast, the data can be captured quantitatively by fitting to a two-component model.\r\nWe find the evidence of the intraband $p \\pm ip$ pairing in the InAs and the emergence of the Bogoliubov-Fermi surfaces due to magnetic field with the characteristic value $B^* = 0.33~\\mathrm{T}$.\r\nFrom the fits, the sheet resistance of Al, the carrier density and mobility in InAs are determined.\r\nBy systematically studying the anisotropy of the circuit response, we find weak anisotropy for $B < B^*$ and increasingly strong anisotropy for $B > B^*$ resulting in a pronounced two-lobe structure in polar plot of frequency versus field angle.\r\nStrong resemblance between the field dependence of dissipation and superfluid density hints at a hidden signature of the Bogoliubov-Fermi surface that is burried in the dissipation data.\r\n\r\nIn the second study, we realize a parametric amplifier with a Josephson field effect transistor as the active element.\r\nThe device's modest construction consists of a gated SNS weak link embedded at the center of a coplanar waveguide resonator.\r\nBy applying a gate voltage, the resonant frequency is field-effect tunable over a range of 2 GHz.\r\nModelling the JoFET minimally as a parallel RL circuit, the dissipation introduced by the JoFET can be quantitatively related to the gate voltage.\r\nWe observed gate-tunable Kerr nonlinearity qualitatively in line with expectation.\r\nThe JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1dB compression point of -125.5 dBm when operated at a fixed resonant frequency.\r\nIn general, the signal-to-noise ratio is improved by 5-7 dB when the JoFET amplifier is activated compared.\r\nThe noise of the measurement chain and insertion loss of relevant circuit elements are calibrated to determine the expected and the real noise performance of the JoFET amplifier.\r\nAs a quantification of the noise performance, the measured total input-referred noise of the JoFET amplifier is in good agreement with the estimated expectation which takes device loss into account.\r\nWe found that the noise performance of the device reported in this document approaches one photon of total input-referred added noise which is the quantum limit imposed in nondegenerate parametric amplifier."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/14547","language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"Bio"}],"supervisor":[{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"publication_identifier":{"issn":["2663 - 337X"]},"month":"11","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10851"},{"id":"13264","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Phan, Duc T","last_name":"Phan","first_name":"Duc T","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-11-30T10:56:04Z","date_created":"2023-11-17T13:45:26Z","year":"2023","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"publication_status":"published","file_date_updated":"2023-11-22T09:46:06Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/"},{"article_processing_charge":"No","day":"09","scopus_import":"1","date_published":"2023-06-09T00:00:00Z","citation":{"ama":"Phan DT, Falthansl-Scheinecker P, Mishra U, et al. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 2023;19(6). doi:10.1103/PhysRevApplied.19.064032","ista":"Phan DT, Falthansl-Scheinecker P, Mishra U, Strickland WM, Langone D, Shabani J, Higginbotham AP. 2023. Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. 19(6), 064032.","apa":"Phan, D. T., Falthansl-Scheinecker, P., Mishra, U., Strickland, W. M., Langone, D., Shabani, J., & Higginbotham, A. P. (2023). Gate-tunable superconductor-semiconductor parametric amplifier. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.19.064032","ieee":"D. T. Phan et al., “Gate-tunable superconductor-semiconductor parametric amplifier,” Physical Review Applied, vol. 19, no. 6. American Physical Society, 2023.","mla":"Phan, Duc T., et al. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied, vol. 19, no. 6, 064032, American Physical Society, 2023, doi:10.1103/PhysRevApplied.19.064032.","short":"D.T. Phan, P. Falthansl-Scheinecker, U. Mishra, W.M. Strickland, D. Langone, J. Shabani, A.P. Higginbotham, Physical Review Applied 19 (2023).","chicago":"Phan, Duc T, Paul Falthansl-Scheinecker, Umang Mishra, W. M. Strickland, D. Langone, J. Shabani, and Andrew P Higginbotham. “Gate-Tunable Superconductor-Semiconductor Parametric Amplifier.” Physical Review Applied. American Physical Society, 2023. https://doi.org/10.1103/PhysRevApplied.19.064032."},"publication":"Physical Review Applied","article_type":"original","issue":"6","abstract":[{"lang":"eng","text":"We build a parametric amplifier with a Josephson field-effect transistor (JoFET) as the active element. The resonant frequency of the device is field-effect tunable over a range of 2 GHz. The JoFET amplifier has 20 dB of gain, 4 MHz of instantaneous bandwidth, and a 1-dB compression point of -125.5 dBm when operated at a fixed resonance frequency.\r\n\r\n"}],"type":"journal_article","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13264","intvolume":" 19","status":"public","title":"Gate-tunable superconductor-semiconductor parametric amplifier","publication_identifier":{"eissn":["2331-7019"]},"month":"06","doi":"10.1103/PhysRevApplied.19.064032","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"main_file_link":[{"url":"https://arxiv.org/abs/2206.05746","open_access":"1"}],"external_id":{"arxiv":["2206.05746"],"isi":["001012022600004"]},"oa":1,"quality_controlled":"1","isi":1,"article_number":"064032","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14547"}]},"author":[{"first_name":"Duc T","last_name":"Phan","id":"29C8C0B4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan, Duc T"},{"id":"85b43b21-15b2-11ec-abd3-e2c252cc2285","last_name":"Falthansl-Scheinecker","first_name":"Paul","full_name":"Falthansl-Scheinecker, Paul"},{"id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","first_name":"Umang","last_name":"Mishra","full_name":"Mishra, Umang"},{"full_name":"Strickland, W. M.","first_name":"W. M.","last_name":"Strickland"},{"full_name":"Langone, D.","last_name":"Langone","first_name":"D."},{"full_name":"Shabani, J.","last_name":"Shabani","first_name":"J."},{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","first_name":"Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"volume":19,"date_created":"2023-07-23T22:01:12Z","date_updated":"2023-11-30T10:56:03Z","year":"2023","acknowledgement":"We thank Shyam Shankar for helpful feedback on the manuscript. We gratefully acknowledge the support of the ISTA nanofabrication facility, the Miba Machine Shop, and the eMachine Shop. The NYU team acknowledges support from Army Research Office Grant No. W911NF2110303.","department":[{"_id":"AnHi"},{"_id":"OnHo"}],"publisher":"American Physical Society","publication_status":"published"},{"day":"10","month":"10","article_processing_charge":"No","date_published":"2023-10-10T00:00:00Z","doi":"10.1101/2023.10.09.561523","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"publication":"bioRxiv","citation":{"ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, 10.1101/2023.10.09.561523.","ieee":"N. Gnyliukh et al., “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” bioRxiv. .","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. https://doi.org/10.1101/2023.10.09.561523","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv. doi:10.1101/2023.10.09.561523","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, n.d. https://doi.org/10.1101/2023.10.09.561523.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” BioRxiv, doi:10.1101/2023.10.09.561523.","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.)."},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2"}],"oa":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins."}],"ec_funded":1,"type":"preprint","author":[{"full_name":"Gnyliukh, Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","last_name":"Gnyliukh","first_name":"Nataliia"},{"full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J"},{"full_name":"Nagel, Marie-Kristin","last_name":"Nagel","first_name":"Marie-Kristin"},{"full_name":"Monzer, Aline","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","last_name":"Monzer","first_name":"Aline"},{"full_name":"Hlavata, Annamaria","id":"36062FEC-F248-11E8-B48F-1D18A9856A87","first_name":"Annamaria","last_name":"Hlavata"},{"last_name":"Isono","first_name":"Erika","full_name":"Isono, Erika"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14510"}]},"date_created":"2023-11-22T10:17:49Z","date_updated":"2023-12-01T13:51:06Z","oa_version":"Preprint","_id":"14591","year":"2023","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"submitted","status":"public","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}]},{"article_number":"102","extern":"1","file_date_updated":"2023-12-04T08:15:43Z","publisher":"Springer Nature","publication_status":"published","year":"2023","volume":15,"date_updated":"2023-12-04T08:17:22Z","date_created":"2023-12-04T08:10:55Z","author":[{"first_name":"Sheng-Jia","last_name":"Lin","full_name":"Lin, Sheng-Jia"},{"full_name":"Vona, Barbara","last_name":"Vona","first_name":"Barbara"},{"full_name":"Lau, Tracy","last_name":"Lau","first_name":"Tracy"},{"full_name":"Huang, Kevin","first_name":"Kevin","last_name":"Huang","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","orcid":"0000-0002-2512-7812"},{"last_name":"Zaki","first_name":"Maha S.","full_name":"Zaki, Maha S."},{"full_name":"Aldeen, Huda Shujaa","last_name":"Aldeen","first_name":"Huda Shujaa"},{"full_name":"Karimiani, Ehsan Ghayoor","last_name":"Karimiani","first_name":"Ehsan Ghayoor"},{"full_name":"Rocca, Clarissa","first_name":"Clarissa","last_name":"Rocca"},{"first_name":"Mahmoud M.","last_name":"Noureldeen","full_name":"Noureldeen, Mahmoud M."},{"first_name":"Ahmed K.","last_name":"Saad","full_name":"Saad, Ahmed K."},{"full_name":"Petree, Cassidy","first_name":"Cassidy","last_name":"Petree"},{"full_name":"Bartolomaeus, Tobias","last_name":"Bartolomaeus","first_name":"Tobias"},{"last_name":"Abou Jamra","first_name":"Rami","full_name":"Abou Jamra, Rami"},{"first_name":"Giovanni","last_name":"Zifarelli","full_name":"Zifarelli, Giovanni"},{"first_name":"Aditi","last_name":"Gotkhindikar","full_name":"Gotkhindikar, Aditi"},{"full_name":"Wentzensen, Ingrid M.","last_name":"Wentzensen","first_name":"Ingrid M."},{"full_name":"Liao, Mingjuan","first_name":"Mingjuan","last_name":"Liao"},{"full_name":"Cork, Emalyn Elise","last_name":"Cork","first_name":"Emalyn Elise"},{"full_name":"Varshney, Pratishtha","first_name":"Pratishtha","last_name":"Varshney"},{"full_name":"Hashemi, Narges","first_name":"Narges","last_name":"Hashemi"},{"full_name":"Mohammadi, Mohammad Hasan","first_name":"Mohammad Hasan","last_name":"Mohammadi"},{"full_name":"Rad, Aboulfazl","first_name":"Aboulfazl","last_name":"Rad"},{"last_name":"Neira","first_name":"Juanita","full_name":"Neira, Juanita"},{"first_name":"Mehran Beiraghi","last_name":"Toosi","full_name":"Toosi, Mehran Beiraghi"},{"full_name":"Knopp, Cordula","first_name":"Cordula","last_name":"Knopp"},{"first_name":"Ingo","last_name":"Kurth","full_name":"Kurth, Ingo"},{"first_name":"Thomas D.","last_name":"Challman","full_name":"Challman, Thomas D."},{"last_name":"Smith","first_name":"Rebecca","full_name":"Smith, Rebecca"},{"first_name":"Asmahan","last_name":"Abdalla","full_name":"Abdalla, Asmahan"},{"first_name":"Thomas","last_name":"Haaf","full_name":"Haaf, Thomas"},{"full_name":"Suri, Mohnish","last_name":"Suri","first_name":"Mohnish"},{"full_name":"Joshi, Manali","first_name":"Manali","last_name":"Joshi"},{"first_name":"Wendy K.","last_name":"Chung","full_name":"Chung, Wendy K."},{"full_name":"Moreno-De-Luca, Andres","last_name":"Moreno-De-Luca","first_name":"Andres"},{"first_name":"Henry","last_name":"Houlden","full_name":"Houlden, Henry"},{"full_name":"Maroofian, Reza","first_name":"Reza","last_name":"Maroofian"},{"first_name":"Gaurav K.","last_name":"Varshney","full_name":"Varshney, Gaurav K."}],"publication_identifier":{"issn":["1756-994X"]},"month":"11","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/s13073-023-01258-4","type":"journal_article","abstract":[{"lang":"eng","text":"Background: Biallelic variants in OGDHL, encoding part of the α-ketoglutarate dehydrogenase complex, have been associated with highly heterogeneous neurological and neurodevelopmental disorders. However, the validity of this association remains to be confirmed. A second OGDHL patient cohort was recruited to carefully assess the gene-disease relationship.\r\nMethods: Using an unbiased genotype-first approach, we screened large, multiethnic aggregated sequencing datasets worldwide for biallelic OGDHL variants. We used CRISPR/Cas9 to generate zebrafish knockouts of ogdhl, ogdh paralogs, and dhtkd1 to investigate functional relationships and impact during development. Functional complementation with patient variant transcripts was conducted to systematically assess protein functionality as a readout for pathogenicity.\r\nResults: A cohort of 14 individuals from 12 unrelated families exhibited highly variable clinical phenotypes, with the majority of them presenting at least one additional variant, potentially accounting for a blended phenotype and complicating phenotypic understanding. We also uncovered extreme clinical heterogeneity and high allele frequencies, occasionally incompatible with a fully penetrant recessive disorder. Human cDNA of previously described and new variants were tested in an ogdhl zebrafish knockout model, adding functional evidence for variant reclassification. We disclosed evidence of hypomorphic alleles as well as a loss-of-function variant without deleterious effects in zebrafish variant testing also showing discordant familial segregation, challenging the relationship of OGDHL as a conventional Mendelian gene. Going further, we uncovered evidence for a complex compensatory relationship among OGDH, OGDHL, and DHTKD1 isoenzymes that are associated with neurodevelopmental disorders and exhibit complex transcriptional compensation patterns with partial functional redundancy.\r\nConclusions: Based on the results of genetic, clinical, and functional studies, we formed three hypotheses in which to frame observations: biallelic OGDHL variants lead to a highly variable monogenic disorder, variants in OGDHL are following a complex pattern of inheritance, or they may not be causative at all. Our study further highlights the continuing challenges of assessing the validity of reported disease-gene associations and effects of variants identified in these genes. This is particularly more complicated in making genetic diagnoses based on identification of variants in genes presenting a highly heterogenous phenotype such as “OGDHL-related disorders”."}],"intvolume":" 15","ddc":["570"],"title":"Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14639","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14640","date_updated":"2023-12-04T08:15:43Z","date_created":"2023-12-04T08:15:43Z","checksum":"279efd212005549aba817a487d56d363","success":1,"file_name":"2023_GenomeMed_Lin.pdf","access_level":"open_access","file_size":14791081,"content_type":"application/pdf","creator":"dernst"}],"keyword":["Genetics (clinical)","Genetics","Molecular Biology","Molecular Medicine"],"has_accepted_license":"1","article_processing_charge":"Yes","day":"23","article_type":"original","citation":{"ama":"Lin S-J, Vona B, Lau T, et al. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 2023;15. doi:10.1186/s13073-023-01258-4","apa":"Lin, S.-J., Vona, B., Lau, T., Huang, K., Zaki, M. S., Aldeen, H. S., … Varshney, G. K. (2023). Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. Springer Nature. https://doi.org/10.1186/s13073-023-01258-4","ieee":"S.-J. Lin et al., “Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity,” Genome Medicine, vol. 15. Springer Nature, 2023.","ista":"Lin S-J, Vona B, Lau T, Huang K, Zaki MS, Aldeen HS, Karimiani EG, Rocca C, Noureldeen MM, Saad AK, Petree C, Bartolomaeus T, Abou Jamra R, Zifarelli G, Gotkhindikar A, Wentzensen IM, Liao M, Cork EE, Varshney P, Hashemi N, Mohammadi MH, Rad A, Neira J, Toosi MB, Knopp C, Kurth I, Challman TD, Smith R, Abdalla A, Haaf T, Suri M, Joshi M, Chung WK, Moreno-De-Luca A, Houlden H, Maroofian R, Varshney GK. 2023. Evaluating the association of biallelic OGDHL variants with significant phenotypic heterogeneity. Genome Medicine. 15, 102.","short":"S.-J. Lin, B. Vona, T. Lau, K. Huang, M.S. Zaki, H.S. Aldeen, E.G. Karimiani, C. Rocca, M.M. Noureldeen, A.K. Saad, C. Petree, T. Bartolomaeus, R. Abou Jamra, G. Zifarelli, A. Gotkhindikar, I.M. Wentzensen, M. Liao, E.E. Cork, P. Varshney, N. Hashemi, M.H. Mohammadi, A. Rad, J. Neira, M.B. Toosi, C. Knopp, I. Kurth, T.D. Challman, R. Smith, A. Abdalla, T. Haaf, M. Suri, M. Joshi, W.K. Chung, A. Moreno-De-Luca, H. Houlden, R. Maroofian, G.K. Varshney, Genome Medicine 15 (2023).","mla":"Lin, Sheng-Jia, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” Genome Medicine, vol. 15, 102, Springer Nature, 2023, doi:10.1186/s13073-023-01258-4.","chicago":"Lin, Sheng-Jia, Barbara Vona, Tracy Lau, Kevin Huang, Maha S. Zaki, Huda Shujaa Aldeen, Ehsan Ghayoor Karimiani, et al. “Evaluating the Association of Biallelic OGDHL Variants with Significant Phenotypic Heterogeneity.” Genome Medicine. Springer Nature, 2023. https://doi.org/10.1186/s13073-023-01258-4."},"publication":"Genome Medicine","date_published":"2023-11-23T00:00:00Z"},{"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","keyword":["Computer Graphics and Computer-Aided Design"],"date_published":"2023-10-01T00:00:00Z","article_type":"original","citation":{"mla":"Makatura, Liane, et al. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics, vol. 42, no. 5, 168, Association for Computing Machinery, 2023, doi:10.1145/3605389.","short":"L. Makatura, B. Wang, Y.-L. Chen, B. Deng, C. Wojtan, B. Bickel, W. Matusik, ACM Transactions on Graphics 42 (2023).","chicago":"Makatura, Liane, Bohan Wang, Yi-Lu Chen, Bolei Deng, Chris Wojtan, Bernd Bickel, and Wojciech Matusik. “Procedural Metamaterials: A Unified Procedural Graph for Metamaterial Design.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3605389.","ama":"Makatura L, Wang B, Chen Y-L, et al. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 2023;42(5). doi:10.1145/3605389","ista":"Makatura L, Wang B, Chen Y-L, Deng B, Wojtan C, Bickel B, Matusik W. 2023. Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. 42(5), 168.","ieee":"L. Makatura et al., “Procedural metamaterials: A unified procedural graph for metamaterial design,” ACM Transactions on Graphics, vol. 42, no. 5. Association for Computing Machinery, 2023.","apa":"Makatura, L., Wang, B., Chen, Y.-L., Deng, B., Wojtan, C., Bickel, B., & Matusik, W. (2023). Procedural metamaterials: A unified procedural graph for metamaterial design. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3605389"},"publication":"ACM Transactions on Graphics","issue":"5","abstract":[{"lang":"eng","text":"We introduce a compact, intuitive procedural graph representation for cellular metamaterials, which are small-scale, tileable structures that can be architected to exhibit many useful material properties. Because the structures’ “architectures” vary widely—with elements such as beams, thin shells, and solid bulks—it is difficult to explore them using existing representations. Generic approaches like voxel grids are versatile, but it is cumbersome to represent and edit individual structures; architecture-specific approaches address these issues, but are incompatible with one another. By contrast, our procedural graph succinctly represents the construction process for any structure using a simple skeleton annotated with spatially varying thickness. To express the highly constrained triply periodic minimal surfaces (TPMS) in this manner, we present the first fully automated version of the conjugate surface construction method, which allows novices to create complex TPMS from intuitive input. We demonstrate our representation’s expressiveness, accuracy, and compactness by constructing a wide range of established structures and hundreds of novel structures with diverse architectures and material properties. We also conduct a user study to verify our representation’s ease-of-use and ability to expand engineers’ capacity for exploration."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"14630","relation":"main_file","date_updated":"2023-11-29T15:16:01Z","date_created":"2023-11-29T15:16:01Z","success":1,"checksum":"0192f597d7a2ceaf89baddfd6190d4c8","file_name":"tog-22-0089-File004.zip","access_level":"open_access","creator":"yichen","file_size":95467870,"content_type":"application/zip"},{"file_size":103731880,"content_type":"application/zip","creator":"yichen","file_name":"tog-22-0089-File005.zip","access_level":"open_access","date_created":"2023-11-29T15:16:01Z","date_updated":"2023-11-29T15:16:01Z","checksum":"7fb024963be81933494f38de191e4710","success":1,"relation":"main_file","file_id":"14631"},{"date_updated":"2023-12-04T08:04:14Z","date_created":"2023-12-04T08:04:14Z","checksum":"b7d6829ce396e21cac9fae0ec7130a6b","success":1,"relation":"main_file","file_id":"14638","content_type":"application/pdf","file_size":57067476,"creator":"dernst","file_name":"2023_ACMToG_Makatura.pdf","access_level":"open_access"}],"intvolume":" 42","title":"Procedural metamaterials: A unified procedural graph for metamaterial design","ddc":["531","006"],"status":"public","_id":"14628","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0730-0301","1557-7368"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1145/3605389","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083"}],"quality_controlled":"1","oa":1,"file_date_updated":"2023-12-04T08:04:14Z","article_number":"168","volume":42,"date_updated":"2023-12-04T08:09:05Z","date_created":"2023-11-29T15:02:03Z","author":[{"full_name":"Makatura, Liane","last_name":"Makatura","first_name":"Liane"},{"last_name":"Wang","first_name":"Bohan","full_name":"Wang, Bohan"},{"full_name":"Chen, Yi-Lu","last_name":"Chen","first_name":"Yi-Lu","id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70"},{"full_name":"Deng, Bolei","first_name":"Bolei","last_name":"Deng"},{"last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"}],"publisher":"Association for Computing Machinery","department":[{"_id":"GradSch"},{"_id":"ChWo"},{"_id":"BeBi"}],"publication_status":"published","acknowledgement":"The authors thank Mina Konaković Luković and Michael Foshey for their early contributions to this project, David Palmer and Paul Zhang for their insightful discussions about minimal surfaces and the CSCM, Julian Panetta for providing the Elastic Textures code, and Hannes Hergeth for his feedback and support. We also thank our user study participants and anonymous reviewers.\r\nThis material is based upon work supported by the National Science Foundation\r\n(NSF) Graduate Research Fellowship under Grant No. 2141064; the MIT Morningside\r\nAcademy for Design Fellowship; the Defense Advanced Research Projects Agency\r\n(DARPA) Grant No. FA8750-20-C-0075; the ERC Consolidator Grant No. 101045083,\r\n“CoDiNA: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena”; and the NewSat project, which is co-funded by the Operational Program for Competitiveness and Internationalisation (COMPETE2020), Portugal 2020, the European Regional Development Fund (ERDF), and the Portuguese Foundation for Science and Technology (FTC) under the MIT Portugal program.","year":"2023"},{"type":"preprint","file_date_updated":"2023-12-05T10:37:02Z","abstract":[{"lang":"eng","text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryo-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how domains of the general transcription factor TFIIF affect complex dynamics and control repressive activity. Together, we reveal how a non-coding RNA can regulate mammalian gene expression."}],"department":[{"_id":"CaBe"}],"publisher":"Institute of Science and Technology Austria","ddc":["572"],"publication_status":"submitted","status":"public","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","_id":"14644","acknowledgement":"We thank B. Kaczmarek and other members of the Bernecky lab for helpful discussions. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade for the wild type TFIIF expression\r\nplasmid. We thank N. Thompson and R. Burgess for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant P34185. This research was further supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Lab Support Facility (LSF), Electron Microscopy Facility (EMF), Scientific Computing (SciComp), and the Preclinical Facility (PCF).","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"14646","date_created":"2023-12-05T10:37:02Z","date_updated":"2023-12-05T10:37:02Z","checksum":"c45608cb97ee36d7b50ba518db8e07b0","success":1,"file_name":"2023_Tluckova_etal_REx.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4892920,"creator":"dernst"}],"date_updated":"2023-12-05T10:37:28Z","date_created":"2023-12-04T14:51:00Z","author":[{"full_name":"Tluckova, Katarina","last_name":"Tluckova","first_name":"Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Testa Salmazo, Anita P","first_name":"Anita P","last_name":"Testa Salmazo","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bernecky","first_name":"Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"}],"has_accepted_license":"1","article_processing_charge":"No","month":"12","day":"05","project":[{"name":"Regulation of mammalian transcription by noncoding RNA","grant_number":"P34185","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"citation":{"ama":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. doi:10.15479/AT:ISTA:14644","apa":"Tluckova, K., Testa Salmazo, A. P., & Bernecky, C. (n.d.). Mechanism of mammalian transcriptional repression by noncoding RNA. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14644","ieee":"K. Tluckova, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA.” Institute of Science and Technology Austria.","ista":"Tluckova K, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. 10.15479/AT:ISTA:14644.","short":"K. Tluckova, A.P. Testa Salmazo, C. Bernecky, (n.d.).","mla":"Tluckova, Katarina, et al. Mechanism of Mammalian Transcriptional Repression by Noncoding RNA. Institute of Science and Technology Austria, doi:10.15479/AT:ISTA:14644.","chicago":"Tluckova, Katarina, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Institute of Science and Technology Austria, n.d. https://doi.org/10.15479/AT:ISTA:14644."},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"date_published":"2023-12-05T00:00:00Z","doi":"10.15479/AT:ISTA:14644"},{"type":"journal_article","abstract":[{"text":"We investigate spin-charge separation of a spin-\r\n1\r\n2\r\n Fermi system confined in a triple well where multiple bands are occupied. We assume that our finite fermionic system is close to fully spin polarized while being doped by a hole and an impurity fermion with opposite spin. Our setup involves ferromagnetic couplings among the particles in different bands, leading to the development of strong spin-transport correlations in an intermediate interaction regime. Interactions are then strong enough to lift the degeneracy among singlet and triplet spin configurations in the well of the spin impurity but not strong enough to prohibit hole-induced magnetic excitations to the singlet state. Despite the strong spin-hole correlations, the system exhibits spin-charge deconfinement allowing for long-range entanglement of the spatial and spin degrees of freedom.","lang":"eng"}],"issue":"4","_id":"14658","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"title":"Spin-charge correlations in finite one-dimensional multiband Fermi systems","status":"public","intvolume":" 5","file":[{"access_level":"open_access","file_name":"2023_PhysReviewResearch_Becker.pdf","creator":"dernst","content_type":"application/pdf","file_size":2362158,"file_id":"14672","relation":"main_file","success":1,"checksum":"ee31c0d0de5d1b65591990ae6705a601","date_created":"2023-12-11T10:49:07Z","date_updated":"2023-12-11T10:49:07Z"}],"oa_version":"Published Version","scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Physical Review Research","citation":{"chicago":"Becker, J. M., Georgios Koutentakis, and P. Schmelcher. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/PhysRevResearch.5.043039.","mla":"Becker, J. M., et al. “Spin-Charge Correlations in Finite One-Dimensional Multiband Fermi Systems.” Physical Review Research, vol. 5, no. 4, 043039, American Physical Society, 2023, doi:10.1103/PhysRevResearch.5.043039.","short":"J.M. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 5 (2023).","ista":"Becker JM, Koutentakis G, Schmelcher P. 2023. Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. 5(4), 043039.","apa":"Becker, J. M., Koutentakis, G., & Schmelcher, P. (2023). Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.5.043039","ieee":"J. M. Becker, G. Koutentakis, and P. Schmelcher, “Spin-charge correlations in finite one-dimensional multiband Fermi systems,” Physical Review Research, vol. 5, no. 4. American Physical Society, 2023.","ama":"Becker JM, Koutentakis G, Schmelcher P. Spin-charge correlations in finite one-dimensional multiband Fermi systems. Physical Review Research. 2023;5(4). doi:10.1103/PhysRevResearch.5.043039"},"article_type":"original","date_published":"2023-10-12T00:00:00Z","article_number":"043039","file_date_updated":"2023-12-11T10:49:07Z","ec_funded":1,"acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG)-EXC 2056-Project ID No. 390715994. G.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","year":"2023","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","author":[{"first_name":"J. M.","last_name":"Becker","full_name":"Becker, J. M."},{"full_name":"Koutentakis, Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","last_name":"Koutentakis","first_name":"Georgios"},{"first_name":"P.","last_name":"Schmelcher","full_name":"Schmelcher, P."}],"date_created":"2023-12-10T23:00:58Z","date_updated":"2023-12-11T10:55:52Z","volume":5,"month":"10","publication_identifier":{"issn":["2643-1564"]},"external_id":{"arxiv":["2305.09529"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"doi":"10.1103/PhysRevResearch.5.043039","language":[{"iso":"eng"}]},{"keyword":["General Physics and Astronomy"],"day":"07","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"SciPost Physics","citation":{"ama":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 2023;15(6). doi:10.21468/scipostphys.15.6.232","apa":"Volosniev, A., Bighin, G., Santos, L., & Peña Ardila, L. A. (2023). Non-equilibrium dynamics of dipolar polarons. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.15.6.232","ieee":"A. Volosniev, G. Bighin, L. Santos, and L. A. Peña Ardila, “Non-equilibrium dynamics of dipolar polarons,” SciPost Physics, vol. 15, no. 6. SciPost Foundation, 2023.","ista":"Volosniev A, Bighin G, Santos L, Peña Ardila LA. 2023. Non-equilibrium dynamics of dipolar polarons. SciPost Physics. 15(6), 232.","short":"A. Volosniev, G. Bighin, L. Santos, L.A. Peña Ardila, SciPost Physics 15 (2023).","mla":"Volosniev, Artem, et al. “Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost Physics, vol. 15, no. 6, 232, SciPost Foundation, 2023, doi:10.21468/scipostphys.15.6.232.","chicago":"Volosniev, Artem, Giacomo Bighin, Luis Santos, and Luisllu A. Peña Ardila. “Non-Equilibrium Dynamics of Dipolar Polarons.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.15.6.232."},"date_published":"2023-12-07T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study the out-of-equilibrium quantum dynamics of dipolar polarons, i.e., impurities immersed in a dipolar Bose-Einstein condensate, after a quench of the impurity-boson interaction. We show that the dipolar nature of the condensate and of the impurity results in anisotropic relaxation dynamics, in particular, anisotropic dressing of the polaron. More relevantly for cold-atom setups, quench dynamics is strongly affected by the interplay between dipolar anisotropy and trap geometry. Our findings pave the way for simulating impurities in anisotropic media utilizing experiments with dipolar mixtures."}],"issue":"6","status":"public","title":"Non-equilibrium dynamics of dipolar polarons","ddc":["530"],"intvolume":" 15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14650","oa_version":"Published Version","file":[{"file_id":"14669","relation":"main_file","success":1,"checksum":"e664372a1fe9d628a9bb1d135ebab7d8","date_updated":"2023-12-11T07:42:04Z","date_created":"2023-12-11T07:42:04Z","access_level":"open_access","file_name":"2023_SciPostPhysics_Volosniev.pdf","creator":"dernst","content_type":"application/pdf","file_size":3543541}],"month":"12","publication_identifier":{"issn":["2542-4653"]},"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"A path-integral approach to composite impurities","grant_number":"M02641","_id":"26986C82-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"external_id":{"arxiv":["2305.17969"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.21468/scipostphys.15.6.232","article_number":"232","file_date_updated":"2023-12-11T07:42:04Z","ec_funded":1,"publication_status":"published","publisher":"SciPost Foundation","department":[{"_id":"MiLe"}],"year":"2023","acknowledgement":"We thank Lauriane Chomaz for useful discussions and comments on the manuscript. We also\r\nthank Ragheed Al Hyder for comments on the manuscript.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF),\r\nunder Project No. M2641-N27. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-\r\n390900948 (the Heidelberg STRUCTURES Excellence Cluster). A. G. V. acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie Skłodowska-Curie Grant Agreement No. 754411. L.A.P.A acknowledges by the PNRR\r\nMUR project PE0000023 - NQSTI and the Deutsche Forschungsgemeinschaft (DFG, German\r\nResearch Foundation) under Germany’s Excellence Strategy - EXC - 2123 Quantum Frontiers390837967 and FOR2247.","date_updated":"2023-12-11T07:44:08Z","date_created":"2023-12-10T13:03:07Z","volume":15,"author":[{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","first_name":"Artem"},{"last_name":"Bighin","first_name":"Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo"},{"full_name":"Santos, Luis","last_name":"Santos","first_name":"Luis"},{"first_name":"Luisllu A.","last_name":"Peña Ardila","full_name":"Peña Ardila, Luisllu A."}]},{"publication_identifier":{"issn":["1387-3806"]},"month":"11","doi":"10.1016/j.ijms.2023.117168","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.ijms.2023.117168"}],"oa":1,"quality_controlled":"1","article_number":"117168","author":[{"first_name":"Florian","last_name":"Kluibenschedl","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","full_name":"Kluibenschedl, Florian"},{"full_name":"Ploner, Anna","first_name":"Anna","last_name":"Ploner"},{"last_name":"Meisenbichler","first_name":"Christina","full_name":"Meisenbichler, Christina"},{"last_name":"Konrat","first_name":"Robert","full_name":"Konrat, Robert"},{"last_name":"Müller","first_name":"Thomas","full_name":"Müller, Thomas"}],"volume":495,"date_created":"2023-12-10T23:00:57Z","date_updated":"2023-12-11T08:16:35Z","year":"2023","acknowledgement":"We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF).","department":[{"_id":"GradSch"}],"publisher":"Elsevier","publication_status":"epub_ahead","article_processing_charge":"Yes (in subscription journal)","day":"23","scopus_import":"1","date_published":"2023-11-23T00:00:00Z","citation":{"chicago":"Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry. Elsevier, 2023. https://doi.org/10.1016/j.ijms.2023.117168.","short":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2023).","mla":"Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry, vol. 495, 117168, Elsevier, 2023, doi:10.1016/j.ijms.2023.117168.","apa":"Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., & Müller, T. (2023). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2023.117168","ieee":"F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” International Journal of Mass Spectrometry, vol. 495. Elsevier, 2023.","ista":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2023. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168.","ama":"Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 2023;495. doi:10.1016/j.ijms.2023.117168"},"publication":"International Journal of Mass Spectrometry","article_type":"original","abstract":[{"lang":"eng","text":"Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen's motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data."}],"type":"journal_article","oa_version":"Published Version","_id":"14653","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 495","status":"public","title":"Advanced motion tracking for interactive mass spectrometry imaging (IMSI)"},{"language":[{"iso":"eng"}],"date_published":"2023-12-01T00:00:00Z","doi":"10.1101/2023.11.30.569337","publication":"bioRxiv","citation":{"mla":"Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2023.11.30.569337.","short":"M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer, S. Tole, BioRxiv (n.d.).","chicago":"Bose, Mahima, Varun Suresh, Urvi Mishra, Ishita Talwar, Anuradha Yadav, Shiona Biswas, Simon Hippenmeyer, and Shubha Tole. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2023.11.30.569337.","ama":"Bose M, Suresh V, Mishra U, et al. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv. doi:10.1101/2023.11.30.569337","ista":"Bose M, Suresh V, Mishra U, Talwar I, Yadav A, Biswas S, Hippenmeyer S, Tole S. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv, 10.1101/2023.11.30.569337.","ieee":"M. Bose et al., “Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Bose, M., Suresh, V., Mishra, U., Talwar, I., Yadav, A., Biswas, S., … Tole, S. (n.d.). Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.11.30.569337"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.11.30.569337"}],"day":"01","month":"12","article_processing_charge":"No","date_updated":"2023-12-11T07:37:17Z","date_created":"2023-12-06T13:07:01Z","oa_version":"Preprint","author":[{"full_name":"Bose, Mahima","last_name":"Bose","first_name":"Mahima"},{"first_name":"Varun","last_name":"Suresh","full_name":"Suresh, Varun"},{"full_name":"Mishra, Urvi","last_name":"Mishra","first_name":"Urvi"},{"full_name":"Talwar, Ishita","last_name":"Talwar","first_name":"Ishita"},{"full_name":"Yadav, Anuradha","first_name":"Anuradha","last_name":"Yadav"},{"full_name":"Biswas, Shiona","last_name":"Biswas","first_name":"Shiona"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Tole, Shubha","last_name":"Tole","first_name":"Shubha"}],"publication_status":"submitted","title":"Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway","status":"public","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"SiHi"}],"_id":"14647","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Dr. Shital Suryavanshi and the animal house staff of the Tata Institute of\r\nFundamental Research (TIFR) for their excellent support; Gord Fishell and Goichi Miyoshi for\r\nthe Foxg1 floxed mouse line; Hiroshi Kawasaki for the plasmids pCAG-FGF8 and pCAGsFGFR3c. We thank Prof. S.K. Lee for the Foxg1lox/lox genotyping primers and protocol. We thank Dr. Deepak Modi and Dr. Vainav Patel for allowing us to use the NIRRCH FACS Facility and the staff of the NIRRCH and TIFR FACS facilities for their assistance.\r\nWe thank Denis Jabaudon for his critical comments on the manuscript and members of the\r\nJabaudon lab for helpful discussions. This work was funded by the Department of Atomic\r\nEnergy (DAE), Govt. of India (Project Identification no. RTI4003, DAE OM no.\r\n1303/2/2019/R&D-II/DAE/2079).","year":"2023","abstract":[{"text":"In the developing vertebrate central nervous system, neurons and glia typically arise sequentially from common progenitors. Here, we report that the transcription factor Forkhead Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and in postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic ligand FGF18 in new born neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons increases Fgf18 expression and enhances gliogenesis in the progenitors. These results fit well with the model that new born neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex.","lang":"eng"}],"type":"preprint"},{"month":"12","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.131.228401","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.03088"}],"external_id":{"arxiv":["2303.03088"]},"oa":1,"article_number":"228401","date_updated":"2023-12-11T07:59:25Z","date_created":"2023-12-10T23:00:57Z","volume":131,"author":[{"first_name":"Valerio","last_name":"Sorichetti","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","orcid":"0000-0002-9645-6576","full_name":"Sorichetti, Valerio"},{"last_name":"Lenz","first_name":"Martin","full_name":"Lenz, Martin"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"AnSa"}],"year":"2023","acknowledgement":"The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable help with understanding the experimental behavior of intermediate filaments, and Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou, and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L. was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03, No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and No. 2021-A0110712066).","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-12-01T00:00:00Z","article_type":"original","publication":"Physical Review Letters","citation":{"short":"V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).","mla":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” Physical Review Letters, vol. 131, no. 22, 228401, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.228401.","chicago":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.228401.","ama":"Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 2023;131(22). doi:10.1103/PhysRevLett.131.228401","apa":"Sorichetti, V., & Lenz, M. (2023). Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.228401","ieee":"V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of semiflexible filaments,” Physical Review Letters, vol. 131, no. 22. American Physical Society, 2023.","ista":"Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 131(22), 228401."},"abstract":[{"lang":"eng","text":"The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division."}],"issue":"22","type":"journal_article","oa_version":"Preprint","status":"public","title":"Transverse fluctuations control the assembly of semiflexible filaments","intvolume":" 131","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14655"},{"publication_identifier":{"eissn":["1469-2120"],"issn":["0024-6093"]},"article_processing_charge":"Yes (via OA deal)","month":"12","day":"04","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2023-12-04T00:00:00Z","doi":"10.1112/blms.12965","article_type":"original","quality_controlled":"1","oa":1,"citation":{"apa":"Ivanov, G., & Naszódi, M. (2023). Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/blms.12965","ieee":"G. Ivanov and M. Naszódi, “Quantitative Steinitz theorem: A polynomial bound,” Bulletin of the London Mathematical Society. London Mathematical Society, 2023.","ista":"Ivanov G, Naszódi M. 2023. Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society.","ama":"Ivanov G, Naszódi M. Quantitative Steinitz theorem: A polynomial bound. Bulletin of the London Mathematical Society. 2023. doi:10.1112/blms.12965","chicago":"Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial Bound.” Bulletin of the London Mathematical Society. London Mathematical Society, 2023. https://doi.org/10.1112/blms.12965.","short":"G. Ivanov, M. Naszódi, Bulletin of the London Mathematical Society (2023).","mla":"Ivanov, Grigory, and Márton Naszódi. “Quantitative Steinitz Theorem: A Polynomial Bound.” Bulletin of the London Mathematical Society, London Mathematical Society, 2023, doi:10.1112/blms.12965."},"external_id":{"arxiv":["2212.04308"]},"main_file_link":[{"url":" https://doi.org/10.1112/blms.12965","open_access":"1"}],"publication":"Bulletin of the London Mathematical Society","abstract":[{"text":"The classical Steinitz theorem states that if the origin belongs to the interior of the convex hull of a set 𝑆⊂ℝ𝑑, then there are at most 2𝑑 points of 𝑆 whose convex hull contains the origin in the interior. Bárány, Katchalski,and Pach proved the following quantitative version of Steinitz’s theorem. Let 𝑄 be a convex polytope in ℝ𝑑 containing the standard Euclidean unit ball 𝐁𝑑. Then there exist at most 2𝑑 vertices of 𝑄 whose convex hull 𝑄′ satisfies 𝑟𝐁𝑑⊂𝑄′ with 𝑟⩾𝑑−2𝑑. They conjectured that 𝑟⩾𝑐𝑑−1∕2 holds with a universal constant 𝑐>0. We prove 𝑟⩾15𝑑2, the first polynomial lower bound on 𝑟. Furthermore, we show that 𝑟 is not greater than 2/√𝑑.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","date_created":"2023-12-10T23:00:58Z","date_updated":"2023-12-11T10:03:54Z","author":[{"full_name":"Ivanov, Grigory","last_name":"Ivanov","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"last_name":"Naszódi","first_name":"Márton","full_name":"Naszódi, Márton"}],"publisher":"London Mathematical Society","department":[{"_id":"UlWa"}],"status":"public","publication_status":"epub_ahead","title":"Quantitative Steinitz theorem: A polynomial bound","acknowledgement":"M.N. was supported by the János Bolyai Scholarship of the Hungarian Academy of Sciences aswell as the National Research, Development and Innovation Fund (NRDI) grants K119670 andK131529, and the ÚNKP-22-5 New National Excellence Program of the Ministry for Innovationand Technology from the source of the NRDI as well as the ELTE TKP 2021-NKTA-62 fundingscheme","_id":"14660","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023"},{"type":"journal_article","abstract":[{"lang":"eng","text":"So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function."}],"issue":"48","_id":"14666","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species","intvolume":" 120","oa_version":"None","file":[{"access_level":"open_access","file_name":"2023_PNAS_Chintaluri.pdf","creator":"dernst","content_type":"application/pdf","file_size":16891602,"file_id":"14678","relation":"main_file","success":1,"checksum":"bf4ec38602a70dae4338077a5a4d497f","date_created":"2023-12-11T12:45:12Z","date_updated":"2023-12-11T12:45:12Z"}],"scopus_import":"1","day":"21","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ama":"Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(48). doi:10.1073/pnas.2306525120","ista":"Chintaluri C, Vogels TP. 2023. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 120(48), e2306525120.","apa":"Chintaluri, C., & Vogels, T. P. (2023). Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2306525120","ieee":"C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48. National Academy of Sciences, 2023.","mla":"Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:10.1073/pnas.2306525120.","short":"C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences of the United States of America 120 (2023).","chicago":"Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2306525120."},"article_type":"original","date_published":"2023-11-21T00:00:00Z","article_number":"e2306525120","file_date_updated":"2023-12-11T12:45:12Z","acknowledgement":"We thank Prof. C. Nazaret and Prof. J.-P. Mazat for sharing the code of their mitochondrial model. We also thank G. Miesenböck, E. Marder, L. Abbott, A. Kempf, P. Hasenhuetl, W. Podlaski, F. Zenke, E. Agnes, P. Bozelos, J. Watson, B. Confavreux, and G. Christodoulou, and the rest of the Vogels Lab for their feedback. This work was funded by Wellcome Trust and Royal Society Sir Henry Dale Research Fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council grant (UKRI-BBSRC BB/N019512/1).","year":"2023","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"TiVo"}],"author":[{"full_name":"Chintaluri, Chaitanya","id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E","first_name":"Chaitanya","last_name":"Chintaluri"},{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","first_name":"Tim P","last_name":"Vogels","full_name":"Vogels, Tim P"}],"related_material":{"link":[{"url":"https://github.com/ccluri/metabolic_spiking","relation":"software"}]},"date_created":"2023-12-10T23:01:00Z","date_updated":"2023-12-11T12:47:41Z","volume":120,"month":"11","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["37988463"]},"quality_controlled":"1","project":[{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","grant_number":"214316/Z/18/Z","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87"}],"doi":"10.1073/pnas.2306525120","language":[{"iso":"eng"}]},{"ddc":["570"],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","status":"public","intvolume":" 43","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14656","oa_version":"Published Version","file":[{"date_created":"2023-12-11T11:30:37Z","date_updated":"2023-12-11T11:30:37Z","checksum":"e2503c8f84be1050e28f64320f1d5bd2","relation":"main_file","embargo":"2024-06-01","file_id":"14674","content_type":"application/pdf","file_size":2280632,"creator":"dernst","embargo_to":"open_access","file_name":"2023_JourNeuroscience_Nardin.pdf","access_level":"closed"}],"type":"journal_article","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"issue":"48","article_type":"original","page":"8140-8156","publication":"The Journal of Neuroscience","citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. Society of Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.0194-23.2023."},"date_published":"2023-11-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publication_status":"published","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"publisher":"Society of Neuroscience","year":"2023","acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","pmid":1,"date_updated":"2023-12-11T11:37:20Z","date_created":"2023-12-10T23:00:58Z","volume":43,"author":[{"full_name":"Nardin, Michele","last_name":"Nardin","first_name":"Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"}],"file_date_updated":"2023-12-11T11:30:37Z","ec_funded":1,"quality_controlled":"1","project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"external_id":{"pmid":["37758476"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.0194-23.2023","month":"11","publication_identifier":{"eissn":["1529-2401"]}},{"file_date_updated":"2023-12-11T11:10:32Z","ec_funded":1,"article_number":"20230355","date_updated":"2023-12-11T11:17:53Z","date_created":"2023-12-10T23:00:58Z","volume":20,"author":[{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"first_name":"Kamran","last_name":"Kaveh","full_name":"Kaveh, Kamran"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"KrCh"}],"acknowledgement":"K.C. acknowledges support from the ERC CoG 863818(ForM-SMArt). J.T. is supported by Center for Foundations ofModern Computer Science (Charles Univ. project UNCE/SCI/004).","year":"2023","pmid":1,"month":"11","publication_identifier":{"eissn":["1742-5662"]},"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2023.0355","quality_controlled":"1","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["38016637"]},"abstract":[{"lang":"eng","text":"Natural selection is usually studied between mutants that differ in reproductive rate, but are subject to the same population structure. Here we explore how natural selection acts on mutants that have the same reproductive rate, but different population structures. In our framework, population structure is given by a graph that specifies where offspring can disperse. The invading mutant disperses offspring on a different graph than the resident wild-type. We find that more densely connected dispersal graphs tend to increase the invader’s fixation probability, but the exact relationship between structure and fixation probability is subtle. We present three main results. First, we prove that if both invader and resident are on complete dispersal graphs, then removing a single edge in the invader’s dispersal graph reduces its fixation probability. Second, we show that for certain island models higher invader’s connectivity increases its fixation probability, but the magnitude of the effect depends on the exact layout of the connections. Third, we show that for lattices the effect of different connectivity is comparable to that of different fitness: for large population size, the invader’s fixation probability is either constant or exponentially small, depending on whether it is more or less connected than the resident."}],"issue":"208","type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1720243,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_RoyalInterface_Tkadlec.pdf","success":1,"checksum":"2eefab13127c7786dbd33303c482a004","date_updated":"2023-12-11T11:10:32Z","date_created":"2023-12-11T11:10:32Z","file_id":"14673","relation":"main_file"}],"ddc":["000","570"],"title":"Evolutionary dynamics of mutants that modify population structure","status":"public","intvolume":" 20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14657","day":"29","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2023-11-29T00:00:00Z","article_type":"original","publication":"Journal of the Royal Society, Interface","citation":{"chicago":"Tkadlec, Josef, Kamran Kaveh, Krishnendu Chatterjee, and Martin A. Nowak. “Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal of the Royal Society, Interface. The Royal Society, 2023. https://doi.org/10.1098/rsif.2023.0355.","mla":"Tkadlec, Josef, et al. “Evolutionary Dynamics of Mutants That Modify Population Structure.” Journal of the Royal Society, Interface, vol. 20, no. 208, 20230355, The Royal Society, 2023, doi:10.1098/rsif.2023.0355.","short":"J. Tkadlec, K. Kaveh, K. Chatterjee, M.A. Nowak, Journal of the Royal Society, Interface 20 (2023).","ista":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. 2023. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. 20(208), 20230355.","ieee":"J. Tkadlec, K. Kaveh, K. Chatterjee, and M. A. Nowak, “Evolutionary dynamics of mutants that modify population structure,” Journal of the Royal Society, Interface, vol. 20, no. 208. The Royal Society, 2023.","apa":"Tkadlec, J., Kaveh, K., Chatterjee, K., & Nowak, M. A. (2023). Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. The Royal Society. https://doi.org/10.1098/rsif.2023.0355","ama":"Tkadlec J, Kaveh K, Chatterjee K, Nowak MA. Evolutionary dynamics of mutants that modify population structure. Journal of the Royal Society, Interface. 2023;20(208). doi:10.1098/rsif.2023.0355"}},{"quality_controlled":"1","external_id":{"pmid":["37917939"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/jacs.3c08666","publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"month":"11","department":[{"_id":"RaKl"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We acknowledge funding from the European Union’s Horizon 2020 Research and Innovation Program under the European Research Council (grant agreement 820008).We also thank the Deutsche Forschungsgemeinschaft (DFG) for support through priority program SPP1807(CL489/3-2) and RESOLV Cluster of Excellence EXC2033 (project number 390677874). A.B.G. acknowledges funding from the Zuckerman STEM Leadership Program. DFT calculations were carried out using resources provided by the Wrocław Center for Networking and Supercomputing, grant 329.","volume":145,"date_updated":"2023-12-11T11:47:07Z","date_created":"2023-12-10T23:00:59Z","author":[{"last_name":"Hema","first_name":"Kuntrapakam","full_name":"Hema, Kuntrapakam"},{"last_name":"Grommet","first_name":"Angela B.","full_name":"Grommet, Angela B."},{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"full_name":"Wang, Jinhua","last_name":"Wang","first_name":"Jinhua"},{"last_name":"Schneider","first_name":"Laura","full_name":"Schneider, Laura"},{"last_name":"Drechsler","first_name":"Christoph","full_name":"Drechsler, Christoph"},{"full_name":"Yanshyna, Oksana","last_name":"Yanshyna","first_name":"Oksana"},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"full_name":"Clever, Guido H.","last_name":"Clever","first_name":"Guido H."},{"full_name":"Klajn, Rafal","first_name":"Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"file_date_updated":"2023-12-11T11:44:54Z","page":"24755-24764","article_type":"original","citation":{"chicago":"Hema, Kuntrapakam, Angela B. Grommet, Michał J. Białek, Jinhua Wang, Laura Schneider, Christoph Drechsler, Oksana Yanshyna, Yael Diskin-Posner, Guido H. Clever, and Rafal Klajn. “Guest Encapsulation Alters the Thermodynamic Landscape of a Coordination Host.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c08666.","mla":"Hema, Kuntrapakam, et al. “Guest Encapsulation Alters the Thermodynamic Landscape of a Coordination Host.” Journal of the American Chemical Society, vol. 145, no. 45, American Chemical Society, 2023, pp. 24755–64, doi:10.1021/jacs.3c08666.","short":"K. Hema, A.B. Grommet, M.J. Białek, J. Wang, L. Schneider, C. Drechsler, O. Yanshyna, Y. Diskin-Posner, G.H. Clever, R. Klajn, Journal of the American Chemical Society 145 (2023) 24755–24764.","ista":"Hema K, Grommet AB, Białek MJ, Wang J, Schneider L, Drechsler C, Yanshyna O, Diskin-Posner Y, Clever GH, Klajn R. 2023. Guest encapsulation alters the thermodynamic landscape of a coordination host. Journal of the American Chemical Society. 145(45), 24755–24764.","ieee":"K. Hema et al., “Guest encapsulation alters the thermodynamic landscape of a coordination host,” Journal of the American Chemical Society, vol. 145, no. 45. American Chemical Society, pp. 24755–24764, 2023.","apa":"Hema, K., Grommet, A. B., Białek, M. J., Wang, J., Schneider, L., Drechsler, C., … Klajn, R. (2023). Guest encapsulation alters the thermodynamic landscape of a coordination host. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c08666","ama":"Hema K, Grommet AB, Białek MJ, et al. Guest encapsulation alters the thermodynamic landscape of a coordination host. Journal of the American Chemical Society. 2023;145(45):24755-24764. doi:10.1021/jacs.3c08666"},"publication":"Journal of the American Chemical Society","date_published":"2023-11-02T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"02","intvolume":" 145","ddc":["540"],"status":"public","title":"Guest encapsulation alters the thermodynamic landscape of a coordination host","_id":"14664","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":4304472,"creator":"dernst","access_level":"open_access","file_name":"2023_JACS_Hema.pdf","checksum":"a1f37df6b83f88f51ba64468ce0c1589","success":1,"date_created":"2023-12-11T11:44:54Z","date_updated":"2023-12-11T11:44:54Z","relation":"main_file","file_id":"14675"}],"oa_version":"Published Version","type":"journal_article","issue":"45","abstract":[{"lang":"eng","text":"The architecture of self-assembled host molecules can profoundly affect the properties of the encapsulated guests. For example, a rigid cage with small windows can efficiently protect its contents from the environment; in contrast, tube-shaped, flexible hosts with large openings and an easily accessible cavity are ideally suited for catalysis. Here, we report a “Janus” nature of a Pd6L4 coordination host previously reported to exist exclusively as a tube isomer (T). We show that upon encapsulating various tetrahedrally shaped guests, T can reconfigure into a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion can be repeated for multiple cycles. Reversible toggling between two vastly different isomers paves the way toward controlling functional properties of coordination hosts “on demand”."}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1021/acscatal.3c03893","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2155-5435"]},"month":"11","acknowledgement":"The authors acknowledge the financial support from the National Natural Science Foundation of China (22008211, 92045303, U21A20298), the National Key Research and Development Project of China (2021YFA1500900, 2022YFE0113800), and Zhejiang Innovation Team (2017R5203).","year":"2023","publisher":"American Chemical Society","department":[{"_id":"MaIb"}],"publication_status":"published","author":[{"first_name":"Jinyan","last_name":"Zhao","full_name":"Zhao, Jinyan"},{"full_name":"Yao, Zihao","first_name":"Zihao","last_name":"Yao"},{"full_name":"Bunting, Rhys","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","orcid":"0000-0001-6928-074X","first_name":"Rhys","last_name":"Bunting"},{"full_name":"Hu, P.","last_name":"Hu","first_name":"P."},{"first_name":"Jianguo","last_name":"Wang","full_name":"Wang, Jianguo"}],"volume":13,"date_updated":"2023-12-11T11:55:35Z","date_created":"2023-12-10T23:00:59Z","file_date_updated":"2023-12-11T11:55:09Z","citation":{"short":"J. Zhao, Z. Yao, R. Bunting, P. Hu, J. Wang, ACS Catalysis 13 (2023) 15054–15073.","mla":"Zhao, Jinyan, et al. “Microkinetic Modeling with Size-Dependent and Adsorbate-Adsorbate Interactions for the Direct Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis, vol. 13, no. 22, American Chemical Society, 2023, pp. 15054–73, doi:10.1021/acscatal.3c03893.","chicago":"Zhao, Jinyan, Zihao Yao, Rhys Bunting, P. Hu, and Jianguo Wang. “Microkinetic Modeling with Size-Dependent and Adsorbate-Adsorbate Interactions for the Direct Synthesis of H₂O₂ over Pd Nanoparticles.” ACS Catalysis. American Chemical Society, 2023. https://doi.org/10.1021/acscatal.3c03893.","ama":"Zhao J, Yao Z, Bunting R, Hu P, Wang J. Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. 2023;13(22):15054-15073. doi:10.1021/acscatal.3c03893","ieee":"J. Zhao, Z. Yao, R. Bunting, P. Hu, and J. Wang, “Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles,” ACS Catalysis, vol. 13, no. 22. American Chemical Society, pp. 15054–15073, 2023.","apa":"Zhao, J., Yao, Z., Bunting, R., Hu, P., & Wang, J. (2023). Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. American Chemical Society. https://doi.org/10.1021/acscatal.3c03893","ista":"Zhao J, Yao Z, Bunting R, Hu P, Wang J. 2023. Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles. ACS Catalysis. 13(22), 15054–15073."},"publication":"ACS Catalysis","page":"15054-15073","article_type":"original","date_published":"2023-11-06T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"06","_id":"14663","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","ddc":["540"],"status":"public","title":"Microkinetic modeling with size-dependent and adsorbate-adsorbate interactions for the direct synthesis of H₂O₂ over Pd nanoparticles","file":[{"date_updated":"2023-12-11T11:55:09Z","date_created":"2023-12-11T11:55:09Z","success":1,"checksum":"a97c771077af71ddfb2249e34530895c","file_id":"14676","relation":"main_file","creator":"dernst","file_size":14813812,"content_type":"application/pdf","file_name":"2023_ACSCatalysis_.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"22","abstract":[{"text":"As a bottleneck in the direct synthesis of hydrogen peroxide, the development of an efficient palladium-based catalyst has garnered great attention. However, elusive active centers and reaction mechanism issues inhibit further optimization of its performance. In this work, advanced microkinetic modeling with the adsorbate–adsorbate interaction and nanoparticle size effect based on first-principles calculations is developed. A full mechanism uncovering the significance of adsorbate–adsorbate interaction is determined on Pd nanoparticles. We demonstrate unambiguously that Pd(100) with main coverage species of O2 and H is beneficial to H2O2 production, being consistent with experimental operando observation, while H2O forms on Pd(111) covered by O species and Pd(211) covered by O and OH species. Kinetic analyses further enable quantitative estimation of the influence of temperature, pressure, and particle size. Large-size Pd nanoparticles are found to achieve a high H2O2 reaction rate when the operating conditions are moderate temperature and higher oxygen partial pressure. We reveal that specific facets of the Pd nanoparticles are crucial factors for their selectivity and activity. Consistent with the experiment, the production of H2O2 is discovered to be more favorable on Pd nanoparticles containing Pd(100) facets. The ratio of H2/O2 induces substantial variations in the coverage of intermediates of O2 and H on Pd(100), resulting in a change in product selectivity.","lang":"eng"}]},{"month":"11","publication_identifier":{"issn":["0246-0203"]},"doi":"10.1214/22-AIHP1304","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2112.11382"}],"external_id":{"arxiv":["2112.11382"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"ec_funded":1,"author":[{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d","first_name":"Hong Chang","last_name":"Ji","full_name":"Ji, Hong Chang"}],"date_updated":"2023-12-11T12:36:56Z","date_created":"2023-12-10T23:01:00Z","volume":59,"acknowledgement":"The first author was partially supported by ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by ERC Advanced Grant “RMTBeyond” No. 101020331.\r\nThe authors are grateful to the anonymous referees and associated editor for carefully reading this paper and providing helpful comments that improved the quality of the article. Also the authors would like to thank Peter Forrester for pointing out the reference [12] that was absent in the previous version of the manuscript.","year":"2023","publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-11-01T00:00:00Z","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","citation":{"ista":"Erdös L, Ji HC. 2023. Functional CLT for non-Hermitian random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 59(4), 2083–2105.","ieee":"L. Erdös and H. C. Ji, “Functional CLT for non-Hermitian random matrices,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 59, no. 4. Institute of Mathematical Statistics, pp. 2083–2105, 2023.","apa":"Erdös, L., & Ji, H. C. (2023). Functional CLT for non-Hermitian random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1304","ama":"Erdös L, Ji HC. Functional CLT for non-Hermitian random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2023;59(4):2083-2105. doi:10.1214/22-AIHP1304","chicago":"Erdös, László, and Hong Chang Ji. “Functional CLT for Non-Hermitian Random Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-AIHP1304.","mla":"Erdös, László, and Hong Chang Ji. “Functional CLT for Non-Hermitian Random Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 59, no. 4, Institute of Mathematical Statistics, 2023, pp. 2083–105, doi:10.1214/22-AIHP1304.","short":"L. Erdös, H.C. Ji, Annales de l’institut Henri Poincare (B) Probability and Statistics 59 (2023) 2083–2105."},"article_type":"original","page":"2083-2105","abstract":[{"lang":"eng","text":"For large dimensional non-Hermitian random matrices X with real or complex independent, identically distributed, centered entries, we consider the fluctuations of f (X) as a matrix where f is an analytic function around the spectrum of X. We prove that for a generic bounded square matrix A, the quantity Tr f (X)A exhibits Gaussian fluctuations as the matrix size grows to infinity, which consists of two independent modes corresponding to the tracial and traceless parts of A. We find a new formula for the variance of the traceless part that involves the Frobenius norm of A and the L2-norm of f on the boundary of the limiting spectrum. "},{"lang":"fre","text":"On étudie les fluctuations de f (X), où X est une matrice aléatoire non-hermitienne de grande taille à coefficients i.i.d. (réels ou complexes), et f une fonction analytique sur un domaine qui contient le spectre de X. On prouve que, pour une matrice carrée générique et bornée A, les fluctuations de la quantité tr f (X)A sont asymptotiquement gaussiennes et comportent deux modes indépendants, correspondant aux composantes traciale et de trace nulle de A. Une nouvelle formule est établie pour la variance de la composante de trace nulle, qui fait intervenir la norme de Frobenius de A et la norme L2 de f sur la frontière du spectre limite."}],"issue":"4","type":"journal_article","oa_version":"Preprint","_id":"14667","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Functional CLT for non-Hermitian random matrices","intvolume":" 59"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14662","intvolume":" 13","ddc":["510"],"status":"public","title":"Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling","file":[{"file_size":201513,"content_type":"application/pdf","creator":"dernst","file_name":"2023_JST_Seiringer.pdf","access_level":"open_access","date_created":"2023-12-11T12:03:12Z","date_updated":"2023-12-11T12:03:12Z","checksum":"9ce96ca87d56ea9a70d2eb9a32839f8d","success":1,"relation":"main_file","file_id":"14677"}],"oa_version":"None","type":"journal_article","issue":"3","abstract":[{"text":"We consider a class of polaron models, including the Fröhlich model, at zero total\r\nmomentum, and show that at sufficiently weak coupling there are no excited eigenvalues below\r\nthe essential spectrum.","lang":"eng"}],"citation":{"chicago":"Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron Models at Weak Coupling.” Journal of Spectral Theory. EMS Press, 2023. https://doi.org/10.4171/JST/469.","mla":"Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron Models at Weak Coupling.” Journal of Spectral Theory, vol. 13, no. 3, EMS Press, 2023, pp. 1045–55, doi:10.4171/JST/469.","short":"R. Seiringer, Journal of Spectral Theory 13 (2023) 1045–1055.","ista":"Seiringer R. 2023. Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. 13(3), 1045–1055.","apa":"Seiringer, R. (2023). Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/469","ieee":"R. Seiringer, “Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling,” Journal of Spectral Theory, vol. 13, no. 3. EMS Press, pp. 1045–1055, 2023.","ama":"Seiringer R. Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. 2023;13(3):1045-1055. doi:10.4171/JST/469"},"publication":"Journal of Spectral Theory","page":"1045-1055","article_type":"original","date_published":"2023-11-25T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"25","year":"2023","department":[{"_id":"RoSe"}],"publisher":"EMS Press","publication_status":"published","author":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"volume":13,"date_updated":"2023-12-11T12:12:14Z","date_created":"2023-12-10T23:00:59Z","file_date_updated":"2023-12-11T12:03:12Z","external_id":{"arxiv":["2210.17123"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.4171/JST/469","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1664-039X"],"eissn":["1664-0403"]},"month":"11"},{"day":"28","month":"11","publication_identifier":{"issn":["0921-4526"]},"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2023-11-28T00:00:00Z","doi":"10.1016/j.physb.2023.415539","article_type":"original","quality_controlled":"1","publication":"Physica B: Condensed Matter","citation":{"ieee":"S. L. Gupta et al., “Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys,” Physica B: Condensed Matter, vol. 674. Elsevier, 2023.","apa":"Gupta, S. L., Singh, S., Kumar, S., Anupam, U., Thakur, S. S., Kumar, A., … Diwaker, D. (2023). Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2023.415539","ista":"Gupta SL, Singh S, Kumar S, Anupam U, Thakur SS, Kumar A, Panwar S, Diwaker D. 2023. Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. 674, 415539.","ama":"Gupta SL, Singh S, Kumar S, et al. Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. 2023;674. doi:10.1016/j.physb.2023.415539","chicago":"Gupta, Shyam Lal, Saurabh Singh, Sumit Kumar, Unknown Anupam, Samjeet Singh Thakur, Ashish Kumar, Sanjay Panwar, and D. Diwaker. “Ab-Initio Stability of Iridium Based Newly Proposed Full and Quaternary Heusler Alloys.” Physica B: Condensed Matter. Elsevier, 2023. https://doi.org/10.1016/j.physb.2023.415539.","short":"S.L. Gupta, S. Singh, S. Kumar, U. Anupam, S.S. Thakur, A. Kumar, S. Panwar, D. Diwaker, Physica B: Condensed Matter 674 (2023).","mla":"Gupta, Shyam Lal, et al. “Ab-Initio Stability of Iridium Based Newly Proposed Full and Quaternary Heusler Alloys.” Physica B: Condensed Matter, vol. 674, 415539, Elsevier, 2023, doi:10.1016/j.physb.2023.415539."},"abstract":[{"lang":"eng","text":"In order to demonstrate the stability of newly proposed iridium-based Ir2Cr(In,Sn) and IrRhCr(In,Sn) heusler alloys, we present ab-initio analysis of these alloys by examining various properties to prove their stability. The stability of these alloys can be inferred from different cohesive and formation energies as well as positive phonon frequencies. Their electronic structure results indicate that they are semi-metals in nature. The magnetic moments are computed using the Slater-Pauling formula and exhibit a high value, with the Cr atom contributing the most in all alloys. Mulliken’s charge analysis results show that our alloys contain a range of linkages, mainly ionic and covalent ones. The ductility and mechanical stability of these alloys are confirmed by elastic constants viz. Poisson’s ratio, Pugh’s ratio, and many different types of elastic moduli."}],"article_number":"415539","type":"journal_article","date_created":"2023-12-10T23:00:56Z","date_updated":"2023-12-12T08:22:23Z","oa_version":"None","volume":674,"author":[{"full_name":"Gupta, Shyam Lal","first_name":"Shyam Lal","last_name":"Gupta"},{"first_name":"Saurabh","last_name":"Singh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269","full_name":"Singh, Saurabh"},{"full_name":"Kumar, Sumit","last_name":"Kumar","first_name":"Sumit"},{"full_name":"Anupam, Unknown","first_name":"Unknown","last_name":"Anupam"},{"full_name":"Thakur, Samjeet Singh","first_name":"Samjeet Singh","last_name":"Thakur"},{"full_name":"Kumar, Ashish","last_name":"Kumar","first_name":"Ashish"},{"last_name":"Panwar","first_name":"Sanjay","full_name":"Panwar, Sanjay"},{"first_name":"D.","last_name":"Diwaker","full_name":"Diwaker, D."}],"publication_status":"epub_ahead","title":"Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys","status":"public","publisher":"Elsevier","intvolume":" 674","department":[{"_id":"MaIb"}],"_id":"14652","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023"},{"day":"20","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2023-10-20T00:00:00Z","publication":"iScience","citation":{"ama":"Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 2023;26(10):107840. doi:10.1016/j.isci.2023.107840","ista":"Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I, Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 26(10), 107840.","apa":"Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R., … Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107840","ieee":"S. Scarpetta et al., “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” iScience, vol. 26, no. 10. Elsevier, p. 107840, 2023.","mla":"Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience, vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:10.1016/j.isci.2023.107840.","short":"S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.","chicago":"Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107840."},"article_type":"original","page":"107840","abstract":[{"lang":"eng","text":"Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.Significance statementWe fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis."}],"issue":"10","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14412","checksum":"f499836af172ecc9865de4bb41fa99d1","success":1,"date_updated":"2023-10-09T07:23:46Z","date_created":"2023-10-09T07:23:46Z","access_level":"open_access","file_name":"2023_iScience_Scarpetta.pdf","content_type":"application/pdf","file_size":4872708,"creator":"dernst"}],"_id":"12487","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","ddc":["570"],"intvolume":" 26","month":"10","publication_identifier":{"eissn":["2589-0042"]},"doi":"10.1016/j.isci.2023.107840","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001082331200001"],"pmid":["37766992"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics"}],"file_date_updated":"2023-10-09T07:23:46Z","ec_funded":1,"author":[{"full_name":"Scarpetta, Silvia","first_name":"Silvia","last_name":"Scarpetta"},{"last_name":"Morrisi","first_name":"Niccolò","full_name":"Morrisi, Niccolò"},{"last_name":"Mutti","first_name":"Carlotta","full_name":"Mutti, Carlotta"},{"first_name":"Nicoletta","last_name":"Azzi","full_name":"Azzi, Nicoletta"},{"last_name":"Trippi","first_name":"Irene","full_name":"Trippi, Irene"},{"first_name":"Rosario","last_name":"Ciliento","full_name":"Ciliento, Rosario"},{"last_name":"Apicella","first_name":"Ilenia","full_name":"Apicella, Ilenia"},{"last_name":"Messuti","first_name":"Giovanni","full_name":"Messuti, Giovanni"},{"full_name":"Angiolelli, Marianna","last_name":"Angiolelli","first_name":"Marianna"},{"last_name":"Lombardi","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio"},{"last_name":"Parrino","first_name":"Liborio","full_name":"Parrino, Liborio"},{"first_name":"Anna Elisabetta","last_name":"Vaudano","full_name":"Vaudano, Anna Elisabetta"}],"date_created":"2023-02-02T10:50:17Z","date_updated":"2023-12-13T11:11:24Z","volume":26,"acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411, and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318. IA acknowledges financial support from the MIUR PRIN 2017WZFTZP.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Elsevier"},{"file_date_updated":"2023-08-14T07:51:47Z","ec_funded":1,"article_number":"37","date_updated":"2023-12-13T11:13:14Z","date_created":"2023-02-28T07:38:17Z","volume":23,"author":[{"full_name":"Metzler, Sina","last_name":"Metzler","first_name":"Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3","last_name":"Kirchner","first_name":"Jessica","full_name":"Kirchner, Jessica"},{"first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"related_material":{"record":[{"id":"12693","relation":"research_data","status":"public"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"SyCr"}],"year":"2023","acknowledgement":"We are thankful to Mike Bidochka for the fungal strain, Lukas Schrader for sharing the C. obscurior genome data for primer development, the Lab Support Facility of ISTA for general laboratory support and help with the permit approval procedures, and the Finca El Quinto for letting us collect ants on their property. We thank the Social Immunity Team at ISTA for help with ant collection and experimental help, in particular Elina Hanhimäki and Marta Gorecka for behavioural observation, and Elisabeth Naderlinger for spore load PCRs. We further thank the Social Immunity Team and Jürgen Heinze for continued discussion and comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology Austria (ISTA). This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 771402 to SC). ","pmid":1,"month":"08","publication_identifier":{"issn":["2730-7182"]},"acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.1186/s12862-023-02137-7","quality_controlled":"1","isi":1,"project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37550612"],"isi":["001042643600002"]},"oa":1,"abstract":[{"lang":"eng","text":"Background: Fighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogen Metarhizium robertsii interfered with fighting success in Cardiocondyla obscurior ant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colony’s worker force.\r\nResults: We found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on.\r\nConclusions: Males of the ant C. obscurior have evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2023_BMCEcology_Metzler.pdf","creator":"dernst","file_size":2004276,"content_type":"application/pdf","file_id":"14048","relation":"main_file","success":1,"checksum":"95966dc7d242d2c85bdd4fe14233dbd8","date_created":"2023-08-14T07:51:47Z","date_updated":"2023-08-14T07:51:47Z"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Trade-offs between immunity and competitive ability in fighting ant males","intvolume":" 23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12696","day":"07","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2023-08-07T00:00:00Z","article_type":"original","publication":"BMC Ecology and Evolution","citation":{"chicago":"Metzler, Sina, Jessica Kirchner, Anna V Grasse, and Sylvia Cremer. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” BMC Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1186/s12862-023-02137-7.","mla":"Metzler, Sina, et al. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” BMC Ecology and Evolution, vol. 23, 37, Springer Nature, 2023, doi:10.1186/s12862-023-02137-7.","short":"S. Metzler, J. Kirchner, A.V. Grasse, S. Cremer, BMC Ecology and Evolution 23 (2023).","ista":"Metzler S, Kirchner J, Grasse AV, Cremer S. 2023. Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. 23, 37.","apa":"Metzler, S., Kirchner, J., Grasse, A. V., & Cremer, S. (2023). Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. Springer Nature. https://doi.org/10.1186/s12862-023-02137-7","ieee":"S. Metzler, J. Kirchner, A. V. Grasse, and S. Cremer, “Trade-offs between immunity and competitive ability in fighting ant males,” BMC Ecology and Evolution, vol. 23. Springer Nature, 2023.","ama":"Metzler S, Kirchner J, Grasse AV, Cremer S. Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. 2023;23. doi:10.1186/s12862-023-02137-7"}},{"type":"journal_article","abstract":[{"text":"Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment.","lang":"eng"}],"_id":"14659","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 16","status":"public","title":"Local cooling and drying induced by Himalayan glaciers under global warming","ddc":["550"],"file":[{"creator":"dernst","file_size":6072603,"content_type":"application/pdf","file_name":"2023_NatureGeoscience_Salerno.pdf","access_level":"open_access","date_updated":"2023-12-11T10:11:19Z","date_created":"2023-12-11T10:11:19Z","success":1,"checksum":"d5ae0d17069eebc6f454c8608cf83e21","file_id":"14671","relation":"main_file"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"04","citation":{"apa":"Salerno, F., Guyennon, N., Yang, K., Shaw, T., Lin, C., Colombo, N., … Pellicciotti, F. (2023). Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. Springer Nature. https://doi.org/10.1038/s41561-023-01331-y","ieee":"F. Salerno et al., “Local cooling and drying induced by Himalayan glaciers under global warming,” Nature Geoscience, vol. 16. Springer Nature, pp. 1120–1127, 2023.","ista":"Salerno F, Guyennon N, Yang K, Shaw T, Lin C, Colombo N, Romano E, Gruber S, Bolch T, Alessandri A, Cristofanelli P, Putero D, Diolaiuti G, Tartari G, Verza G, Thakuri S, Balsamo G, Miles ES, Pellicciotti F. 2023. Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. 16, 1120–1127.","ama":"Salerno F, Guyennon N, Yang K, et al. Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. 2023;16:1120-1127. doi:10.1038/s41561-023-01331-y","chicago":"Salerno, Franco, Nicolas Guyennon, Kun Yang, Thomas Shaw, Changgui Lin, Nicola Colombo, Emanuele Romano, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” Nature Geoscience. Springer Nature, 2023. https://doi.org/10.1038/s41561-023-01331-y.","short":"F. Salerno, N. Guyennon, K. Yang, T. Shaw, C. Lin, N. Colombo, E. Romano, S. Gruber, T. Bolch, A. Alessandri, P. Cristofanelli, D. Putero, G. Diolaiuti, G. Tartari, G. Verza, S. Thakuri, G. Balsamo, E.S. Miles, F. Pellicciotti, Nature Geoscience 16 (2023) 1120–1127.","mla":"Salerno, Franco, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” Nature Geoscience, vol. 16, Springer Nature, 2023, pp. 1120–27, doi:10.1038/s41561-023-01331-y."},"publication":"Nature Geoscience","page":"1120-1127","article_type":"original","date_published":"2023-12-04T00:00:00Z","file_date_updated":"2023-12-11T10:11:19Z","acknowledgement":"This work was carried out within the framework of the EV-K2-CNR and Nepal Academy of Science and Technology. K.Y. was supported by the Second Tibetan Plateau Scientific Expedition and Research Program (grant no. 2019QZKK0206). N.C. was supported by the project NODES, which has received funding from the MUR–M4C2 1.5 of PNRR funded by the European Union - NextGeneration EU (Grant agreement no. ECS00000036). T.E.S. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant no. 101026058. F.P. has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme grant no. 772751, RAVEN, ‘Rapid mass losses of debris-covered glaciers in High Mountain Asia’ and has been supported by the SNSF grant ‘High-elevation precipitation in High Mountain Asia’ (grant no. 183633). A.A. was supported by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 101004156 (CONFESS project) and by the European Union’s Horizon Europe research and innovation program under grant agreement no. 101081193 (OptimESM project). We thank H. Wehrli for valuable comments and suggestions and J. Giannitrapani for the graphic support. We thank A. Da Polenza and K. Bista of EV-K2-CNR for believing that studying the high elevations is relevant for the whole globe.","year":"2023","department":[{"_id":"FrPe"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/wind-of-climate-change/"}]},"author":[{"last_name":"Salerno","first_name":"Franco","full_name":"Salerno, Franco"},{"last_name":"Guyennon","first_name":"Nicolas","full_name":"Guyennon, Nicolas"},{"full_name":"Yang, Kun","last_name":"Yang","first_name":"Kun"},{"id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","orcid":"0000-0001-7640-6152","first_name":"Thomas","last_name":"Shaw","full_name":"Shaw, Thomas"},{"last_name":"Lin","first_name":"Changgui","full_name":"Lin, Changgui"},{"last_name":"Colombo","first_name":"Nicola","full_name":"Colombo, Nicola"},{"full_name":"Romano, Emanuele","last_name":"Romano","first_name":"Emanuele"},{"full_name":"Gruber, Stephan","last_name":"Gruber","first_name":"Stephan"},{"full_name":"Bolch, Tobias","last_name":"Bolch","first_name":"Tobias"},{"full_name":"Alessandri, Andrea","last_name":"Alessandri","first_name":"Andrea"},{"full_name":"Cristofanelli, Paolo","first_name":"Paolo","last_name":"Cristofanelli"},{"full_name":"Putero, Davide","first_name":"Davide","last_name":"Putero"},{"first_name":"Guglielmina","last_name":"Diolaiuti","full_name":"Diolaiuti, Guglielmina"},{"first_name":"Gianni","last_name":"Tartari","full_name":"Tartari, Gianni"},{"full_name":"Verza, Gianpietro","last_name":"Verza","first_name":"Gianpietro"},{"last_name":"Thakuri","first_name":"Sudeep","full_name":"Thakuri, Sudeep"},{"first_name":"Gianpaolo","last_name":"Balsamo","full_name":"Balsamo, Gianpaolo"},{"first_name":"Evan S.","last_name":"Miles","full_name":"Miles, Evan S."},{"full_name":"Pellicciotti, Francesca","first_name":"Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","orcid":"0000-0002-5554-8087"}],"volume":16,"date_updated":"2023-12-13T11:01:10Z","date_created":"2023-12-10T23:00:58Z","publication_identifier":{"eissn":["1752-0908"],"issn":["1752-0894"]},"month":"12","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1038/s41561-023-01331-y","language":[{"iso":"eng"}]},{"_id":"12786","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics","intvolume":" 14","oa_version":"Published Version","file":[{"file_id":"12797","relation":"main_file","date_created":"2023-04-03T06:38:56Z","date_updated":"2023-04-03T06:38:56Z","success":1,"checksum":"0a97b31191432dae5853bbb5ccb7698d","file_name":"2023_NatureComm_Zhang.pdf","access_level":"open_access","creator":"dernst","file_size":2613996,"content_type":"application/pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators."}],"publication":"Nature Communications","citation":{"ieee":"D. Zhang et al., “Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Zhang, D., Lape, R., Shaikh, S. A., Kohegyi, B. K., Watson, J., Cais, O., … Greger, I. H. (2023). Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37259-5","ista":"Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson J, Cais O, Nakagawa T, Greger IH. 2023. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 14, 1659.","ama":"Zhang D, Lape R, Shaikh SA, et al. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 2023;14. doi:10.1038/s41467-023-37259-5","chicago":"Zhang, Danyang, Remigijus Lape, Saher A. Shaikh, Bianka K. Kohegyi, Jake Watson, Ondrej Cais, Terunaga Nakagawa, and Ingo H. Greger. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37259-5.","short":"D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa, I.H. Greger, Nature Communications 14 (2023).","mla":"Zhang, Danyang, et al. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” Nature Communications, vol. 14, 1659, Springer Nature, 2023, doi:10.1038/s41467-023-37259-5."},"article_type":"original","date_published":"2023-03-25T00:00:00Z","scopus_import":"1","day":"25","has_accepted_license":"1","article_processing_charge":"No","acknowledgement":"We thank James Krieger for generating the ‘proDy’ interaction maps in Fig. 5B and S7C, and Jan-Niklas Dohrke for critically reading the manuscript. We thank members of the Greger lab for insightful comments during this study. We acknowledge Trevor Rutherford for confirming ligand integrity by NMR. We are also grateful to LMB scientific computing and the EM facility for their support. This research was funded in part by the Wellcome Trust (223194/Z/21/Z) to I.H.G. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Further funding came from the Medical Research Council (MRU105174197) to I.H.G, and NIH grant (R56/R01MH123474) to T.N.","year":"2023","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Springer Nature","author":[{"last_name":"Zhang","first_name":"Danyang","full_name":"Zhang, Danyang"},{"full_name":"Lape, Remigijus","first_name":"Remigijus","last_name":"Lape"},{"full_name":"Shaikh, Saher A.","first_name":"Saher A.","last_name":"Shaikh"},{"full_name":"Kohegyi, Bianka K.","last_name":"Kohegyi","first_name":"Bianka K."},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake"},{"first_name":"Ondrej","last_name":"Cais","full_name":"Cais, Ondrej"},{"last_name":"Nakagawa","first_name":"Terunaga","full_name":"Nakagawa, Terunaga"},{"last_name":"Greger","first_name":"Ingo H.","full_name":"Greger, Ingo H."}],"date_created":"2023-04-02T22:01:09Z","date_updated":"2023-12-13T11:15:58Z","volume":14,"article_number":"1659","file_date_updated":"2023-04-03T06:38:56Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001066658700003"]},"isi":1,"quality_controlled":"1","doi":"10.1038/s41467-023-37259-5","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["2041-1723"]}},{"day":"28","month":"02","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:12693","citation":{"chicago":"Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12693.","mla":"Cremer, Sylvia. Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12693.","short":"S. Cremer, (2023).","ista":"Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12693.","apa":"Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12693","ieee":"S. Cremer, “Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males .” Institute of Science and Technology Austria, 2023.","ama":"Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . 2023. doi:10.15479/AT:ISTA:12693"},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"file_date_updated":"2023-02-28T06:34:12Z","abstract":[{"text":"See Readme File for further 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Sylvia"}],"related_material":{"record":[{"id":"12696","relation":"used_in_publication","status":"public"}]},"contributor":[{"contributor_type":"data_collector","last_name":"Metzler","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jessica","contributor_type":"data_collector","last_name":"Kirchner","id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse","contributor_type":"data_collector"}],"ddc":["570"],"status":"public","title":"Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ","publisher":"Institute of Science and Technology Austria","department":[{"_id":"SyCr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12693","year":"2023"},{"file_date_updated":"2023-06-26T10:15:44Z","author":[{"full_name":"Xu, Jiayuan","last_name":"Xu","first_name":"Jiayuan"},{"first_name":"Nana","last_name":"Liu","full_name":"Liu, 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Andreassen","first_name":"Ole","full_name":"A. Andreassen, Ole"},{"full_name":"T. Westlye, Lars","last_name":"T. Westlye","first_name":"Lars"},{"full_name":"Van Der Meer, Dennis","last_name":"Van Der Meer","first_name":"Dennis"},{"first_name":"Sara","last_name":"Fernandez","full_name":"Fernandez, Sara"},{"full_name":"Kjelkenes, Rikka","last_name":"Kjelkenes","first_name":"Rikka"},{"first_name":"Helga","last_name":"Ask","full_name":"Ask, Helga"},{"last_name":"Rapp","first_name":"Michael","full_name":"Rapp, Michael"},{"last_name":"Tschorn","first_name":"Mira","full_name":"Tschorn, Mira"},{"full_name":"Böttger, Sarah Jane","last_name":"Böttger","first_name":"Sarah Jane"},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"id":"4406F586-F248-11E8-B48F-1D18A9856A87","first_name":"Lena","last_name":"Marr","full_name":"Marr, Lena"},{"full_name":"Slater, Mel","last_name":"Slater","first_name":"Mel"},{"last_name":"Viapiana","first_name":"Guillem Feixas","full_name":"Viapiana, Guillem Feixas"},{"first_name":"Francisco Eiroa","last_name":"Orosa","full_name":"Orosa, Francisco Eiroa"},{"first_name":"Jaime","last_name":"Gallego","full_name":"Gallego, Jaime"},{"last_name":"Pastor","first_name":"Alvaro","full_name":"Pastor, Alvaro"},{"full_name":"Forstner, Andreas","first_name":"Andreas","last_name":"Forstner"},{"full_name":"Hoffmann, Per","first_name":"Per","last_name":"Hoffmann"},{"full_name":"M. Nöthen, Markus","first_name":"Markus","last_name":"M. Nöthen"},{"first_name":"Andreas","last_name":"J. Forstner","full_name":"J. Forstner, Andreas"},{"first_name":"Isabelle","last_name":"Claus","full_name":"Claus, Isabelle"},{"first_name":"Abbi","last_name":"Miller","full_name":"Miller, Abbi"},{"last_name":"Heilmann-Heimbach","first_name":"Stefanie","full_name":"Heilmann-Heimbach, Stefanie"},{"last_name":"Sommer","first_name":"Peter","full_name":"Sommer, Peter"},{"last_name":"Boye","first_name":"Mona","full_name":"Boye, Mona"},{"last_name":"Wilbertz","first_name":"Johannes","full_name":"Wilbertz, Johannes"},{"full_name":"Schmitt, Karen","last_name":"Schmitt","first_name":"Karen"},{"first_name":"Viktor","last_name":"Jirsa","full_name":"Jirsa, Viktor"},{"last_name":"Petkoski","first_name":"Spase","full_name":"Petkoski, Spase"},{"full_name":"Pitel, Séverine","last_name":"Pitel","first_name":"Séverine"},{"full_name":"Otten, Lisa","first_name":"Lisa","last_name":"Otten"},{"first_name":"Anastasios Polykarpos","last_name":"Athanasiadis","full_name":"Athanasiadis, Anastasios Polykarpos"},{"full_name":"Pearmund, Charlie","last_name":"Pearmund","first_name":"Charlie"},{"last_name":"Spanlang","first_name":"Bernhard","full_name":"Spanlang, Bernhard"},{"full_name":"Alvarez, Elena","first_name":"Elena","last_name":"Alvarez"},{"full_name":"Sanchez, Mavi","last_name":"Sanchez","first_name":"Mavi"},{"full_name":"Giner, Arantxa","last_name":"Giner","first_name":"Arantxa"},{"last_name":"Hese","first_name":"Sören","full_name":"Hese, Sören"},{"full_name":"Renner, Paul","first_name":"Paul","last_name":"Renner"},{"first_name":"Tianye","last_name":"Jia","full_name":"Jia, Tianye"},{"last_name":"Gong","first_name":"Yanting","full_name":"Gong, Yanting"},{"first_name":"Yunman","last_name":"Xia","full_name":"Xia, Yunman"},{"full_name":"Chang, Xiao","last_name":"Chang","first_name":"Xiao"},{"full_name":"Calhoun, Vince","first_name":"Vince","last_name":"Calhoun"},{"full_name":"Liu, Jingyu","first_name":"Jingyu","last_name":"Liu"},{"full_name":"Thompson, Paul","first_name":"Paul","last_name":"Thompson"},{"last_name":"Clinton","first_name":"Nicholas","full_name":"Clinton, Nicholas"},{"last_name":"Desrivieres","first_name":"Sylvane","full_name":"Desrivieres, Sylvane"},{"full_name":"H. Young, Allan","last_name":"H. Young","first_name":"Allan"},{"full_name":"Stahl, Bernd","first_name":"Bernd","last_name":"Stahl"},{"full_name":"Ogoh, George","last_name":"Ogoh","first_name":"George"}],"volume":29,"date_created":"2023-06-25T22:00:46Z","date_updated":"2023-12-13T11:25:55Z","acknowledgement":"This work received support from the European Union-funded Horizon Europe project ‘environMENTAL’ (no. 101057429 to G.S., A.M. and M.M.N.) and cofunding by UK Research and Innovation under the UK Government’s Horizon Europe funding guarantee (nos. 10041392 and 10038599) for study design and data analysis; the Horizon 2020-funded European Research Council Advanced Grant ‘STRATIFY’ (no. 695313 to G.S. for study design and data analysis); the Human Brain Project (HBP SGA3, no. 945539 to G.S. for study design and data analysis); the National Institutes of Health (grant no. R01DA049238 to G.S. for study design and data analysis); the German Research Foundation (COPE; grant no. 675346 to G.S. for study design and data analysis); the National Natural Science Foundation of China (grant no. 82001797 to J.X., grant no. 82030053 to C.Y., grant no. 82202093 to J.T. and grant no. 82150710554 to G.S. for study design, data analysis and preparation of the manuscript); National Key Research and Development Program of China (grant no. 2018YFC1314301 to C.Y. for study design and data analysis); Tianjin Applied Basic Research Diversified Investment Foundation (grant no. 21JCYBJC01360 to J.X. for study design and data analysis); Tianjin Health Technology Project (grant no. TJWJ2021QN002 to J.X. for preparation of the manuscript); Science & Technology Development Fund of the Tianjin Education Commission for Higher Education (grant no. 2019KJ195 to J.X. for preparation of the manuscript); the Tianjin Medical University ‘Clinical Talent Training 123 Climbing Plan’ to J.X. for the preparation of the manuscript; Tianjin Key Medical Discipline (Specialty) Construction Project (grant no. TJYXZDXK-001A to C.Y. for preparation of the manuscript); the National Key R&D Program of China (grant no. 2022YFE0209400 to L.Y. for study design and data analysis); the Tsinghua University Initiative Scientific Research Program (grant no. 2021Z11GHX002 to L.Y. for study design and data analysis); the National Key Scientific and Technological Infrastructure Project ‘Earth System Science Numerical Simulator Facility’ (EarthLab to L.Y. for study design and data analysis); the Chinese National High-end Foreign Expert Recruitment Plan to G.S.; and the Alexander von Humboldt Foundation to G.S. for study design and data analysis.","year":"2023","publisher":"Springer Nature","department":[{"_id":"GaNo"}],"publication_status":"published","publication_identifier":{"issn":["1078-8956"],"eissn":["1546-170X"]},"month":"06","doi":"10.1038/s41591-023-02365-w","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001013172700001"]},"isi":1,"quality_controlled":"1","abstract":[{"text":"Urban-living individuals are exposed to many environmental factors that may combine and interact to influence mental health. While individual factors of an urban environment have been investigated in isolation, no attempt has been made to model how complex, real-life exposure to living in the city relates to brain and mental health, and how this is moderated by genetic factors. Using the data of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation analyses to investigate the relationships between urban environments and psychiatric symptoms. We found an environmental profile of social deprivation, air pollution, street network and urban land-use density that was positively correlated with an affective symptom group (r = 0.22, Pperm < 0.001), mediated by brain volume differences consistent with reward processing, and moderated by genes enriched for stress response, including CRHR1, explaining 2.01% of the variance in brain volume differences. Protective factors such as greenness and generous destination accessibility were negatively correlated with an anxiety symptom group (r = 0.10, Pperm < 0.001), mediated by brain regions necessary for emotion regulation and moderated by EXD3, explaining 1.65% of the variance. The third urban environmental profile was correlated with an emotional instability symptom group (r = 0.03, Pperm < 0.001). Our findings suggest that different environmental profiles of urban living may influence specific psychiatric symptom groups through distinct neurobiological pathways.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"bcd3225b2731c3442fa98987fd3bd46d","success":1,"date_created":"2023-06-26T10:15:44Z","date_updated":"2023-06-26T10:15:44Z","relation":"main_file","file_id":"13171","content_type":"application/pdf","file_size":7365360,"creator":"dernst","access_level":"open_access","file_name":"2023_NatureMedicine_Xu.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13168","intvolume":" 29","title":"Effects of urban living environments on mental health in adults","ddc":["570"],"status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"15","scopus_import":"1","date_published":"2023-06-15T00:00:00Z","citation":{"chicago":"Xu, Jiayuan, Nana Liu, Elli Polemiti, Liliana Garcia-Mondragon, Jie Tang, Xiaoxuan Liu, Tristram Lett, et al. “Effects of Urban Living Environments on Mental Health in Adults.” Nature Medicine. Springer Nature, 2023. https://doi.org/10.1038/s41591-023-02365-w.","mla":"Xu, Jiayuan, et al. “Effects of Urban Living Environments on Mental Health in Adults.” Nature Medicine, vol. 29, Springer Nature, 2023, pp. 1456–67, doi:10.1038/s41591-023-02365-w.","short":"J. Xu, N. Liu, E. Polemiti, L. Garcia-Mondragon, J. Tang, X. Liu, T. Lett, L. Yu, M.M. Nöthen, J. Feng, C. Yu, A. Marquand, G. Schumann, H. Walter, A. Heinz, M. Ralser, S. Twardziok, N. Vaidya, E. Serin, M. Jentsch, E. Hitchen, R. Eils, U.H. Taron, T. Schütz, K. Schepanski, J. Banks, T. Banaschewski, K. Jansone, N. Christmann, A. Meyer-Lindenberg, H. Tost, N. Holz, E. Schwarz, A. Stringaris, M. Neidhart, F. Nees, S. Siehl, O. A. Andreassen, L. T. Westlye, D. Van Der Meer, S. Fernandez, R. Kjelkenes, H. Ask, M. Rapp, M. Tschorn, S.J. Böttger, G. Novarino, L. Marr, M. Slater, G.F. Viapiana, F.E. Orosa, J. Gallego, A. Pastor, A. Forstner, P. Hoffmann, M. M. Nöthen, A. J. Forstner, I. Claus, A. Miller, S. Heilmann-Heimbach, P. Sommer, M. Boye, J. Wilbertz, K. Schmitt, V. Jirsa, S. Petkoski, S. Pitel, L. Otten, A.P. Athanasiadis, C. Pearmund, B. Spanlang, E. Alvarez, M. Sanchez, A. Giner, S. Hese, P. Renner, T. Jia, Y. Gong, Y. Xia, X. Chang, V. Calhoun, J. Liu, P. Thompson, N. Clinton, S. Desrivieres, A. H. Young, B. Stahl, G. Ogoh, Nature Medicine 29 (2023) 1456–1467.","ista":"Xu J, Liu N, Polemiti E, Garcia-Mondragon L, Tang J, Liu X, Lett T, Yu L, Nöthen MM, Feng J, Yu C, Marquand A, Schumann G, Walter H, Heinz A, Ralser M, Twardziok S, Vaidya N, Serin E, Jentsch M, Hitchen E, Eils R, Taron UH, Schütz T, Schepanski K, Banks J, Banaschewski T, Jansone K, Christmann N, Meyer-Lindenberg A, Tost H, Holz N, Schwarz E, Stringaris A, Neidhart M, Nees F, Siehl S, A. Andreassen O, T. Westlye L, Van Der Meer D, Fernandez S, Kjelkenes R, Ask H, Rapp M, Tschorn M, Böttger SJ, Novarino G, Marr L, Slater M, Viapiana GF, Orosa FE, Gallego J, Pastor A, Forstner A, Hoffmann P, M. Nöthen M, J. Forstner A, Claus I, Miller A, Heilmann-Heimbach S, Sommer P, Boye M, Wilbertz J, Schmitt K, Jirsa V, Petkoski S, Pitel S, Otten L, Athanasiadis AP, Pearmund C, Spanlang B, Alvarez E, Sanchez M, Giner A, Hese S, Renner P, Jia T, Gong Y, Xia Y, Chang X, Calhoun V, Liu J, Thompson P, Clinton N, Desrivieres S, H. Young A, Stahl B, Ogoh G. 2023. Effects of urban living environments on mental health in adults. Nature Medicine. 29, 1456–1467.","ieee":"J. Xu et al., “Effects of urban living environments on mental health in adults,” Nature Medicine, vol. 29. Springer Nature, pp. 1456–1467, 2023.","apa":"Xu, J., Liu, N., Polemiti, E., Garcia-Mondragon, L., Tang, J., Liu, X., … Ogoh, G. (2023). Effects of urban living environments on mental health in adults. Nature Medicine. Springer Nature. https://doi.org/10.1038/s41591-023-02365-w","ama":"Xu J, Liu N, Polemiti E, et al. Effects of urban living environments on mental health in adults. Nature Medicine. 2023;29:1456-1467. doi:10.1038/s41591-023-02365-w"},"publication":"Nature Medicine","page":"1456-1467","article_type":"original"},{"page":"12345-12352","citation":{"mla":"Liao, Kang, et al. “Learning Deposition Policies for Fused Multi-Material 3D Printing.” 2023 IEEE International Conference on Robotics and Automation, vol. 2023, IEEE, 2023, pp. 12345–52, doi:10.1109/ICRA48891.2023.10160465.","short":"K. Liao, T. Tricard, M. Piovarci, H.-P. Seidel, V. Babaei, in:, 2023 IEEE International Conference on Robotics and Automation, IEEE, 2023, pp. 12345–12352.","chicago":"Liao, Kang, Thibault Tricard, Michael Piovarci, Hans-Peter Seidel, and Vahid Babaei. “Learning Deposition Policies for Fused Multi-Material 3D Printing.” In 2023 IEEE International Conference on Robotics and Automation, 2023:12345–52. IEEE, 2023. https://doi.org/10.1109/ICRA48891.2023.10160465.","ama":"Liao K, Tricard T, Piovarci M, Seidel H-P, Babaei V. Learning deposition policies for fused multi-material 3D printing. In: 2023 IEEE International Conference on Robotics and Automation. Vol 2023. IEEE; 2023:12345-12352. doi:10.1109/ICRA48891.2023.10160465","ista":"Liao K, Tricard T, Piovarci M, Seidel H-P, Babaei V. 2023. Learning deposition policies for fused multi-material 3D printing. 2023 IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation vol. 2023, 12345–12352.","ieee":"K. Liao, T. Tricard, M. Piovarci, H.-P. Seidel, and V. Babaei, “Learning deposition policies for fused multi-material 3D printing,” in 2023 IEEE International Conference on Robotics and Automation, London, United Kingdom, 2023, vol. 2023, pp. 12345–12352.","apa":"Liao, K., Tricard, T., Piovarci, M., Seidel, H.-P., & Babaei, V. (2023). Learning deposition policies for fused multi-material 3D printing. In 2023 IEEE International Conference on Robotics and Automation (Vol. 2023, pp. 12345–12352). London, United Kingdom: IEEE. https://doi.org/10.1109/ICRA48891.2023.10160465"},"publication":"2023 IEEE International Conference on Robotics and Automation","date_published":"2023-07-04T00:00:00Z","keyword":["reinforcement learning","deposition","control","color","multi-filament"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"04","intvolume":" 2023","status":"public","ddc":["004"],"title":"Learning deposition policies for fused multi-material 3D printing","_id":"12976","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"file_size":5367986,"content_type":"application/pdf","creator":"mpiovarc","file_name":"Liao2023.pdf","access_level":"open_access","date_updated":"2023-05-16T09:12:05Z","date_created":"2023-05-16T09:12:05Z","checksum":"daeaa67124777d88487f933ea3f77164","success":1,"relation":"main_file","file_id":"12977"}],"type":"conference","abstract":[{"lang":"eng","text":"3D printing based on continuous deposition of materials, such as filament-based 3D printing, has seen widespread adoption thanks to its versatility in working with a wide range of materials. An important shortcoming of this type of technology is its limited multi-material capabilities. While there are simple hardware designs that enable multi-material printing in principle, the required software is heavily underdeveloped. A typical hardware design fuses together individual materials fed into a single chamber from multiple inlets before they are deposited. This design, however, introduces a time delay between the intended material mixture and its actual deposition. In this work, inspired by diverse path planning research in robotics, we show that this mechanical challenge can be addressed via improved printer control. We propose to formulate the search for optimal multi-material printing policies in a reinforcement\r\nlearning setup. We put forward a simple numerical deposition model that takes into account the non-linear material mixing and delayed material deposition. To validate our system we focus on color fabrication, a problem known for its strict requirements for varying material mixtures at a high spatial frequency. We demonstrate that our learned control policy outperforms state-of-the-art hand-crafted algorithms."}],"project":[{"grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["001048371104068"]},"language":[{"iso":"eng"}],"doi":"10.1109/ICRA48891.2023.10160465","conference":{"name":"ICRA: International Conference on Robotics and Automation","end_date":"2023-06-02","location":"London, United Kingdom","start_date":"2023-05-29"},"publication_identifier":{"issn":["1050-4729"],"eisbn":["9798350323658"]},"month":"07","department":[{"_id":"BeBi"}],"publisher":"IEEE","publication_status":"published","year":"2023","acknowledgement":"This work is graciously supported by FWF Lise Meitner (Grant M 3319). Kang Liao sincerely thank Emiliano Luci, Chunyu Lin, and Yao Zhao for their huge support.","volume":2023,"date_updated":"2023-12-13T11:20:00Z","date_created":"2023-05-16T09:14:09Z","author":[{"last_name":"Liao","first_name":"Kang","full_name":"Liao, Kang"},{"first_name":"Thibault","last_name":"Tricard","full_name":"Tricard, Thibault"},{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","orcid":"0000-0002-5062-4474","first_name":"Michael","last_name":"Piovarci","full_name":"Piovarci, Michael"},{"full_name":"Seidel, Hans-Peter","last_name":"Seidel","first_name":"Hans-Peter"},{"full_name":"Babaei, Vahid","first_name":"Vahid","last_name":"Babaei"}],"file_date_updated":"2023-05-16T09:12:05Z"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"14","article_type":"original","citation":{"chicago":"Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39317-4.","short":"K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).","mla":"Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications, vol. 14, 3506, Springer Nature, 2023, doi:10.1038/s41467-023-39317-4.","ieee":"K. R. B. Gert et al., “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39317-4","ista":"Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y, Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 14, 3506.","ama":"Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 2023;14. doi:10.1038/s41467-023-39317-4"},"publication":"Nature Communications","date_published":"2023-06-14T00:00:00Z","type":"journal_article","abstract":[{"text":"Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization.","lang":"eng"}],"intvolume":" 14","status":"public","ddc":["570"],"title":"Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries","_id":"13164","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2023_NatureComm_Gert.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1555006,"creator":"dernst","relation":"main_file","file_id":"13172","date_created":"2023-06-26T10:26:04Z","date_updated":"2023-06-26T10:26:04Z","checksum":"d6165f41c7f1c2c04b04256ec9f003fb","success":1}],"oa_version":"Published Version","publication_identifier":{"eissn":["2041-1723"]},"month":"06","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001048208600023"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-39317-4","article_number":"3506","file_date_updated":"2023-06-26T10:26:04Z","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"publication_status":"published","year":"2023","acknowledgement":"We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis; Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award (RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.","volume":14,"date_created":"2023-06-25T22:00:45Z","date_updated":"2023-12-13T11:26:34Z","author":[{"full_name":"Gert, Krista R.B.","first_name":"Krista R.B.","last_name":"Gert"},{"full_name":"Panser, Karin","first_name":"Karin","last_name":"Panser"},{"full_name":"Surm, Joachim","first_name":"Joachim","last_name":"Surm"},{"full_name":"Steinmetz, Benjamin S.","last_name":"Steinmetz","first_name":"Benjamin S."},{"last_name":"Schleiffer","first_name":"Alexander","full_name":"Schleiffer, Alexander"},{"full_name":"Jovine, Luca","last_name":"Jovine","first_name":"Luca"},{"last_name":"Moran","first_name":"Yehu","full_name":"Moran, Yehu"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Andrea","last_name":"Pauli","full_name":"Pauli, Andrea"}]},{"doi":"10.2140/pjm.2023.325.331","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001104766900001"],"arxiv":["2001.02987"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"month":"11","publication_identifier":{"eissn":["0030-8730"]},"author":[{"orcid":"0000-0002-0854-0306","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","last_name":"Verzobio","first_name":"Matteo","full_name":"Verzobio, Matteo"}],"date_created":"2023-01-16T11:46:19Z","date_updated":"2023-12-13T11:18:14Z","volume":325,"acknowledgement":"This paper is part of the author’s PhD thesis at Università of Pisa. Moreover, this\r\nproject has received funding from the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement\r\nNo. 101034413. I thank the referee for many helpful comments.","year":"2023","publication_status":"published","department":[{"_id":"TiBr"}],"publisher":"Mathematical Sciences Publishers","file_date_updated":"2023-11-13T09:50:41Z","ec_funded":1,"date_published":"2023-11-03T00:00:00Z","publication":"Pacific Journal of Mathematics","citation":{"ieee":"M. Verzobio, “Some effectivity results for primitive divisors of elliptic divisibility sequences,” Pacific Journal of Mathematics, vol. 325, no. 2. Mathematical Sciences Publishers, pp. 331–351, 2023.","apa":"Verzobio, M. (2023). Some effectivity results for primitive divisors of elliptic divisibility sequences. Pacific Journal of Mathematics. Mathematical Sciences Publishers. https://doi.org/10.2140/pjm.2023.325.331","ista":"Verzobio M. 2023. Some effectivity results for primitive divisors of elliptic divisibility sequences. Pacific Journal of Mathematics. 325(2), 331–351.","ama":"Verzobio M. Some effectivity results for primitive divisors of elliptic divisibility sequences. Pacific Journal of Mathematics. 2023;325(2):331-351. doi:10.2140/pjm.2023.325.331","chicago":"Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic Divisibility Sequences.” Pacific Journal of Mathematics. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.325.331.","short":"M. Verzobio, Pacific Journal of Mathematics 325 (2023) 331–351.","mla":"Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic Divisibility Sequences.” Pacific Journal of Mathematics, vol. 325, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–51, doi:10.2140/pjm.2023.325.331."},"article_type":"original","page":"331-351","day":"03","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_PacificJourMaths_Verzobio.pdf","creator":"dernst","file_size":389897,"content_type":"application/pdf","file_id":"14525","relation":"main_file","success":1,"checksum":"b6218d16a72742d8bb38d6fc3c9bb8c6","date_created":"2023-11-13T09:50:41Z","date_updated":"2023-11-13T09:50:41Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12313","ddc":["510"],"status":"public","title":"Some effectivity results for primitive divisors of elliptic divisibility sequences","intvolume":" 325","abstract":[{"lang":"eng","text":"Let P be a nontorsion point on an elliptic curve defined over a number field K and consider the sequence {Bn}n∈N of the denominators of x(nP). We prove that every term of the sequence of the Bn has a primitive divisor for n greater than an effectively computable constant that we will explicitly compute. This constant will depend only on the model defining the curve."}],"issue":"2","type":"journal_article"},{"abstract":[{"text":"We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"13152","date_created":"2023-06-19T09:37:40Z","date_updated":"2023-06-19T09:37:40Z","checksum":"4a543fe4b3f9e747cc52167c17bfb524","success":1,"file_name":"2023_ElectronCommProbability_Schiavo.pdf","access_level":"open_access","file_size":271434,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","status":"public","title":"A Mecke-type characterization of the Dirichlet–Ferguson measure","ddc":["510"],"intvolume":" 28","_id":"13145","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-05-05T00:00:00Z","article_type":"original","page":"1-12","publication":"Electronic Communications in Probability","citation":{"chicago":"Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-ECP528.","mla":"Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” Electronic Communications in Probability, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–12, doi:10.1214/23-ECP528.","short":"L. Dello Schiavo, E. Lytvynov, Electronic Communications in Probability 28 (2023) 1–12.","ista":"Dello Schiavo L, Lytvynov E. 2023. A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. 28, 1–12.","apa":"Dello Schiavo, L., & Lytvynov, E. (2023). A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-ECP528","ieee":"L. Dello Schiavo and E. Lytvynov, “A Mecke-type characterization of the Dirichlet–Ferguson measure,” Electronic Communications in Probability, vol. 28. Institute of Mathematical Statistics, pp. 1–12, 2023.","ama":"Dello Schiavo L, Lytvynov E. A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. 2023;28:1-12. doi:10.1214/23-ECP528"},"file_date_updated":"2023-06-19T09:37:40Z","date_updated":"2023-12-13T11:24:57Z","date_created":"2023-06-18T22:00:48Z","volume":28,"author":[{"orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo"},{"first_name":"Eugene","last_name":"Lytvynov","full_name":"Lytvynov, Eugene"}],"publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"Institute of Mathematical Statistics","acknowledgement":"Research supported by the Sfb 1060 The Mathematics of Emergent Effects (University of Bonn). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through project ESPRIT 208.","year":"2023","month":"05","publication_identifier":{"eissn":["1083-589X"]},"language":[{"iso":"eng"}],"doi":"10.1214/23-ECP528","quality_controlled":"1","isi":1,"project":[{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001042025400001"]},"oa":1},{"volume":69,"date_created":"2023-04-16T22:01:09Z","date_updated":"2023-12-13T11:16:46Z","author":[{"full_name":"Zhang, Yihan","first_name":"Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258"},{"full_name":"Vatedka, Shashank","last_name":"Vatedka","first_name":"Shashank"}],"department":[{"_id":"MaMo"}],"publisher":"IEEE","publication_status":"published","year":"2023","acknowledgement":"YZ thanks Jiajin Li for making the observation given by Equation (23). He also would like to thank Nir Ailon and Ely Porat for several helpful conversations throughout this project, and Alexander Barg for insightful comments on the manuscript.\r\nYZ has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]. The work of SV was supported by a seed grant from IIT Hyderabad and the start-up research grant from the Science and Engineering Research Board, India (SRG/2020/000910).","language":[{"iso":"eng"}],"doi":"10.1109/TIT.2023.3260950","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04407","open_access":"1"}],"external_id":{"isi":["001017307000023"],"arxiv":["2211.04407"]},"oa":1,"publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"month":"07","oa_version":"Preprint","intvolume":" 69","status":"public","title":"Multiple packing: Lower bounds via infinite constellations","_id":"12838","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7","abstract":[{"text":"We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L ∈ Z ≽2 . A multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L – 1 balls of radius √ nN around points in C . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we derive the best known lower bounds on the optimal density of list-decodable infinite constellations for constant L under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory.","lang":"eng"}],"type":"journal_article","date_published":"2023-07-01T00:00:00Z","page":"4513-4527","article_type":"original","citation":{"mla":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Infinite Constellations.” IEEE Transactions on Information Theory, vol. 69, no. 7, IEEE, 2023, pp. 4513–27, doi:10.1109/TIT.2023.3260950.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 69 (2023) 4513–4527.","chicago":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Infinite Constellations.” IEEE Transactions on Information Theory. IEEE, 2023. https://doi.org/10.1109/TIT.2023.3260950.","ama":"Zhang Y, Vatedka S. Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. 2023;69(7):4513-4527. doi:10.1109/TIT.2023.3260950","ista":"Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. 69(7), 4513–4527.","apa":"Zhang, Y., & Vatedka, S. (2023). Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3260950","ieee":"Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via infinite constellations,” IEEE Transactions on Information Theory, vol. 69, no. 7. IEEE, pp. 4513–4527, 2023."},"publication":"IEEE Transactions on Information Theory","article_processing_charge":"No","day":"01","scopus_import":"1"},{"year":"2023","acknowledgement":"The authors would like to thank the anonymous reviewers for their valuable comments and helpful suggestions. This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093.","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Association for Computing Machinery","author":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Mahyar","last_name":"Karimi","full_name":"Karimi, Mahyar"},{"full_name":"Kueffner, Konstantin","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","orcid":"0000-0001-8974-2542","first_name":"Konstantin","last_name":"Kueffner"},{"full_name":"Mallik, Kaushik","last_name":"Mallik","first_name":"Kaushik","orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598"}],"date_created":"2023-07-16T22:01:09Z","date_updated":"2023-12-13T11:30:31Z","file_date_updated":"2023-07-18T07:43:10Z","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.04699"],"isi":["001062819300057"]},"isi":1,"quality_controlled":"1","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"conference":{"name":"FAccT: Conference on Fairness, Accountability and Transparency","end_date":"2023-06-15","location":"Chicago, IL, United States","start_date":"2023-06-12"},"doi":"10.1145/3593013.3594028","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"isbn":["9781450372527"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13228","title":"Runtime monitoring of dynamic fairness properties","status":"public","ddc":["000"],"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4100596,"file_name":"2023_ACM_HenzingerT.pdf","access_level":"open_access","date_created":"2023-07-18T07:43:10Z","date_updated":"2023-07-18T07:43:10Z","success":1,"checksum":"96c759db9cdf94b81e37871a66a6ff48","file_id":"13245","relation":"main_file"}],"type":"conference","abstract":[{"text":"A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox.","lang":"eng"}],"publication":"FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency","citation":{"mla":"Henzinger, Thomas A., et al. “Runtime Monitoring of Dynamic Fairness Properties.” FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association for Computing Machinery, 2023, pp. 604–14, doi:10.1145/3593013.3594028.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association for Computing Machinery, 2023, pp. 604–614.","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Runtime Monitoring of Dynamic Fairness Properties.” In FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, 604–14. Association for Computing Machinery, 2023. https://doi.org/10.1145/3593013.3594028.","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Runtime monitoring of dynamic fairness properties. In: FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency. Association for Computing Machinery; 2023:604-614. doi:10.1145/3593013.3594028","ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Runtime monitoring of dynamic fairness properties. FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency. FAccT: Conference on Fairness, Accountability and Transparency, 604–614.","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Runtime monitoring of dynamic fairness properties. In FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency (pp. 604–614). Chicago, IL, United States: Association for Computing Machinery. https://doi.org/10.1145/3593013.3594028","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Runtime monitoring of dynamic fairness properties,” in FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Chicago, IL, United States, 2023, pp. 604–614."},"page":"604-614","date_published":"2023-06-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1"},{"_id":"13225","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"title":"Correlation energy of a weakly interacting Fermi gas with large interaction potential","status":"public","intvolume":" 247","oa_version":"Published Version","file":[{"file_name":"2023_ArchiveRationalMechAnalysis_Benedikter.pdf","access_level":"open_access","file_size":851626,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14535","date_created":"2023-11-14T13:12:12Z","date_updated":"2023-11-14T13:12:12Z","checksum":"2b45828d854a253b14bf7aa196ec55e9","success":1}],"type":"journal_article","abstract":[{"text":"Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy.","lang":"eng"}],"issue":"4","publication":"Archive for Rational Mechanics and Analysis","citation":{"ama":"Benedikter NP, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. 2023;247(4). doi:10.1007/s00205-023-01893-6","ista":"Benedikter NP, Porta M, Schlein B, Seiringer R. 2023. Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. 247(4), 65.","ieee":"N. P. Benedikter, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas with large interaction potential,” Archive for Rational Mechanics and Analysis, vol. 247, no. 4. Springer Nature, 2023.","apa":"Benedikter, N. P., Porta, M., Schlein, B., & Seiringer, R. (2023). Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01893-6","mla":"Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” Archive for Rational Mechanics and Analysis, vol. 247, no. 4, 65, Springer Nature, 2023, doi:10.1007/s00205-023-01893-6.","short":"N.P. Benedikter, M. Porta, B. Schlein, R. Seiringer, Archive for Rational Mechanics and Analysis 247 (2023).","chicago":"Benedikter, Niels P, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” Archive for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01893-6."},"article_type":"original","date_published":"2023-08-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","year":"2023","acknowledgement":"RS was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227). MP acknowledges financial support from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, Grant Agreement No. 802901). BS acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC AdG CLaQS (Grant Agreement No. 834782). NB and MP were supported by Gruppo Nazionale per la Fisica Matematica (GNFM) of Italy. NB was supported by the European Research Council’s Starting Grant FERMIMATH (Grant Agreement No. 101040991).\r\nOpen access funding provided by Università degli Studi di Milano within the CRUI-CARE Agreement.","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"author":[{"orcid":"0000-0002-1071-6091","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","last_name":"Benedikter","first_name":"Niels P","full_name":"Benedikter, Niels P"},{"full_name":"Porta, Marcello","last_name":"Porta","first_name":"Marcello"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"date_created":"2023-07-16T22:01:08Z","date_updated":"2023-12-13T11:31:14Z","volume":247,"article_number":"65","file_date_updated":"2023-11-14T13:12:12Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001024369000001"],"arxiv":["2106.13185"]},"isi":1,"quality_controlled":"1","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"doi":"10.1007/s00205-023-01893-6","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]}},{"isi":1,"quality_controlled":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"external_id":{"arxiv":["2208.00199"],"isi":["001022878900002"]},"language":[{"iso":"eng"}],"doi":"10.1007/s11005-023-01698-4","month":"07","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"It is a pleasure to thank Martin Kolb, Simone Rademacher, Robert Seiringer and Stefan Teufel for helpful discussions. Moreover, we thank the referee for many constructive comments. L.B. gratefully acknowledges funding from the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We thank the Mathematical Research Institute Oberwolfach, where part of this work was done, for their hospitality.\r\nOpen Access funding enabled and organized by Projekt DEAL.","date_created":"2023-07-16T22:01:08Z","date_updated":"2023-12-13T11:31:50Z","volume":113,"author":[{"full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","last_name":"Bossmann","first_name":"Lea"},{"full_name":"Petrat, Sören P","last_name":"Petrat","first_name":"Sören P","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87"}],"article_number":"77","ec_funded":1,"article_type":"original","publication":"Letters in Mathematical Physics","citation":{"short":"L. Bossmann, S.P. Petrat, Letters in Mathematical Physics 113 (2023).","mla":"Bossmann, Lea, and Sören P. Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” Letters in Mathematical Physics, vol. 113, no. 4, 77, Springer Nature, 2023, doi:10.1007/s11005-023-01698-4.","chicago":"Bossmann, Lea, and Sören P Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” Letters in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s11005-023-01698-4.","ama":"Bossmann L, Petrat SP. Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. 2023;113(4). doi:10.1007/s11005-023-01698-4","ieee":"L. Bossmann and S. P. Petrat, “Weak Edgeworth expansion for the mean-field Bose gas,” Letters in Mathematical Physics, vol. 113, no. 4. Springer Nature, 2023.","apa":"Bossmann, L., & Petrat, S. P. (2023). Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-023-01698-4","ista":"Bossmann L, Petrat SP. 2023. Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. 113(4), 77."},"date_published":"2023-07-03T00:00:00Z","scopus_import":"1","day":"03","article_processing_charge":"Yes (via OA deal)","title":"Weak Edgeworth expansion for the mean-field Bose gas","status":"public","intvolume":" 113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13226","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion.","lang":"eng"}],"issue":"4"},{"file_date_updated":"2023-07-18T08:43:07Z","article_number":"3968","author":[{"last_name":"Hassani","first_name":"Farid","orcid":"0000-0001-6937-5773","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid"},{"orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","first_name":"Matilda","full_name":"Peruzzo, Matilda"},{"first_name":"Lucky","last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615","full_name":"Kapoor, Lucky"},{"first_name":"Andrea","last_name":"Trioni","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","full_name":"Trioni, Andrea"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin","full_name":"Zemlicka, Martin"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"date_updated":"2023-12-13T11:32:25Z","date_created":"2023-07-16T22:01:08Z","volume":14,"year":"2023","acknowledgement":"The authors thank J. Koch for discussions and support with the scQubits python package, I. Rozhansky and A. Poddubny for important insights into photon-assisted tunneling, S. Barzanjeh and G. Arnold for theory, E. Redchenko, S. Pepic, the MIBA workshop and the IST nanofabrication facility for technical contributions, as well as L. Drmic, P. Zielinski and R. Sett for software development. We acknowledge the prompt support of Quantum Machines to implement active state preparation with their OPX+. This work was supported by a NOMIS foundation research grant (J.F.), the Austrian Science Fund (FWF) through BeyondC F7105 (J.F.) and IST Austria.","pmid":1,"publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"Springer Nature","month":"07","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-023-39656-2","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001024729900009"],"pmid":["37407570"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Integrating superconducting quantum circuits","call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2023_NatureComm_Hassani.pdf","access_level":"open_access","creator":"dernst","file_size":2899592,"content_type":"application/pdf","file_id":"13248","relation":"main_file","date_updated":"2023-07-18T08:43:07Z","date_created":"2023-07-18T08:43:07Z","success":1,"checksum":"a85773b5fe23516f60f7d5d31b55c200"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13227","title":"Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours","ddc":["530"],"status":"public","intvolume":" 14","day":"05","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2023-07-05T00:00:00Z","publication":"Nature Communications","citation":{"short":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, J.M. Fink, Nature Communications 14 (2023).","mla":"Hassani, Farid, et al. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications, vol. 14, 3968, Springer Nature, 2023, doi:10.1038/s41467-023-39656-2.","chicago":"Hassani, Farid, Matilda Peruzzo, Lucky Kapoor, Andrea Trioni, Martin Zemlicka, and Johannes M Fink. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39656-2.","ama":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 2023;14. doi:10.1038/s41467-023-39656-2","ieee":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, and J. M. Fink, “Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Hassani, F., Peruzzo, M., Kapoor, L., Trioni, A., Zemlicka, M., & Fink, J. M. (2023). Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39656-2","ista":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. 2023. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 14, 3968."},"article_type":"original"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2023-05-01T00:00:00Z","page":"294-298","publication":"2023 IEEE Information Theory Workshop","citation":{"apa":"Xu, Y., Hou, T. Q., Liang, S. S., & Mondelli, M. (2023). Approximate message passing for multi-layer estimation in rotationally invariant models. In 2023 IEEE Information Theory Workshop (pp. 294–298). Saint-Malo, France: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ITW55543.2023.10160238","ieee":"Y. Xu, T. Q. Hou, S. S. Liang, and M. Mondelli, “Approximate message passing for multi-layer estimation in rotationally invariant models,” in 2023 IEEE Information Theory Workshop, Saint-Malo, France, 2023, pp. 294–298.","ista":"Xu Y, Hou TQ, Liang SS, Mondelli M. 2023. Approximate message passing for multi-layer estimation in rotationally invariant models. 2023 IEEE Information Theory Workshop. ITW: Information Theory Workshop, 294–298.","ama":"Xu Y, Hou TQ, Liang SS, Mondelli M. Approximate message passing for multi-layer estimation in rotationally invariant models. In: 2023 IEEE Information Theory Workshop. Institute of Electrical and Electronics Engineers; 2023:294-298. doi:10.1109/ITW55543.2023.10160238","chicago":"Xu, Yizhou, Tian Qi Hou, Shan Suo Liang, and Marco Mondelli. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” In 2023 IEEE Information Theory Workshop, 294–98. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/ITW55543.2023.10160238.","short":"Y. Xu, T.Q. Hou, S.S. Liang, M. Mondelli, in:, 2023 IEEE Information Theory Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–298.","mla":"Xu, Yizhou, et al. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” 2023 IEEE Information Theory Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–98, doi:10.1109/ITW55543.2023.10160238."},"abstract":[{"lang":"eng","text":"We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm."}],"type":"conference","oa_version":"Preprint","status":"public","title":"Approximate message passing for multi-layer estimation in rotationally invariant models","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13321","month":"05","publication_identifier":{"eissn":["2475-4218"],"isbn":["9798350301496"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-04-28","location":"Saint-Malo, France","start_date":"2023-04-23","name":"ITW: Information Theory Workshop"},"doi":"10.1109/ITW55543.2023.10160238","isi":1,"quality_controlled":"1","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"oa":1,"external_id":{"isi":["001031733100053"],"arxiv":["2212.01572"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.01572"}],"date_created":"2023-07-30T22:01:04Z","date_updated":"2023-12-13T11:35:46Z","author":[{"full_name":"Xu, Yizhou","first_name":"Yizhou","last_name":"Xu"},{"full_name":"Hou, Tian Qi","first_name":"Tian Qi","last_name":"Hou"},{"first_name":"Shan Suo","last_name":"Liang","full_name":"Liang, Shan Suo"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"}],"publication_status":"published","department":[{"_id":"MaMo"}],"publisher":"Institute of Electrical and Electronics Engineers","year":"2023","acknowledgement":"Marco Mondelli was partially supported by the 2019 Lopez-Loreta prize."},{"publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"month":"03","doi":"10.1145/3575859","language":[{"iso":"eng"}],"external_id":{"arxiv":["2201.02374"],"isi":["001018739600002"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.02374"}],"isi":1,"quality_controlled":"1","article_number":"26","author":[{"last_name":"Zhong","first_name":"Fanchao","full_name":"Zhong, Fanchao"},{"last_name":"Xu","first_name":"Yonglai","full_name":"Xu, Yonglai"},{"full_name":"Zhao, Haisen","last_name":"Zhao","first_name":"Haisen","orcid":"0000-0002-6389-1045","id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4"},{"full_name":"Lu, Lin","first_name":"Lin","last_name":"Lu"}],"volume":42,"date_created":"2023-07-23T22:01:13Z","date_updated":"2023-12-13T11:34:59Z","acknowledgement":"This work was supported in part by grants from the NSFC (61972232), Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). ","year":"2023","department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","publication_status":"published","article_processing_charge":"No","day":"17","scopus_import":"1","date_published":"2023-03-17T00:00:00Z","citation":{"ista":"Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 42(3), 26.","ieee":"F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based fabrication of surface models,” ACM Transactions on Graphics, vol. 42, no. 3. Association for Computing Machinery, 2023.","apa":"Zhong, F., Xu, Y., Zhao, H., & Lu, L. (2023). As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3575859","ama":"Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 2023;42(3). doi:10.1145/3575859","chicago":"Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3575859.","mla":"Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” ACM Transactions on Graphics, vol. 42, no. 3, 26, Association for Computing Machinery, 2023, doi:10.1145/3575859.","short":"F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023)."},"publication":"ACM Transactions on Graphics","article_type":"original","issue":"3","abstract":[{"text":"In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"13265","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 42","title":"As-Continuous-As-Possible extrusion-based fabrication of surface models","status":"public"},{"article_processing_charge":"No","day":"24","scopus_import":"1","date_published":"2023-07-24T00:00:00Z","citation":{"mla":"Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” Mathematische Annalen, Springer Nature, 2023, doi:10.1007/s00208-023-02680-0.","short":"A. Volberg, H. Zhang, Mathematische Annalen (2023).","chicago":"Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” Mathematische Annalen. Springer Nature, 2023. https://doi.org/10.1007/s00208-023-02680-0.","ama":"Volberg A, Zhang H. Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen. 2023. doi:10.1007/s00208-023-02680-0","ista":"Volberg A, Zhang H. 2023. Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen.","ieee":"A. Volberg and H. Zhang, “Noncommutative Bohnenblust–Hille inequalities,” Mathematische Annalen. Springer Nature, 2023.","apa":"Volberg, A., & Zhang, H. (2023). Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-023-02680-0"},"publication":"Mathematische Annalen","article_type":"original","abstract":[{"text":"Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13318","title":"Noncommutative Bohnenblust–Hille inequalities","status":"public","publication_identifier":{"eissn":["1432-1807"],"issn":["0025-5831"]},"month":"07","doi":"10.1007/s00208-023-02680-0","language":[{"iso":"eng"}],"external_id":{"arxiv":["2210.14468"],"isi":["001035665500001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-023-02680-0"}],"oa":1,"project":[{"_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","grant_number":"M03337","name":"Curvature-dimension in noncommutative analysis"}],"quality_controlled":"1","isi":1,"author":[{"first_name":"Alexander","last_name":"Volberg","full_name":"Volberg, Alexander"},{"first_name":"Haonan","last_name":"Zhang","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","full_name":"Zhang, Haonan"}],"date_updated":"2023-12-13T11:36:20Z","date_created":"2023-07-30T22:01:03Z","year":"2023","acknowledgement":"The research of A.V. is supported by NSF DMS-1900286, DMS-2154402 and by Hausdorff Center for Mathematics. H.Z. is supported by the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. This work is partially supported by NSF DMS-1929284 while both authors were in residence at the Institute for Computational and Experimental Research in Mathematics in Providence, RI, during the Harmonic Analysis and Convexity program.","department":[{"_id":"JaMa"}],"publisher":"Springer Nature","publication_status":"epub_ahead"},{"month":"07","publication_identifier":{"issn":["1424-0637"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2108.05785"}],"external_id":{"arxiv":["2108.05785"],"isi":["001025709100001"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Curvature-dimension in noncommutative analysis","grant_number":"M03337","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6"}],"doi":"10.1007/s00023-023-01345-7","language":[{"iso":"eng"}],"ec_funded":1,"year":"2023","acknowledgement":"I am grateful to Boguslaw Zegarliński for asking me the questions in [3] and for helpful communication. I also want to thank Paata Ivanisvili for drawing [25] to my attention and for useful correspondence. Many thanks to the anonymous referee for the valuable comments and for pointing out some errors in an earlier version of the paper. This work is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337.","publication_status":"epub_ahead","department":[{"_id":"JaMa"}],"publisher":"Springer Nature","author":[{"full_name":"Zhang, Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","last_name":"Zhang","first_name":"Haonan"}],"date_updated":"2023-12-13T11:33:46Z","date_created":"2023-07-23T22:01:15Z","scopus_import":"1","day":"08","article_processing_charge":"No","publication":"Annales Henri Poincare","citation":{"chicago":"Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-023-01345-7.","mla":"Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” Annales Henri Poincare, Springer Nature, 2023, doi:10.1007/s00023-023-01345-7.","short":"H. Zhang, Annales Henri Poincare (2023).","ista":"Zhang H. 2023. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare.","ieee":"H. Zhang, “Some convexity and monotonicity results of trace functionals,” Annales Henri Poincare. Springer Nature, 2023.","apa":"Zhang, H. (2023). Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-023-01345-7","ama":"Zhang H. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. 2023. doi:10.1007/s00023-023-01345-7"},"article_type":"original","date_published":"2023-07-08T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s,\r\nfor parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13271","status":"public","title":"Some convexity and monotonicity results of trace functionals","oa_version":"Preprint"},{"citation":{"mla":"Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Nature Communications, vol. 14, 4153, Springer Nature, 2023, doi:10.1038/s41467-023-39625-9.","short":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023).","chicago":"Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39625-9.","ama":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 2023;14. doi:10.1038/s41467-023-39625-9","ista":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153.","apa":"Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., & Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39625-9","ieee":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” Nature Communications, vol. 14. Springer Nature, 2023."},"publication":"Nature Communications","article_type":"original","date_published":"2023-07-12T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13258","intvolume":" 14","status":"public","title":"The effect of environmental information on evolution of cooperation in stochastic games","ddc":["000"],"oa_version":"Published Version","file":[{"file_size":1601682,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_NatureComm_Kleshnina.pdf","checksum":"5aceefdfe76686267b93ae4fe81899f1","success":1,"date_created":"2023-07-31T11:32:36Z","date_updated":"2023-07-31T11:32:36Z","relation":"main_file","file_id":"13337"}],"type":"journal_article","abstract":[{"text":"Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation.","lang":"eng"}],"external_id":{"pmid":["37438341"],"isi":["001029450400031"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41467-023-39625-9","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"month":"07","pmid":1,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).","year":"2023","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"13336"}]},"author":[{"id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina","first_name":"Maria","full_name":"Kleshnina, Maria"},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"first_name":"Stepan","last_name":"Simsa","id":"409d615c-2f95-11ee-b934-90a352102c1e","orcid":"0000-0001-6687-1210","full_name":"Simsa, Stepan"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"volume":14,"date_updated":"2023-12-13T11:42:38Z","date_created":"2023-07-23T22:01:11Z","article_number":"4153","ec_funded":1,"file_date_updated":"2023-07-31T11:32:36Z"},{"scopus_import":"1","day":"30","article_processing_charge":"Yes","has_accepted_license":"1","article_type":"original","page":"i513-i522","publication":"Bioinformatics","citation":{"apa":"Trinh, V. G., Benhamou, B., Henzinger, T. A., & Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad262","ieee":"V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” Bioinformatics, vol. 39, no. Supplement_1. Oxford Academic, pp. i513–i522, 2023.","ista":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522.","ama":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 2023;39(Supplement_1):i513-i522. doi:10.1093/bioinformatics/btad262","chicago":"Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad262.","short":"V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522.","mla":"Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” Bioinformatics, vol. 39, no. Supplement_1, Oxford Academic, 2023, pp. i513–22, doi:10.1093/bioinformatics/btad262."},"date_published":"2023-06-30T00:00:00Z","type":"journal_article","abstract":[{"text":"Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models.","lang":"eng"}],"issue":"Supplement_1","status":"public","title":"Trap spaces of multi-valued networks: Definition, computation, and applications","ddc":["000"],"intvolume":" 39","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13263","oa_version":"Published Version","file":[{"file_id":"13335","relation":"main_file","date_updated":"2023-07-31T11:09:05Z","date_created":"2023-07-31T11:09:05Z","success":1,"checksum":"ba3abe1171df1958413b7c7f957f5486","file_name":"2023_Bioinformatics_Trinh.pdf","access_level":"open_access","creator":"dernst","file_size":641736,"content_type":"application/pdf"}],"month":"06","publication_identifier":{"eissn":["1367-4811"],"issn":["1367-4803"]},"quality_controlled":"1","isi":1,"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37387165"],"isi":["001027457000060"]},"language":[{"iso":"eng"}],"doi":"10.1093/bioinformatics/btad262","file_date_updated":"2023-07-31T11:09:05Z","ec_funded":1,"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Oxford Academic","acknowledgement":"This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413].","year":"2023","pmid":1,"date_created":"2023-07-23T22:01:12Z","date_updated":"2023-12-13T11:41:52Z","volume":39,"author":[{"first_name":"Van Giang","last_name":"Trinh","full_name":"Trinh, Van Giang"},{"first_name":"Belaid","last_name":"Benhamou","full_name":"Benhamou, Belaid"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Pastva, Samuel","first_name":"Samuel","last_name":"Pastva","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","orcid":"0000-0003-1993-0331"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/giang-trinh/trap-mvn"}]}},{"publication_identifier":{"eissn":["2050-084X"]},"month":"07","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37477116"],"isi":["001035372800001"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.7554/eLife.84850","language":[{"iso":"eng"}],"article_number":"e84850","file_date_updated":"2023-07-31T07:43:00Z","pmid":1,"acknowledgement":"This work was supported by JSPS KAKENHI grant #18K062291, and the Takeda Science Foundation to JYT., as well as JSPS KAKENHI grant #19K065710, the Takeda Science Foundation, and Life Science Foundation of Japan to JT.","year":"2023","department":[{"_id":"DaSi"}],"publisher":"eLife Sciences Publications","publication_status":"published","author":[{"full_name":"Toshima, Junko Y.","last_name":"Toshima","first_name":"Junko Y."},{"full_name":"Tsukahara, Ayana","last_name":"Tsukahara","first_name":"Ayana"},{"full_name":"Nagano, Makoto","first_name":"Makoto","last_name":"Nagano"},{"last_name":"Tojima","first_name":"Takuro","full_name":"Tojima, Takuro"},{"orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E"},{"full_name":"Nakano, Akihiko","last_name":"Nakano","first_name":"Akihiko"},{"last_name":"Toshima","first_name":"Jiro","full_name":"Toshima, Jiro"}],"volume":12,"date_updated":"2023-12-13T11:37:36Z","date_created":"2023-07-30T22:01:02Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"21","citation":{"chicago":"Toshima, Junko Y., Ayana Tsukahara, Makoto Nagano, Takuro Tojima, Daria E Siekhaus, Akihiko Nakano, and Jiro Toshima. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.84850.","short":"J.Y. Toshima, A. Tsukahara, M. Nagano, T. Tojima, D.E. Siekhaus, A. Nakano, J. Toshima, ELife 12 (2023).","mla":"Toshima, Junko Y., et al. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife, vol. 12, e84850, eLife Sciences Publications, 2023, doi:10.7554/eLife.84850.","apa":"Toshima, J. Y., Tsukahara, A., Nagano, M., Tojima, T., Siekhaus, D. E., Nakano, A., & Toshima, J. (2023). The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.84850","ieee":"J. Y. Toshima et al., “The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network,” eLife, vol. 12. eLife Sciences Publications, 2023.","ista":"Toshima JY, Tsukahara A, Nagano M, Tojima T, Siekhaus DE, Nakano A, Toshima J. 2023. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 12, e84850.","ama":"Toshima JY, Tsukahara A, Nagano M, et al. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 2023;12. doi:10.7554/eLife.84850"},"publication":"eLife","article_type":"original","date_published":"2023-07-21T00:00:00Z","type":"journal_article","abstract":[{"text":"Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13316","intvolume":" 12","status":"public","ddc":["570"],"title":"The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network","file":[{"content_type":"application/pdf","file_size":11980913,"creator":"dernst","file_name":"2023_eLife_Toshima.pdf","access_level":"open_access","date_created":"2023-07-31T07:43:00Z","date_updated":"2023-07-31T07:43:00Z","checksum":"2af111a00cf5e3a956f7f0fd13199b15","success":1,"relation":"main_file","file_id":"13324"}],"oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13317","ddc":["510","530"],"status":"public","title":"Eigenstate thermalisation hypothesis for translation invariant spin systems","intvolume":" 190","file":[{"checksum":"c2ef6b2aecfee1ad6d03fab620507c2c","success":1,"date_updated":"2023-07-31T07:49:31Z","date_created":"2023-07-31T07:49:31Z","relation":"main_file","file_id":"13325","content_type":"application/pdf","file_size":612755,"creator":"dernst","access_level":"open_access","file_name":"2023_JourStatPhysics_Sugimoto.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction.","lang":"eng"}],"issue":"7","publication":"Journal of Statistical Physics","citation":{"ista":"Sugimoto S, Henheik SJ, Riabov V, Erdös L. 2023. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 190(7), 128.","ieee":"S. Sugimoto, S. J. Henheik, V. Riabov, and L. Erdös, “Eigenstate thermalisation hypothesis for translation invariant spin systems,” Journal of Statistical Physics, vol. 190, no. 7. Springer Nature, 2023.","apa":"Sugimoto, S., Henheik, S. J., Riabov, V., & Erdös, L. (2023). Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-023-03132-4","ama":"Sugimoto S, Henheik SJ, Riabov V, Erdös L. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 2023;190(7). doi:10.1007/s10955-023-03132-4","chicago":"Sugimoto, Shoki, Sven Joscha Henheik, Volodymyr Riabov, and László Erdös. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics. Springer Nature, 2023. https://doi.org/10.1007/s10955-023-03132-4.","mla":"Sugimoto, Shoki, et al. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics, vol. 190, no. 7, 128, Springer Nature, 2023, doi:10.1007/s10955-023-03132-4.","short":"S. Sugimoto, S.J. Henheik, V. Riabov, L. Erdös, Journal of Statistical Physics 190 (2023)."},"article_type":"original","date_published":"2023-07-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","acknowledgement":"LE, JH, and VR were supported by ERC Advanced Grant “RMTBeyond” No. 101020331. SS was supported by KAKENHI Grant Number JP22J14935 from the Japan Society for the Promotion of Science (JSPS) and Forefront Physics and Mathematics Program to Drive Transformation (FoPM), a World-leading Innovative Graduate Study (WINGS) Program, the University of Tokyo.\r\nOpen access funding provided by The University of Tokyo.","year":"2023","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Springer Nature","author":[{"first_name":"Shoki","last_name":"Sugimoto","full_name":"Sugimoto, Shoki"},{"id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","orcid":"0000-0003-1106-327X","first_name":"Sven Joscha","last_name":"Henheik","full_name":"Henheik, Sven Joscha"},{"full_name":"Riabov, Volodymyr","last_name":"Riabov","first_name":"Volodymyr","id":"1949f904-edfb-11eb-afb5-e2dfddabb93b"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"}],"date_created":"2023-07-30T22:01:02Z","date_updated":"2023-12-13T11:38:44Z","volume":190,"article_number":"128","file_date_updated":"2023-07-31T07:49:31Z","ec_funded":1,"external_id":{"arxiv":["2304.04213"],"isi":["001035677200002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020"}],"doi":"10.1007/s10955-023-03132-4","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["0022-4715"],"eissn":["1572-9613"]}},{"publication":"SciPost Physics","citation":{"ieee":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, and A. Volosniev, “Magnetic impurity in a one-dimensional few-fermion system,” SciPost Physics, vol. 14, no. 1. SciPost Foundation, 2023.","apa":"Rammelmüller, L., Huber, D., Čufar, M., Brand, J., Hammer, H.-W., & Volosniev, A. (2023). Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.14.1.006","ista":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. 2023. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 14(1), 006.","ama":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 2023;14(1). doi:10.21468/scipostphys.14.1.006","chicago":"Rammelmüller, Lukas, David Huber, Matija Čufar, Joachim Brand, Hans-Werner Hammer, and Artem Volosniev. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.14.1.006.","short":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, A. Volosniev, SciPost Physics 14 (2023).","mla":"Rammelmüller, Lukas, et al. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics, vol. 14, no. 1, 006, SciPost Foundation, 2023, doi:10.21468/scipostphys.14.1.006."},"article_type":"original","date_published":"2023-01-24T00:00:00Z","scopus_import":"1","keyword":["General Physics and Astronomy"],"day":"24","has_accepted_license":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13278","title":"Magnetic impurity in a one-dimensional few-fermion system","ddc":["530"],"status":"public","intvolume":" 14","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1163444,"access_level":"open_access","file_name":"2023_SciPostPhysics_Rammelmueller.pdf","success":1,"checksum":"ffdb70b9ae7aa45ea4ea6096ecbd6431","date_created":"2023-07-31T08:44:38Z","date_updated":"2023-07-31T08:44:38Z","file_id":"13328","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity \"breaks\" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms."}],"issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001000325800008"],"arxiv":["2204.01606"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.21468/scipostphys.14.1.006","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":["2542-4653"]},"year":"2023","publication_status":"published","publisher":"SciPost Foundation","department":[{"_id":"MiLe"}],"author":[{"full_name":"Rammelmüller, Lukas","first_name":"Lukas","last_name":"Rammelmüller"},{"full_name":"Huber, David","last_name":"Huber","first_name":"David"},{"last_name":"Čufar","first_name":"Matija","full_name":"Čufar, Matija"},{"full_name":"Brand, Joachim","last_name":"Brand","first_name":"Joachim"},{"full_name":"Hammer, Hans-Werner","last_name":"Hammer","first_name":"Hans-Werner"},{"last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"date_updated":"2023-12-13T11:39:32Z","date_created":"2023-07-24T10:48:23Z","volume":14,"article_number":"006","file_date_updated":"2023-07-31T08:44:38Z"},{"article_number":"034002","date_updated":"2023-12-13T11:40:19Z","date_created":"2023-07-24T09:43:59Z","volume":131,"author":[{"full_name":"Paranjape, Chaitanya S","first_name":"Chaitanya S","last_name":"Paranjape","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yalniz, Gökhan","first_name":"Gökhan","last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","orcid":"0000-0002-8490-9312"},{"full_name":"Duguet, Yohann","first_name":"Yohann","last_name":"Duguet"},{"last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"acknowledgement":"We thank Baofang Song as well as the developers of Channelflow for sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful discussions. This work was supported by a grant from the Simons Foundation (662960, B. H.).","year":"2023","month":"07","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.131.034002","isi":1,"quality_controlled":"1","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"oa":1,"external_id":{"arxiv":["2306.05098"],"isi":["001052929900004"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2306.05098","open_access":"1"}],"abstract":[{"text":"Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Preprint","title":"Direct path from turbulence to time-periodic solutions","status":"public","intvolume":" 131","_id":"13274","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"21","article_processing_charge":"No","keyword":["General Physics and Astronomy"],"date_published":"2023-07-21T00:00:00Z","article_type":"original","publication":"Physical Review Letters","citation":{"mla":"Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters, vol. 131, no. 3, 034002, American Physical Society, 2023, doi:10.1103/physrevlett.131.034002.","short":"C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review Letters 131 (2023).","chicago":"Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur, and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.131.034002.","ama":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 2023;131(3). doi:10.1103/physrevlett.131.034002","ista":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002.","apa":"Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., & Hof, B. (2023). Direct path from turbulence to time-periodic solutions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.131.034002","ieee":"C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct path from turbulence to time-periodic solutions,” Physical Review Letters, vol. 131, no. 3. American Physical Society, 2023."}},{"date_published":"2023-06-29T00:00:00Z","citation":{"short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:10.1126/science.adf5568.","chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adf5568.","ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 2023;380(6652):1357-1362. doi:10.1126/science.adf5568","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adf5568","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” Science, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023.","ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362."},"publication":"Science","page":"1357-1362","article_type":"original","article_processing_charge":"No","day":"29","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13261","intvolume":" 380","title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","status":"public","issue":"6652","abstract":[{"lang":"eng","text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression."}],"type":"journal_article","doi":"10.1126/science.adf5568","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["001106405600028"]},"main_file_link":[{"url":"https://doi.org/10.1126/science.adf5568","open_access":"1"}],"project":[{"grant_number":"343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1095-9203"]},"month":"06","author":[{"orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","first_name":"David","full_name":"Brückner, David"},{"first_name":"Hongtao","last_name":"Chen","full_name":"Chen, Hongtao"},{"last_name":"Barinov","first_name":"Lev","full_name":"Barinov, Lev"},{"last_name":"Zoller","first_name":"Benjamin","full_name":"Zoller, Benjamin"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"}],"volume":380,"date_created":"2023-07-23T22:01:12Z","date_updated":"2023-12-13T11:41:07Z","acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","year":"2023","department":[{"_id":"EdHa"}],"publisher":"American Association for the Advancement of Science","publication_status":"published"},{"type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13336","year":"2023","publisher":"Zenodo","department":[{"_id":"KrCh"}],"title":"kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games","status":"public","ddc":["000"],"related_material":{"record":[{"id":"13258","relation":"used_in_publication","status":"public"}]},"author":[{"id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina","first_name":"Maria","full_name":"Kleshnina, Maria"}],"oa_version":"Published Version","date_created":"2023-07-31T11:30:46Z","date_updated":"2023-12-13T11:42:37Z","article_processing_charge":"No","month":"06","day":"20","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8059564","open_access":"1"}],"citation":{"ama":"Kleshnina M. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. 2023. doi:10.5281/ZENODO.8059564","ieee":"M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games.” Zenodo, 2023.","apa":"Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. Zenodo. https://doi.org/10.5281/ZENODO.8059564","ista":"Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games, Zenodo, 10.5281/ZENODO.8059564.","short":"M. Kleshnina, (2023).","mla":"Kleshnina, Maria. Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games. Zenodo, 2023, doi:10.5281/ZENODO.8059564.","chicago":"Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8059564."},"oa":1,"date_published":"2023-06-20T00:00:00Z","doi":"10.5281/ZENODO.8059564"},{"_id":"13443","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["520"],"status":"public","title":"Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations","intvolume":" 952","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_AstrophysicalJour_Mathur.pdf","creator":"dernst","file_size":4192386,"content_type":"application/pdf","file_id":"13448","relation":"main_file","success":1,"checksum":"f12452834d7ed6748dbf5ace18af4723","date_created":"2023-08-02T07:42:26Z","date_updated":"2023-08-02T07:42:26Z"}],"type":"journal_article","abstract":[{"text":"The ages of solar-like stars have been at the center of many studies such as exoplanet characterization or Galactic-archeology. While ages are usually computed from stellar evolution models, relations linking ages to other stellar properties, such as rotation and magnetic activity, have been investigated. With the large catalog of 55,232 rotation periods, Prot, and photometric magnetic activity index, Sph from Kepler data, we have the opportunity to look for such magneto-gyro-chronology relations. Stellar ages are obtained with two stellar evolution codes that include treatment of angular momentum evolution, hence using Prot as input in addition to classical atmospheric parameters. We explore two different ways of predicting stellar ages on three subsamples with spectroscopic observations: solar analogs, late-F and G dwarfs, and K dwarfs. We first perform a Bayesian analysis to derive relations between Sph and ages between 1 and 5 Gyr, and other stellar properties. For late-F and G dwarfs, and K dwarfs, the multivariate regression favors the model with Prot and Sph with median differences of 0.1% and 0.2%, respectively. We also apply Machine Learning techniques with a Random Forest algorithm to predict ages up to 14 Gyr with the same set of input parameters. For late-F, G and K dwarfs together, predicted ages are on average within 5.3% of the model ages and improve to 3.1% when including Prot. These are very promising results for a quick age estimation for solar-like stars with photometric observations, especially with current and future space missions.","lang":"eng"}],"issue":"2","publication":"The Astrophysical Journal","citation":{"ista":"Mathur S, Claytor ZR, Santos ÂRG, García RA, Amard L, Bugnet LA, Corsaro E, Bonanno A, Breton SN, Godoy-Rivera D, Pinsonneault MH, van Saders J. 2023. Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. 952(2), 131.","ieee":"S. Mathur et al., “Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations,” The Astrophysical Journal, vol. 952, no. 2. American Astronomical Society, 2023.","apa":"Mathur, S., Claytor, Z. R., Santos, Â. R. G., García, R. A., Amard, L., Bugnet, L. A., … van Saders, J. (2023). Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/acd118","ama":"Mathur S, Claytor ZR, Santos ÂRG, et al. Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. 2023;952(2). doi:10.3847/1538-4357/acd118","chicago":"Mathur, Savita, Zachary R. Claytor, Ângela R. G. Santos, Rafael A. García, Louis Amard, Lisa Annabelle Bugnet, Enrico Corsaro, et al. “Magnetic Activity Evolution of Solar-like Stars. I. Sph–Age Relation Derived from Kepler Observations.” The Astrophysical Journal. American Astronomical Society, 2023. https://doi.org/10.3847/1538-4357/acd118.","mla":"Mathur, Savita, et al. “Magnetic Activity Evolution of Solar-like Stars. I. Sph–Age Relation Derived from Kepler Observations.” The Astrophysical Journal, vol. 952, no. 2, 131, American Astronomical Society, 2023, doi:10.3847/1538-4357/acd118.","short":"S. Mathur, Z.R. Claytor, Â.R.G. Santos, R.A. García, L. Amard, L.A. Bugnet, E. Corsaro, A. Bonanno, S.N. Breton, D. Godoy-Rivera, M.H. Pinsonneault, J. van Saders, The Astrophysical Journal 952 (2023)."},"article_type":"original","date_published":"2023-08-01T00:00:00Z","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"day":"01","has_accepted_license":"1","article_processing_charge":"Yes","year":"2023","acknowledgement":"This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is provided by the NASA Science Mission Directorate. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–26555. We acknowledge that this research was supported in part by the National Science Foundation under grant No. NSF PHY-1748958. S.M. acknowledges support from the Spanish Ministry of Science and Innovation (MICINN) with the Ramón y Cajal fellowship No. RYC-2015-17697, the grant No. PID2019-107061GB-C66, and through AEI under the Severo Ochoa Centres of Excellence Programme 2020–2023 (CEX2019-000920-S). S.M. and D.G.R. acknowledge support from the Spanish Ministry of Science and Innovation (MICINN) with the grant No. PID2019-107187GB-I00. Z.R.C. acknowledges support from National Aeronautics and Space Administration via the TESS Guest Investigator Program (grant No. 80NSSC18K18584). The work presented here was partially supported by the NASA grant NNX17AF27G. A.R.G.S. acknowledges the support by FCT through national funds and by FEDER through COMPETE2020 by the following grants: UIDB/04434/2020 and UIDP/04434/2020. A.R.G.S. is supported by FCT through the work contract No. 2020.02480.CEECIND/CP1631/CT0001. R.A.G., L.A., and S.N.B. acknowledge the support from PLATO and GOLF CNES grants. S.N.B. acknowledges support from PLATO ASI-INAF agreement No. 2015-019-R.1-2018.","publication_status":"published","department":[{"_id":"LiBu"}],"publisher":"American Astronomical Society","author":[{"full_name":"Mathur, Savita","first_name":"Savita","last_name":"Mathur"},{"last_name":"Claytor","first_name":"Zachary R.","full_name":"Claytor, Zachary R."},{"full_name":"Santos, Ângela R. G.","last_name":"Santos","first_name":"Ângela R. G."},{"full_name":"García, Rafael A.","first_name":"Rafael A.","last_name":"García"},{"first_name":"Louis","last_name":"Amard","full_name":"Amard, Louis"},{"full_name":"Bugnet, Lisa Annabelle","first_name":"Lisa Annabelle","last_name":"Bugnet","id":"d9edb345-f866-11ec-9b37-d119b5234501","orcid":"0000-0003-0142-4000"},{"last_name":"Corsaro","first_name":"Enrico","full_name":"Corsaro, Enrico"},{"last_name":"Bonanno","first_name":"Alfio","full_name":"Bonanno, Alfio"},{"first_name":"Sylvain N.","last_name":"Breton","full_name":"Breton, Sylvain N."},{"first_name":"Diego","last_name":"Godoy-Rivera","full_name":"Godoy-Rivera, Diego"},{"full_name":"Pinsonneault, Marc H.","last_name":"Pinsonneault","first_name":"Marc H."},{"full_name":"van Saders, Jennifer","last_name":"van Saders","first_name":"Jennifer"}],"date_updated":"2023-12-13T12:00:15Z","date_created":"2023-08-01T14:19:16Z","volume":952,"article_number":"131","file_date_updated":"2023-08-02T07:42:26Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001034185700001"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.3847/1538-4357/acd118","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]}},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"07","citation":{"ama":"Ogura N, Sasagawa Y, Ito T, et al. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. 2023;9(27):eadg6983. doi:10.1126/sciadv.adg6983","ieee":"N. Ogura et al., “WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus,” Science Advances, vol. 9, no. 27. American Association for the Advancement of Science, p. eadg6983, 2023.","apa":"Ogura, N., Sasagawa, Y., Ito, T., Tameshige, T., Kawai, S., Sano, M., … Ikeuchi, M. (2023). WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adg6983","ista":"Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A, Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. 2023. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. 9(27), eadg6983.","short":"N. Ogura, Y. Sasagawa, T. Ito, T. Tameshige, S. Kawai, M. Sano, Y. Doll, A. Iwase, A. Kawamura, T. Suzuki, I. Nikaido, K. Sugimoto, M. Ikeuchi, Science Advances 9 (2023) eadg6983.","mla":"Ogura, Nao, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” Science Advances, vol. 9, no. 27, American Association for the Advancement of Science, 2023, p. eadg6983, doi:10.1126/sciadv.adg6983.","chicago":"Ogura, Nao, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai, Masaki Sano, Yuki Doll, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg6983."},"publication":"Science Advances","page":"eadg6983","article_type":"original","date_published":"2023-07-07T00:00:00Z","type":"journal_article","issue":"27","abstract":[{"text":"Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency.","lang":"eng"}],"_id":"13259","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","ddc":["580"],"status":"public","title":"WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus","oa_version":"Published Version","file":[{"file_size":1759993,"content_type":"application/pdf","creator":"dernst","file_name":"2023_ScienceAdvance_Ogura.pdf","access_level":"open_access","date_updated":"2023-08-01T06:40:35Z","date_created":"2023-08-01T06:40:35Z","checksum":"f59217e1083767777318b5d0cc5e141d","success":1,"relation":"main_file","file_id":"13338"}],"publication_identifier":{"eissn":["2375-2548"]},"month":"07","external_id":{"pmid":["37418524"],"isi":["001030983100012"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1126/sciadv.adg6983","language":[{"iso":"eng"}],"file_date_updated":"2023-08-01T06:40:35Z","pmid":1,"year":"2023","acknowledgement":"Wethank Y.Iwayama, K.Ohtawa, K.Fukumoto,andN. Mataga (RIKENRRD) for technical assistance in Quartz-Seq2analyses; M. Mouri(RIKENCSRS)for technical support with plasmid construction and transactivation assay; Y. Ikeda (NAIST) for technical support with tissue culture; and A. Furuta for technical support in bulk RNA-seq analysis. We also thank the Single-cell Omics Laboratory for technical consultation in scRNA-seq analyses, the members of the Laboratory for Bioinformatics Research at the RIKEN Center for Biosystems Dynamics Research, and A. Matsushima and T. Ichikawa for IT infrastructure management. This work was supported by JSPS KAKENHI(17K15146,19H05670,20K06712,20H04894,20H05431,and 22H04713 to M.I. and 20H03284 and 20H05911 to K.S.), by the JST FOREST Program (JPMJFR214H to M.I.), by The Naito Foundation to M.I.; by Takeda Science Foundation to M.I,and by the Shiseido Female Researcher Science Grant to M.I. This work was partially supported by RIKENE pigenome Control Program, Medical Research Center Initiative for High Depth Omics, and JST CREST(JPMJCR16G3and JPMJCR1926)to I.N.","publisher":"American Association for the Advancement of Science","publication_status":"published","author":[{"first_name":"Nao","last_name":"Ogura","full_name":"Ogura, Nao"},{"last_name":"Sasagawa","first_name":"Yohei","full_name":"Sasagawa, Yohei"},{"last_name":"Ito","first_name":"Tasuku","orcid":"0000-0002-2482-9089","id":"d5a17a4a-e534-11eb-93ec-91fa2aa9bd57","full_name":"Ito, Tasuku"},{"full_name":"Tameshige, Toshiaki","first_name":"Toshiaki","last_name":"Tameshige"},{"first_name":"Satomi","last_name":"Kawai","full_name":"Kawai, Satomi"},{"last_name":"Sano","first_name":"Masaki","full_name":"Sano, Masaki"},{"last_name":"Doll","first_name":"Yuki","full_name":"Doll, Yuki"},{"last_name":"Iwase","first_name":"Akira","full_name":"Iwase, Akira"},{"full_name":"Kawamura, Ayako","last_name":"Kawamura","first_name":"Ayako"},{"full_name":"Suzuki, Takamasa","first_name":"Takamasa","last_name":"Suzuki"},{"first_name":"Itoshi","last_name":"Nikaido","full_name":"Nikaido, Itoshi"},{"full_name":"Sugimoto, Keiko","first_name":"Keiko","last_name":"Sugimoto"},{"full_name":"Ikeuchi, Momoko","first_name":"Momoko","last_name":"Ikeuchi"}],"volume":9,"date_updated":"2023-12-13T11:59:29Z","date_created":"2023-07-23T22:01:11Z"},{"date_published":"2023-07-27T00:00:00Z","publication":"GigaScience","citation":{"chicago":"Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova, Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience. Oxford Academic, 2023. https://doi.org/10.1093/gigascience/giad045.","short":"W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko, M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro, V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero, J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023).","mla":"Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience, vol. 12, Oxford Academic, 2023, doi:10.1093/gigascience/giad045.","ieee":"W. Wolfsberger et al., “Scientists without borders: Lessons from Ukraine,” GigaScience, vol. 12. Oxford Academic, 2023.","apa":"Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko, O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine. GigaScience. Oxford Academic. https://doi.org/10.1093/gigascience/giad045","ista":"Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience. 12.","ama":"Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders: Lessons from Ukraine. GigaScience. 2023;12. doi:10.1093/gigascience/giad045"},"article_type":"original","day":"27","article_processing_charge":"Yes","scopus_import":"1","oa_version":"Published Version","_id":"13976","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Scientists without borders: Lessons from Ukraine","status":"public","intvolume":" 12","abstract":[{"lang":"eng","text":"Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades’ worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery."}],"type":"journal_article","doi":"10.1093/gigascience/giad045","language":[{"iso":"eng"}],"external_id":{"isi":["001081086100001"],"pmid":["37496156"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/gigascience/giad045"}],"isi":1,"quality_controlled":"1","month":"07","publication_identifier":{"eissn":["2047-217X"]},"author":[{"full_name":"Wolfsberger, Walter","last_name":"Wolfsberger","first_name":"Walter"},{"last_name":"Chhugani","first_name":"Karishma","full_name":"Chhugani, Karishma"},{"first_name":"Khrystyna","last_name":"Shchubelka","full_name":"Shchubelka, Khrystyna"},{"last_name":"Frolova","first_name":"Alina","full_name":"Frolova, Alina"},{"full_name":"Salyha, Yuriy","first_name":"Yuriy","last_name":"Salyha"},{"full_name":"Zlenko, Oksana","first_name":"Oksana","last_name":"Zlenko"},{"full_name":"Arych, Mykhailo","last_name":"Arych","first_name":"Mykhailo"},{"first_name":"Dmytro","last_name":"Dziuba","full_name":"Dziuba, Dmytro"},{"last_name":"Parkhomenko","first_name":"Andrii","full_name":"Parkhomenko, Andrii"},{"full_name":"Smolanka, Volodymyr","last_name":"Smolanka","first_name":"Volodymyr"},{"first_name":"Zeynep H.","last_name":"Gümüş","full_name":"Gümüş, Zeynep H."},{"full_name":"Sezgin, Efe","first_name":"Efe","last_name":"Sezgin"},{"last_name":"Diaz-Lameiro","first_name":"Alondra","full_name":"Diaz-Lameiro, Alondra"},{"full_name":"Toth, Viktor R.","first_name":"Viktor R.","last_name":"Toth"},{"full_name":"Maci, Megi","last_name":"Maci","first_name":"Megi"},{"full_name":"Bortz, Eric","last_name":"Bortz","first_name":"Eric"},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Morton, Patricia M.","last_name":"Morton","first_name":"Patricia M."},{"last_name":"Łabaj","first_name":"Paweł P.","full_name":"Łabaj, Paweł P."},{"first_name":"Veronika","last_name":"Romero","full_name":"Romero, Veronika"},{"first_name":"Jakub","last_name":"Hlávka","full_name":"Hlávka, Jakub"},{"full_name":"Mangul, Serghei","last_name":"Mangul","first_name":"Serghei"},{"full_name":"Oleksyk, Taras K.","last_name":"Oleksyk","first_name":"Taras K."}],"date_updated":"2023-12-13T12:01:46Z","date_created":"2023-08-06T22:01:13Z","volume":12,"year":"2023","acknowledgement":"Our article is dedicated to all freedom-loving people around the world and to the people of Ukraine who fight for our freedom. Special thanks to Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful review, valuable criticism, and useful suggestions while preparing this manuscript, and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered their time. No funding supported work on this article.","pmid":1,"publication_status":"epub_ahead","publisher":"Oxford Academic","department":[{"_id":"FyKo"}]},{"type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We construct families of log K3 surfaces and study the arithmetic of their members. We use this to produce explicit surfaces with an order 5 Brauer–Manin obstruction to the integral Hasse principle."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13973","intvolume":" 73","status":"public","ddc":["510"],"title":"Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1529821,"file_name":"2023_AnnalesFourier_Lyczak.pdf","access_level":"open_access","date_created":"2023-08-07T07:19:42Z","date_updated":"2023-08-07T07:19:42Z","success":1,"checksum":"daf53fc614c894422e4c0fb3d2a2ae3e","file_id":"13977","relation":"main_file"}],"scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"12","citation":{"ieee":"J. Lyczak, “Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces,” Annales de l’Institut Fourier, vol. 73, no. 2. Association des Annales de l’Institut Fourier, pp. 447–478, 2023.","apa":"Lyczak, J. (2023). Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. Association des Annales de l’Institut Fourier. https://doi.org/10.5802/aif.3529","ista":"Lyczak J. 2023. Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. 73(2), 447–478.","ama":"Lyczak J. Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. 2023;73(2):447-478. doi:10.5802/aif.3529","chicago":"Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle on Log K3 Surfaces.” Annales de l’Institut Fourier. Association des Annales de l’Institut Fourier, 2023. https://doi.org/10.5802/aif.3529.","short":"J. Lyczak, Annales de l’Institut Fourier 73 (2023) 447–478.","mla":"Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle on Log K3 Surfaces.” Annales de l’Institut Fourier, vol. 73, no. 2, Association des Annales de l’Institut Fourier, 2023, pp. 447–78, doi:10.5802/aif.3529."},"publication":"Annales de l'Institut Fourier","page":"447-478","article_type":"original","date_published":"2023-05-12T00:00:00Z","ec_funded":1,"file_date_updated":"2023-08-07T07:19:42Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","acknowledgement":"This paper was completed as part of a project which received funding from the\r\nEuropean Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie grant agreement No. 754411.","year":"2023","publisher":"Association des Annales de l'Institut Fourier","department":[{"_id":"TiBr"}],"publication_status":"published","author":[{"full_name":"Lyczak, Julian","id":"3572849A-F248-11E8-B48F-1D18A9856A87","first_name":"Julian","last_name":"Lyczak"}],"volume":73,"date_created":"2023-08-06T22:01:12Z","date_updated":"2023-12-13T12:03:04Z","publication_identifier":{"issn":["0373-0956"]},"month":"05","oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"external_id":{"isi":["001000279500001"],"arxiv":["2005.14013"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"doi":"10.5802/aif.3529","language":[{"iso":"eng"}]},{"doi":"10.1007/s00454-023-00532-x","language":[{"iso":"eng"}],"external_id":{"isi":["001038546500001"],"arxiv":["1812.04911"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1812.04911"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"month":"07","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"},{"full_name":"Gärtner, Bernd","first_name":"Bernd","last_name":"Gärtner"},{"first_name":"Andrey","last_name":"Kupavskii","full_name":"Kupavskii, Andrey"},{"full_name":"Valtr, Pavel","last_name":"Valtr","first_name":"Pavel"},{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"related_material":{"record":[{"id":"6647","status":"public","relation":"earlier_version"}]},"date_created":"2023-08-06T22:01:12Z","date_updated":"2023-12-13T12:03:35Z","acknowledgement":"Part of the research leading to this paper was done during the 16th Gremo Workshop on Open Problems (GWOP), Waltensburg, Switzerland, June 12–16, 2018. We thank Patrick Schnider for suggesting the problem, and Stefan Felsner, Malte Milatz, and Emo Welzl for fruitful discussions during the workshop. We also thank Stefan Felsner and Manfred Scheucher for finding, communicating the example from Sect. 3.3, and the kind permission to include their visualization of the point set. We thank Dömötör Pálvölgyi, the SoCG reviewers, and DCG reviewers for various helpful comments.\r\nR. Fulek gratefully acknowledges support from Austrian Science Fund (FWF), Project M2281-N35. A. Kupavskii was supported by the Advanced Postdoc.Mobility Grant no. P300P2_177839 of the Swiss National Science Foundation. Research by P. Valtr was supported by the Grant no. 18-19158 S of the Czech Science Foundation (GAČR).","year":"2023","publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"date_published":"2023-07-27T00:00:00Z","publication":"Discrete and Computational Geometry","citation":{"ama":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. Discrete and Computational Geometry. 2023. doi:10.1007/s00454-023-00532-x","ista":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2023. The crossing Tverberg theorem. Discrete and Computational Geometry.","ieee":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” Discrete and Computational Geometry. Springer Nature, 2023.","apa":"Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2023). The crossing Tverberg theorem. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00532-x","mla":"Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” Discrete and Computational Geometry, Springer Nature, 2023, doi:10.1007/s00454-023-00532-x.","short":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, Discrete and Computational Geometry (2023).","chicago":"Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00532-x."},"article_type":"original","day":"27","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"13974","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The crossing Tverberg theorem","status":"public","abstract":[{"text":"The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r−1)+1 points in Rd, one can find a partition X=X1∪⋯∪Xr of X, such that the convex hulls of the Xi, i=1,…,r, all share a common point. In this paper, we prove a trengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span ⌊n/3⌋ vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Álvarez-Rebollar et al. guarantees ⌊n/6⌋pairwise crossing triangles. Our result generalizes to a result about simplices in Rd, d≥2.","lang":"eng"}],"type":"journal_article"},{"oa_version":"Published Version","ddc":["510"],"status":"public","title":"Spectrum of Lévy–Khintchine random laplacian matrices","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13975","abstract":[{"lang":"eng","text":"We consider the spectrum of random Laplacian matrices of the form Ln=An−Dn where An\r\n is a real symmetric random matrix and Dn is a diagonal matrix whose entries are equal to the corresponding row sums of An. If An is a Wigner matrix with entries in the domain of attraction of a Gaussian distribution, the empirical spectral measure of Ln is known to converge to the free convolution of a semicircle distribution and a standard real Gaussian distribution. We consider real symmetric random matrices An with independent entries (up to symmetry) whose row sums converge to a purely non-Gaussian infinitely divisible distribution, which fall into the class of Lévy–Khintchine random matrices first introduced by Jung [Trans Am Math Soc, 370, (2018)]. Our main result shows that the empirical spectral measure of Ln converges almost surely to a deterministic limit. A key step in the proof is to use the purely non-Gaussian nature of the row sums to build a random operator to which Ln converges in an appropriate sense. This operator leads to a recursive distributional equation uniquely describing the Stieltjes transform of the limiting empirical spectral measure."}],"type":"journal_article","date_published":"2023-07-26T00:00:00Z","article_type":"original","publication":"Journal of Theoretical Probability","citation":{"mla":"Campbell, Andrew J., and Sean O’Rourke. “Spectrum of Lévy–Khintchine Random Laplacian Matrices.” Journal of Theoretical Probability, Springer Nature, 2023, doi:10.1007/s10959-023-01275-4.","short":"A.J. Campbell, S. O’Rourke, Journal of Theoretical Probability (2023).","chicago":"Campbell, Andrew J, and Sean O’Rourke. “Spectrum of Lévy–Khintchine Random Laplacian Matrices.” Journal of Theoretical Probability. Springer Nature, 2023. https://doi.org/10.1007/s10959-023-01275-4.","ama":"Campbell AJ, O’Rourke S. Spectrum of Lévy–Khintchine random laplacian matrices. Journal of Theoretical Probability. 2023. doi:10.1007/s10959-023-01275-4","ista":"Campbell AJ, O’Rourke S. 2023. Spectrum of Lévy–Khintchine random laplacian matrices. Journal of Theoretical Probability.","apa":"Campbell, A. J., & O’Rourke, S. (2023). Spectrum of Lévy–Khintchine random laplacian matrices. Journal of Theoretical Probability. Springer Nature. https://doi.org/10.1007/s10959-023-01275-4","ieee":"A. J. Campbell and S. O’Rourke, “Spectrum of Lévy–Khintchine random laplacian matrices,” Journal of Theoretical Probability. Springer Nature, 2023."},"day":"26","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_created":"2023-08-06T22:01:13Z","date_updated":"2023-12-13T12:00:50Z","author":[{"full_name":"Campbell, Andrew J","id":"582b06a9-1f1c-11ee-b076-82ffce00dde4","last_name":"Campbell","first_name":"Andrew J"},{"first_name":"Sean","last_name":"O’Rourke","full_name":"O’Rourke, Sean"}],"publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"LaEr"}],"year":"2023","acknowledgement":"The first author thanks Yizhe Zhu for pointing out reference [30]. We thank David Renfrew for comments on an earlier draft. We thank the anonymous referee for a careful reading and helpful comments.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","language":[{"iso":"eng"}],"doi":"10.1007/s10959-023-01275-4","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s10959-023-01275-4","open_access":"1"}],"external_id":{"isi":["001038341000001"],"arxiv":["2210.07927"]},"month":"07","publication_identifier":{"issn":["0894-9840"],"eissn":["1572-9230"]}},{"oa_version":"Preprint","status":"public","title":"Magnetotropic susceptibility","intvolume":" 108","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13257","abstract":[{"text":"The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2023-07-15T00:00:00Z","article_type":"original","publication":"Physical Review B","citation":{"ama":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility. Physical Review B. 2023;108(3). doi:10.1103/PhysRevB.108.035111","apa":"Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., & Modic, K. A. (2023). Magnetotropic susceptibility. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.035111","ieee":"A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic susceptibility,” Physical Review B, vol. 108, no. 3. American Physical Society, 2023.","ista":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility. Physical Review B. 108(3), 035111.","short":"A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108 (2023).","mla":"Shekhter, A., et al. “Magnetotropic Susceptibility.” Physical Review B, vol. 108, no. 3, 035111, American Physical Society, 2023, doi:10.1103/PhysRevB.108.035111.","chicago":"Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic Susceptibility.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.035111."},"day":"15","article_processing_charge":"No","scopus_import":"1","date_created":"2023-07-23T22:01:10Z","date_updated":"2023-12-13T11:58:57Z","volume":108,"author":[{"last_name":"Shekhter","first_name":"A.","full_name":"Shekhter, A."},{"last_name":"Mcdonald","first_name":"R. D.","full_name":"Mcdonald, R. D."},{"first_name":"B. J.","last_name":"Ramshaw","full_name":"Ramshaw, B. J."},{"full_name":"Modic, Kimberly A","first_name":"Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","orcid":"0000-0001-9760-3147"}],"publication_status":"published","department":[{"_id":"KiMo"}],"publisher":"American Physical Society","year":"2023","acknowledgement":"We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating discussions. The work at the Los Alamos National Laboratory is supported by National Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National Science Foundation under Grant No.\r\nDMR-1752784.","article_number":"035111","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.108.035111","quality_controlled":"1","isi":1,"external_id":{"isi":["001062708600002"],"arxiv":["2208.10038"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.10038"}],"oa":1,"month":"07","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]}},{"article_number":"e202300683","date_created":"2023-08-06T22:01:12Z","date_updated":"2023-12-13T12:02:26Z","author":[{"first_name":"Line","last_name":"Næsborg","full_name":"Næsborg, Line"},{"full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","last_name":"Pieber","first_name":"Bartholomäus"},{"first_name":"Oliver S.","last_name":"Wenger","full_name":"Wenger, Oliver S."}],"publication_status":"epub_ahead","department":[{"_id":"BaPi"}],"publisher":"Wiley","year":"2023","month":"07","publication_identifier":{"eissn":["1867-3899"],"issn":["1867-3880"]},"language":[{"iso":"eng"}],"doi":"10.1002/cctc.202300683","isi":1,"quality_controlled":"1","external_id":{"isi":["001037859900001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/cctc.202300683"}],"oa":1,"abstract":[{"lang":"eng","text":"This Special Collection is dedicated to the field of photocatalytic synthesis and contains a diverse selection of original research contributions. It includes studies on catalyst development, mechanistic investigations, method development and the use of enabling technologies, illustrating the many facets of state-of-the-art research in photocatalytic synthesis. Further, emerging topics are surveyed and discussed in three reviews and a concept article."}],"type":"journal_article","oa_version":"Published Version","status":"public","title":"Special Collection: Photocatalytic synthesis","_id":"13972","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"27","article_processing_charge":"No","scopus_import":"1","date_published":"2023-07-27T00:00:00Z","article_type":"letter_note","publication":"ChemCatChem","citation":{"mla":"Næsborg, Line, et al. “Special Collection: Photocatalytic Synthesis.” ChemCatChem, e202300683, Wiley, 2023, doi:10.1002/cctc.202300683.","short":"L. Næsborg, B. Pieber, O.S. Wenger, ChemCatChem (2023).","chicago":"Næsborg, Line, Bartholomäus Pieber, and Oliver S. Wenger. “Special Collection: Photocatalytic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202300683.","ama":"Næsborg L, Pieber B, Wenger OS. Special Collection: Photocatalytic synthesis. ChemCatChem. 2023. doi:10.1002/cctc.202300683","ista":"Næsborg L, Pieber B, Wenger OS. 2023. Special Collection: Photocatalytic synthesis. ChemCatChem., e202300683.","ieee":"L. Næsborg, B. Pieber, and O. S. Wenger, “Special Collection: Photocatalytic synthesis,” ChemCatChem. Wiley, 2023.","apa":"Næsborg, L., Pieber, B., & Wenger, O. S. (2023). Special Collection: Photocatalytic synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202300683"}},{"publication_identifier":{"eissn":["2296-424X"]},"month":"07","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001038636400001"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.3389/fphy.2023.1202132","article_number":"1202132","file_date_updated":"2023-08-07T07:48:11Z","publisher":"Frontiers","department":[{"_id":"MaIb"}],"publication_status":"published","year":"2023","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863–BORGES. We further thank the office of the Federal Government of Lower Austria, K3-Group–Culture, Science and Education, for their financial support as part of the project “Responsive Wound Dressing”. We gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 888067).\r\nWe thank the Electron Microscopy Facility at IST Austria for their support with sputter coating the FO tips and Bernhard Pichler from AIT for software development to facilitate data evaluation.","volume":11,"date_updated":"2023-12-13T12:04:10Z","date_created":"2023-08-06T22:01:11Z","author":[{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"first_name":"Marie Helene","last_name":"Steger-Polt","full_name":"Steger-Polt, Marie Helene"},{"full_name":"Reiner-Rozman, Ciril","first_name":"Ciril","last_name":"Reiner-Rozman"},{"first_name":"Stefan","last_name":"Fossati","full_name":"Fossati, Stefan"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","first_name":"Seungho","last_name":"Lee","full_name":"Lee, Seungho"},{"full_name":"Aspermair, Patrik","first_name":"Patrik","last_name":"Aspermair"},{"full_name":"Kleber, Christoph","last_name":"Kleber","first_name":"Christoph"},{"full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"full_name":"Dostalek, Jakub","first_name":"Jakub","last_name":"Dostalek"},{"last_name":"Knoll","first_name":"Wolfgang","full_name":"Knoll, Wolfgang"}],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"14","article_type":"original","citation":{"ama":"Hasler R, Steger-Polt MH, Reiner-Rozman C, et al. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. 2023;11. doi:10.3389/fphy.2023.1202132","ista":"Hasler R, Steger-Polt MH, Reiner-Rozman C, Fossati S, Lee S, Aspermair P, Kleber C, Ibáñez M, Dostalek J, Knoll W. 2023. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. 11, 1202132.","apa":"Hasler, R., Steger-Polt, M. H., Reiner-Rozman, C., Fossati, S., Lee, S., Aspermair, P., … Knoll, W. (2023). Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. Frontiers. https://doi.org/10.3389/fphy.2023.1202132","ieee":"R. Hasler et al., “Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing,” Frontiers in Physics, vol. 11. Frontiers, 2023.","mla":"Hasler, Roger, et al. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” Frontiers in Physics, vol. 11, 1202132, Frontiers, 2023, doi:10.3389/fphy.2023.1202132.","short":"R. Hasler, M.H. Steger-Polt, C. Reiner-Rozman, S. Fossati, S. Lee, P. Aspermair, C. Kleber, M. Ibáñez, J. Dostalek, W. Knoll, Frontiers in Physics 11 (2023).","chicago":"Hasler, Roger, Marie Helene Steger-Polt, Ciril Reiner-Rozman, Stefan Fossati, Seungho Lee, Patrik Aspermair, Christoph Kleber, Maria Ibáñez, Jakub Dostalek, and Wolfgang Knoll. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” Frontiers in Physics. Frontiers, 2023. https://doi.org/10.3389/fphy.2023.1202132."},"publication":"Frontiers in Physics","date_published":"2023-07-14T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The use of multimodal readout mechanisms next to label-free real-time monitoring of biomolecular interactions can provide valuable insight into surface-based reaction mechanisms. To this end, the combination of an electrolyte-gated field-effect transistor (EG-FET) with a fiber optic-coupled surface plasmon resonance (FO-SPR) probe serving as gate electrode has been investigated to deconvolute surface mass and charge density variations associated to surface reactions. However, applying an electrochemical potential on such gold-coated FO-SPR gate electrodes can induce gradual morphological changes of the thin gold film, leading to an irreversible blue-shift of the SPR wavelength and a substantial signal drift. We show that mild annealing leads to optical and electronic signal stabilization (20-fold lower signal drift than as-sputtered fiber optic gates) and improved overall analytical performance characteristics. The thermal treatment prevents morphological changes of the thin gold-film occurring during operation, hence providing reliable and stable data immediately upon gate voltage application. Thus, the readout output of both transducing principles, the optical FO-SPR and electronic EG-FET, stays constant throughout the whole sensing time-window and the long-term effect of thermal treatment is also improved, providing stable signals even after 1 year of storage. Annealing should therefore be considered a necessary modification for applying fiber optic gate electrodes in real-time multimodal investigations of surface reactions at the solid-liquid interface."}],"intvolume":" 11","ddc":["530"],"status":"public","title":"Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing","_id":"13968","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"2023_FrontiersPhysics_Hasler.pdf","file_size":2421758,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"13978","checksum":"fb36dda665e57bab006a000bf0faacd5","success":1,"date_created":"2023-08-07T07:48:11Z","date_updated":"2023-08-07T07:48:11Z"}],"oa_version":"Published Version"},{"issue":"3","abstract":[{"text":"Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"14046","checksum":"c549cd8f0dd02ed60477a05ca045f481","success":1,"date_created":"2023-08-14T07:24:17Z","date_updated":"2023-08-14T07:24:17Z","access_level":"open_access","file_name":"2023_JourMathFluidMech_Bulicek.pdf","file_size":845748,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","intvolume":" 25","status":"public","title":"On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14042","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2023-08-01T00:00:00Z","article_type":"original","citation":{"ama":"Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 2023;25(3). doi:10.1007/s00021-023-00803-w","ieee":"M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary,” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3. Springer Nature, 2023.","apa":"Bulíček, M., Málek, J., & Maringová, E. (2023). On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. Springer Nature. https://doi.org/10.1007/s00021-023-00803-w","ista":"Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72.","short":"M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics 25 (2023).","mla":"Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3, 72, Springer Nature, 2023, doi:10.1007/s00021-023-00803-w.","chicago":"Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics. Springer Nature, 2023. https://doi.org/10.1007/s00021-023-00803-w."},"publication":"Journal of Mathematical Fluid Mechanics","file_date_updated":"2023-08-14T07:24:17Z","article_number":"72","volume":25,"date_updated":"2023-12-13T12:08:08Z","date_created":"2023-08-13T22:01:13Z","author":[{"first_name":"Miroslav","last_name":"Bulíček","full_name":"Bulíček, Miroslav"},{"last_name":"Málek","first_name":"Josef","full_name":"Málek, Josef"},{"full_name":"Maringová, Erika","first_name":"Erika","last_name":"Maringová","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4"}],"publisher":"Springer Nature","department":[{"_id":"JuFi"}],"publication_status":"published","acknowledgement":"M. Bulíček and J. Málek acknowledge the support of the project No. 20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing supported by the National Technical Library in Prague.","year":"2023","publication_identifier":{"eissn":["1422-6952"],"issn":["1422-6928"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1007/s00021-023-00803-w","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2301.12834"],"isi":["001040354900001"]}},{"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001042544100001"],"pmid":["37542157"]},"language":[{"iso":"eng"}],"doi":"10.1038/s42003-023-05181-7","month":"08","publication_identifier":{"eissn":["2399-3642"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"CaHe"},{"_id":"Bio"}],"year":"2023","acknowledgement":"We thank Marton Gulyas (ELTE Eötvös University) for development of videomicroscopy experiment manager and image analysis software. Authors are grateful to Gabor Forgacs (University of Missouri) for critical reading of earlier versions of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University) for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project No 227878 to TV, the National Research Development and Innovation Fund of Hungary, K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access funding provided by Eötvös Loránd University.","pmid":1,"date_updated":"2023-12-13T12:07:33Z","date_created":"2023-08-13T22:01:13Z","volume":6,"author":[{"first_name":"Elod","last_name":"Méhes","full_name":"Méhes, Elod"},{"full_name":"Mones, Enys","last_name":"Mones","first_name":"Enys"},{"first_name":"Máté","last_name":"Varga","full_name":"Varga, Máté"},{"full_name":"Zsigmond, Áron","first_name":"Áron","last_name":"Zsigmond"},{"last_name":"Biri-Kovács","first_name":"Beáta","full_name":"Biri-Kovács, Beáta"},{"full_name":"Nyitray, László","first_name":"László","last_name":"Nyitray"},{"first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa"},{"first_name":"Gabriel","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Vicsek, Tamás","last_name":"Vicsek","first_name":"Tamás"}],"article_number":"817","file_date_updated":"2023-08-14T07:17:36Z","article_type":"original","publication":"Communications Biology","citation":{"chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology. Springer Nature, 2023. https://doi.org/10.1038/s42003-023-05181-7.","mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology, vol. 6, 817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7.","short":"E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).","ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817.","ieee":"E. Méhes et al., “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” Communications Biology, vol. 6. Springer Nature, 2023.","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-023-05181-7","ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 2023;6. doi:10.1038/s42003-023-05181-7"},"date_published":"2023-08-04T00:00:00Z","scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"Yes","title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","status":"public","ddc":["570"],"intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14041","file":[{"file_id":"14045","relation":"main_file","date_updated":"2023-08-14T07:17:36Z","date_created":"2023-08-14T07:17:36Z","success":1,"checksum":"1f9324f736bdbb76426b07736651c4cd","file_name":"2023_CommBiology_Mehes.pdf","access_level":"open_access","creator":"dernst","file_size":10181997,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering.","lang":"eng"}]},{"_id":"14039","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"The membrane surface as a platform that organizes cellular and biochemical processes","intvolume":" 58","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14049","date_updated":"2023-08-14T07:57:55Z","date_created":"2023-08-14T07:57:55Z","checksum":"d8c5dc97cd40c26da2ec98ae723ab368","success":1,"file_name":"2023_DevelopmentalCell_Leonard.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3184217,"creator":"dernst"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them."}],"issue":"15","publication":"Developmental Cell","citation":{"ama":"Leonard TA, Loose M, Martens S. The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. 2023;58(15):1315-1332. doi:10.1016/j.devcel.2023.06.001","ista":"Leonard TA, Loose M, Martens S. 2023. The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. 58(15), 1315–1332.","ieee":"T. A. Leonard, M. Loose, and S. Martens, “The membrane surface as a platform that organizes cellular and biochemical processes,” Developmental Cell, vol. 58, no. 15. Elsevier, pp. 1315–1332, 2023.","apa":"Leonard, T. A., Loose, M., & Martens, S. (2023). The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.001","mla":"Leonard, Thomas A., et al. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” Developmental Cell, vol. 58, no. 15, Elsevier, 2023, pp. 1315–32, doi:10.1016/j.devcel.2023.06.001.","short":"T.A. Leonard, M. Loose, S. Martens, Developmental Cell 58 (2023) 1315–1332.","chicago":"Leonard, Thomas A., Martin Loose, and Sascha Martens. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.001."},"article_type":"original","page":"1315-1332","date_published":"2023-08-07T00:00:00Z","scopus_import":"1","day":"07","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","year":"2023","acknowledgement":"We acknowledge funding from the Austrian Science Fund (FWF F79, P32814-B, and P35061-B to S.M.; P34607-B to M.L.; and P30584-B and P33066-B to T.A.L.) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 101045340 to M.L.). We are grateful for comments on the manuscript by Justyna Sawa-Makarska, Verena Baumann, Marko Kojic, Philipp Radler, Ronja Reinhardt, and Sumire Antonioli.","pmid":1,"publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Elsevier","author":[{"first_name":"Thomas A.","last_name":"Leonard","full_name":"Leonard, Thomas A."},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"},{"last_name":"Martens","first_name":"Sascha","full_name":"Martens, Sascha"}],"date_updated":"2023-12-13T12:09:20Z","date_created":"2023-08-13T22:01:12Z","volume":58,"file_date_updated":"2023-08-14T07:57:55Z","external_id":{"isi":["001059110400001"],"pmid":["37419118"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"},{"name":"Synthetic and structural biology of Rab GTPase networks","grant_number":"101045340","_id":"bd6ae2ca-d553-11ed-ba76-a4aa239da5ee"}],"doi":"10.1016/j.devcel.2023.06.001","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]}},{"file":[{"creator":"dernst","content_type":"application/pdf","file_size":2315325,"file_name":"2023_NatureComm_Zhao.pdf","access_level":"open_access","date_updated":"2023-08-14T07:01:12Z","date_created":"2023-08-14T07:01:12Z","success":1,"checksum":"3b9043df3d51c300f9be95eac3ff9d0b","file_id":"14044","relation":"main_file"}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","intvolume":" 14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14040","abstract":[{"text":"Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.","lang":"eng"}],"type":"journal_article","date_published":"2023-08-04T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ama":"Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6","apa":"Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6","ieee":"Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature Communications, vol. 14. Springer Nature, 2023.","ista":"Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 14, 4681.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).","mla":"Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications, vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6.","chicago":"Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6."},"day":"04","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_created":"2023-08-13T22:01:13Z","date_updated":"2023-12-13T12:06:56Z","volume":14,"author":[{"first_name":"Ziyu","last_name":"Zhao","full_name":"Zhao, Ziyu"},{"full_name":"Vercellino, Irene","orcid":"0000-0001-5618-3449","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","last_name":"Vercellino","first_name":"Irene"},{"full_name":"Knoppová, Jana","last_name":"Knoppová","first_name":"Jana"},{"first_name":"Roman","last_name":"Sobotka","full_name":"Sobotka, Roman"},{"full_name":"Murray, James W.","first_name":"James W.","last_name":"Murray"},{"first_name":"Peter J.","last_name":"Nixon","full_name":"Nixon, Peter J."},{"first_name":"Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"},{"last_name":"Komenda","first_name":"Josef","full_name":"Komenda, Josef"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"LeSa"}],"acknowledgement":"P.J.N. and J.W.M. are grateful for the support of the Biotechnology & Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J. Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project 19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster.","year":"2023","file_date_updated":"2023-08-14T07:01:12Z","article_number":"4681","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-40388-6","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001042606700004"]},"month":"08","publication_identifier":{"eissn":["2041-1723"]}},{"date_published":"2023-07-01T00:00:00Z","citation":{"ama":"Kretinsky J, Meggendorfer T, Weininger M. Stopping criteria for value iteration on stochastic games with quantitative objectives. In: 38th Annual ACM/IEEE Symposium on Logic in Computer Science. Vol 2023. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/LICS56636.2023.10175771","ieee":"J. Kretinsky, T. Meggendorfer, and M. Weininger, “Stopping criteria for value iteration on stochastic games with quantitative objectives,” in 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Boston, MA, United States, 2023, vol. 2023.","apa":"Kretinsky, J., Meggendorfer, T., & Weininger, M. (2023). Stopping criteria for value iteration on stochastic games with quantitative objectives. In 38th Annual ACM/IEEE Symposium on Logic in Computer Science (Vol. 2023). Boston, MA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS56636.2023.10175771","ista":"Kretinsky J, Meggendorfer T, Weininger M. 2023. Stopping criteria for value iteration on stochastic games with quantitative objectives. 38th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science vol. 2023.","short":"J. Kretinsky, T. Meggendorfer, M. Weininger, in:, 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2023.","mla":"Kretinsky, Jan, et al. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” 38th Annual ACM/IEEE Symposium on Logic in Computer Science, vol. 2023, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/LICS56636.2023.10175771.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, and Maximilian Weininger. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” In 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Vol. 2023. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LICS56636.2023.10175771."},"publication":"38th Annual ACM/IEEE Symposium on Logic in Computer Science","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 2023","title":"Stopping criteria for value iteration on stochastic games with quantitative objectives","status":"public","_id":"13967","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"A classic solution technique for Markov decision processes (MDP) and stochastic games (SG) is value iteration (VI). Due to its good practical performance, this approximative approach is typically preferred over exact techniques, even though no practical bounds on the imprecision of the result could be given until recently. As a consequence, even the most used model checkers could return arbitrarily wrong results. Over the past decade, different works derived stopping criteria, indicating when the precision reaches the desired level, for various settings, in particular MDP with reachability, total reward, and mean payoff, and SG with reachability.In this paper, we provide the first stopping criteria for VI on SG with total reward and mean payoff, yielding the first anytime algorithms in these settings. To this end, we provide the solution in two flavours: First through a reduction to the MDP case and second directly on SG. The former is simpler and automatically utilizes any advances on MDP. The latter allows for more local computations, heading towards better practical efficiency.Our solution unifies the previously mentioned approaches for MDP and SG and their underlying ideas. To achieve this, we isolate objective-specific subroutines as well as identify objective-independent concepts. These structural concepts, while surprisingly simple, form the very essence of the unified solution."}],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1109/LICS56636.2023.10175771","conference":{"end_date":"2023-06-29","start_date":"2023-06-26","location":"Boston, MA, United States","name":"LICS: Symposium on Logic in Computer Science"},"isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["2304.09930"],"isi":["001036707700042"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.09930"}],"publication_identifier":{"issn":["1043-6871"],"isbn":["9798350335873"]},"month":"07","volume":2023,"date_updated":"2023-12-13T12:06:10Z","date_created":"2023-08-06T22:01:10Z","author":[{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"},{"full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","first_name":"Tobias"},{"id":"02ab0197-cc70-11ed-ab61-918e71f56881","last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"}],"publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"This research was funded in part by DFG projects 383882557 “SUV” and 427755713 “GOPro”.","year":"2023"},{"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-08-01T00:00:00Z","article_type":"original","citation":{"ista":"Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 81(8), 102087.","ieee":"E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms and implications of long-term epigenetic inheritance,” Current Opinion in Genetics and Development, vol. 81, no. 8. Elsevier, 2023.","apa":"Hollwey, E., Briffa, A., Howard, M., & Zilberman, D. (2023). Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2023.102087","ama":"Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 2023;81(8). doi:10.1016/j.gde.2023.102087","chicago":"Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development. Elsevier, 2023. https://doi.org/10.1016/j.gde.2023.102087.","mla":"Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development, vol. 81, no. 8, 102087, Elsevier, 2023, doi:10.1016/j.gde.2023.102087.","short":"E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics and Development 81 (2023)."},"publication":"Current Opinion in Genetics and Development","issue":"8","abstract":[{"lang":"eng","text":"Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2023_CurrentOpinionGenetics_Hollwey.pdf","creator":"dernst","content_type":"application/pdf","file_size":2568632,"file_id":"13980","relation":"main_file","success":1,"checksum":"a294cd9506b80ed6ef218ef44ed32765","date_created":"2023-08-07T08:32:26Z","date_updated":"2023-08-07T08:32:26Z"}],"oa_version":"Published Version","intvolume":" 81","title":"Concepts, mechanisms and implications of long-term epigenetic inheritance","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13965","publication_identifier":{"issn":["0959-437X"],"eissn":["1879-0380"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1016/j.gde.2023.102087","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37441873"],"isi":["001047020200001"]},"file_date_updated":"2023-08-07T08:32:26Z","article_number":"102087","volume":81,"date_created":"2023-08-06T22:01:10Z","date_updated":"2023-12-13T12:05:31Z","author":[{"last_name":"Hollwey","first_name":"Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd","full_name":"Hollwey, Elizabeth"},{"first_name":"Amy","last_name":"Briffa","full_name":"Briffa, Amy"},{"full_name":"Howard, Martin","first_name":"Martin","last_name":"Howard"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel"}],"publisher":"Elsevier","department":[{"_id":"DaZi"}],"pmid":1,"year":"2023"},{"month":"08","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"doi":"10.15479/at:ista:14058","supervisor":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","grant_number":"25817"}],"file_date_updated":"2023-08-18T10:47:55Z","ec_funded":1,"author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9803"},{"id":"12933","status":"public","relation":"research_data"},{"id":"6831","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14077"}]},"date_updated":"2023-12-13T12:15:36Z","date_created":"2023-08-15T10:20:40Z","year":"2023","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"day":"15","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-08-15T00:00:00Z","citation":{"short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","mla":"Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14058.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14058.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","apa":"Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria."},"page":"230","abstract":[{"text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_id":"14075","relation":"source_file","date_updated":"2023-08-17T06:55:24Z","date_created":"2023-08-16T18:15:17Z","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_name":"Thesis_latex_forpdfa.zip","access_level":"closed","creator":"gpuixeus","content_type":"application/zip","file_size":10891454},{"creator":"gpuixeus","file_size":19856686,"content_type":"application/pdf","access_level":"open_access","file_name":"PhDThesis_PuixeuG.pdf","success":1,"checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","date_created":"2023-08-18T10:47:55Z","date_updated":"2023-08-18T10:47:55Z","file_id":"14079","relation":"main_file"}],"oa_version":"Published Version","_id":"14058","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","status":"public","ddc":["576"]},{"publication_identifier":{"issn":["2160-1836"]},"month":"08","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/g3journal/jkad121","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001002997200001"]},"ec_funded":1,"file_date_updated":"2023-11-07T09:00:19Z","volume":13,"date_updated":"2023-12-13T12:15:37Z","date_created":"2023-08-18T06:52:14Z","related_material":{"record":[{"id":"12933","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"14058"}]},"author":[{"full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"publication_status":"published","acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","year":"2023","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"scopus_import":"1","date_published":"2023-08-01T00:00:00Z","article_type":"original","citation":{"ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press, 2023.","apa":"Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121.","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023. https://doi.org/10.1093/g3journal/jkad121."},"publication":"G3: Genes, Genomes, Genetics","issue":"8","abstract":[{"lang":"eng","text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns."}],"type":"journal_article","file":[{"creator":"dernst","content_type":"application/pdf","file_size":845642,"access_level":"open_access","file_name":"2023_G3_Puixeu.pdf","success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","date_created":"2023-11-07T09:00:19Z","date_updated":"2023-11-07T09:00:19Z","file_id":"14498","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 13","ddc":["570"],"status":"public","title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","_id":"14077","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file":[{"creator":"dernst","file_size":18665315,"content_type":"application/pdf","access_level":"closed","file_name":"2023_JourCellScience_Higashi.pdf","embargo_to":"open_access","checksum":"a399389b7e3d072f1788b63e612a10b3","date_updated":"2023-08-21T07:37:54Z","date_created":"2023-08-21T07:37:54Z","file_id":"14092","embargo":"2024-08-10","relation":"main_file"}],"oa_version":"None","_id":"14082","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"ZnUMBA - a live imaging method to detect local barrier breaches","intvolume":" 136","abstract":[{"lang":"eng","text":"Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision."}],"issue":"15","type":"journal_article","date_published":"2023-08-01T00:00:00Z","publication":"Journal of Cell Science","citation":{"ieee":"T. Higashi et al., “ZnUMBA - a live imaging method to detect local barrier breaches,” Journal of Cell Science, vol. 136, no. 15. The Company of Biologists, 2023.","apa":"Higashi, T., Stephenson, R. E., Schwayer, C., Huljev, K., Higashi, A. Y., Heisenberg, C.-P. J., … Miller, A. L. (2023). ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.260668","ista":"Higashi T, Stephenson RE, Schwayer C, Huljev K, Higashi AY, Heisenberg C-PJ, Chiba H, Miller AL. 2023. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 136(15), jcs260668.","ama":"Higashi T, Stephenson RE, Schwayer C, et al. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 2023;136(15). doi:10.1242/jcs.260668","chicago":"Higashi, Tomohito, Rachel E. Stephenson, Cornelia Schwayer, Karla Huljev, Atsuko Y. Higashi, Carl-Philipp J Heisenberg, Hideki Chiba, and Ann L. Miller. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.260668.","short":"T. Higashi, R.E. Stephenson, C. Schwayer, K. Huljev, A.Y. Higashi, C.-P.J. Heisenberg, H. Chiba, A.L. Miller, Journal of Cell Science 136 (2023).","mla":"Higashi, Tomohito, et al. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” Journal of Cell Science, vol. 136, no. 15, jcs260668, The Company of Biologists, 2023, doi:10.1242/jcs.260668."},"article_type":"original","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","author":[{"last_name":"Higashi","first_name":"Tomohito","full_name":"Higashi, Tomohito"},{"full_name":"Stephenson, Rachel E.","last_name":"Stephenson","first_name":"Rachel E."},{"full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226","first_name":"Cornelia","last_name":"Schwayer"},{"id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","last_name":"Huljev","first_name":"Karla","full_name":"Huljev, Karla"},{"full_name":"Higashi, Atsuko Y.","first_name":"Atsuko Y.","last_name":"Higashi"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"},{"full_name":"Chiba, Hideki","first_name":"Hideki","last_name":"Chiba"},{"full_name":"Miller, Ann L.","last_name":"Miller","first_name":"Ann L."}],"date_created":"2023-08-20T22:01:13Z","date_updated":"2023-12-13T12:11:18Z","volume":136,"acknowledgement":"The authors thank their respective lab members for feedback and helpful discussions. We thank the bioimaging and zebrafish facilities of IST Austria for their support.\r\nThis work was supported by the National Institutes of Health [R01GM112794 to A.L.M.], by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science [21K06156 to T.H.], by the Grant Program for Biomedical Engineering Research from the Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering [to T.H.] and by funding from the European Research Council [advanced grant 742573 to C.-P.H.]. ","year":"2023","publication_status":"published","publisher":"The Company of Biologists","department":[{"_id":"CaHe"},{"_id":"EvBe"}],"file_date_updated":"2023-08-21T07:37:54Z","ec_funded":1,"article_number":"jcs260668","doi":"10.1242/jcs.260668","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001070149000001"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"month":"08","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]}},{"date_published":"2023-08-01T00:00:00Z","page":"8651-8662","article_type":"original","citation":{"ista":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. 2023. Practical limitations of Ethereum’s layer-2. IEEE Access. 11, 8651–8662.","ieee":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, and L. Rodrigues, “Practical limitations of Ethereum’s layer-2,” IEEE Access, vol. 11. Institute of Electrical and Electronics Engineers, pp. 8651–8662, 2023.","apa":"Neiheiser, R., Inacio, G., Rech, L., Montez, C., Matos, M., & Rodrigues, L. (2023). Practical limitations of Ethereum’s layer-2. IEEE Access. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/access.2023.3237897","ama":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. Practical limitations of Ethereum’s layer-2. IEEE Access. 2023;11:8651-8662. doi:10.1109/access.2023.3237897","chicago":"Neiheiser, Ray, Gustavo Inacio, Luciana Rech, Carlos Montez, Miguel Matos, and Luis Rodrigues. “Practical Limitations of Ethereum’s Layer-2.” IEEE Access. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/access.2023.3237897.","mla":"Neiheiser, Ray, et al. “Practical Limitations of Ethereum’s Layer-2.” IEEE Access, vol. 11, Institute of Electrical and Electronics Engineers, 2023, pp. 8651–62, doi:10.1109/access.2023.3237897.","short":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, L. Rodrigues, IEEE Access 11 (2023) 8651–8662."},"publication":"IEEE Access","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","keyword":["General Engineering","General Materials Science","General Computer Science","Electrical and Electronic Engineering"],"scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2023-08-22T06:37:48Z","date_created":"2023-08-22T06:37:48Z","success":1,"checksum":"4b80b0ff212edf7e5842fbdd53784432","file_id":"14166","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1289285,"file_name":"2023_IEEEAccess_Neiheiser.pdf","access_level":"open_access"}],"intvolume":" 11","title":"Practical limitations of Ethereum’s layer-2","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13988","abstract":[{"text":"Most permissionless blockchains inherently suffer from throughput limitations. Layer-2 systems, such as side-chains or Rollups, have been proposed as a possible strategy to overcome this limitation. Layer-2 systems interact with the main-chain in two ways. First, users can move funds from/to the main-chain to/from the layer-2. Second, layer-2 systems periodically synchronize with the main-chain to keep some form of log of their activity on the main-chain - this log is key for security. Due to this interaction with the main-chain, which is necessary and recurrent, layer-2 systems impose some load on the main-chain. The impact of such load on the main-chain has been, so far, poorly understood. In addition to that, layer-2 approaches typically sacrifice decentralization and security in favor of higher throughput. This paper presents an experimental study that analyzes the current state of Ethereum layer-2 projects. Our goal is to assess the load they impose on Ethereum and to understand their scalability potential in the long-run. Our analysis shows that the impact of any given layer-2 on the main-chain is the result of both technical aspects (how state is logged on the main-chain) and user behavior (how often users decide to transfer funds between the layer-2 and the main-chain). Based on our observations, we infer that without efficient mechanisms that allow users to transfer funds in a secure and fast manner directly from one layer-2 project to another, current layer-2 systems will not be able to scale Ethereum effectively, regardless of their technical solutions. Furthermore, from our results, we conclude that the layer-2 systems that offer similar security guarantees as Ethereum have limited scalability potential, while approaches that offer better performance, sacrifice security and lead to an increase in centralization which runs against the end-goals of permissionless blockchains.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1109/access.2023.3237897","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000927831000001"]},"oa":1,"publication_identifier":{"issn":["2169-3536"]},"month":"08","volume":11,"date_created":"2023-08-09T12:09:57Z","date_updated":"2023-12-13T12:14:52Z","author":[{"first_name":"Ray","last_name":"Neiheiser","id":"f09651b9-fec0-11ec-b5d8-934aff0e52a4","orcid":"0000-0001-7227-8309","full_name":"Neiheiser, Ray"},{"full_name":"Inacio, Gustavo","first_name":"Gustavo","last_name":"Inacio"},{"first_name":"Luciana","last_name":"Rech","full_name":"Rech, Luciana"},{"first_name":"Carlos","last_name":"Montez","full_name":"Montez, Carlos"},{"first_name":"Miguel","last_name":"Matos","full_name":"Matos, Miguel"},{"full_name":"Rodrigues, Luis","last_name":"Rodrigues","first_name":"Luis"}],"publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"ElKo"}],"publication_status":"published","acknowledgement":"This work was supported in part by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior (CAPES)—Brazil (CAPES), in part by the Fundação para a Ciência e Tecnologia (FCT) under Project UIDB/50021/2020 and Grant 2020.05270.BD, in part by the Project COSMOS (via the Orçamento de Estado (OE) with ref. PTDC/EEI-COM/29271/2017 and via the ‘‘Programa Operacional Regional de Lisboa na sua componente Fundo Europeu de Desenvolvimento Regional (FEDER)’’ with ref. Lisboa-01-0145-FEDER-029271), and in part by the project Angainor with reference LISBOA-01-0145-FEDER-031456 as well as supported by Meta Platforms for the project key Transparency at Scale.","year":"2023","file_date_updated":"2023-08-22T06:37:48Z"}]