[{"publication":"40th International Symposium on Computational Geometry","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":766562,"date_created":"2024-06-17T08:46:33Z","date_updated":"2024-06-17T08:46:33Z","creator":"dernst","success":1,"checksum":"5442d44fb89d77477a87668d6e61aac9","file_id":"17152","relation":"main_file","file_name":"2024_LIPICS_Edelsbrunner.pdf"}],"publication_identifier":{"isbn":["9783959773164"],"issn":["1868-8969"]},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2310.14801"]},"year":"2024","article_processing_charge":"No","oa":1,"ddc":["510"],"day":"01","author":[{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert"},{"first_name":"János","full_name":"Pach, János","last_name":"Pach","id":"E62E3130-B088-11EA-B919-BF823C25FEA4"}],"title":"Maximum Betti numbers of Čech complexes","abstract":[{"lang":"eng","text":"The Upper Bound Theorem for convex polytopes implies that the p-th Betti number of the Čech complex of any set of N points in ℝ^d and any radius satisfies β_p = O(N^m), with m = min{p+1, ⌈d/2⌉}. We construct sets in even and odd dimensions, which prove that this upper bound is asymptotically tight. For example, we describe a set of N = 2(n+1) points in ℝ³ and two radii such that the first Betti number of the Čech complex at one radius is (n+1)² - 1, and the second Betti number of the Čech complex at the other radius is n². In particular, there is an arrangement of n contruent balls in ℝ³ that enclose a quadratic number of voids, which answers a long-standing open question in computational geometry."}],"acknowledgement":"The first author is supported by the European Research Council (ERC), grant no. 788183, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant no. {I 02979-N35.} The second author is supported by the European Research Council (ERC), grant \"GeoScape\" and by the Hungarian Science Foundation (NKFIH), grant K-131529. Both authors are supported by the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.\r\nThe authors thank Matt Kahle for communicating the question about extremal Čech complexes, Ben Schweinhart for early discussions on the linked circles construction in three dimensions, and Gábor Tardos for helpful remarks and suggestions.","publication_status":"published","department":[{"_id":"HeEd"}],"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2024-06-17T08:46:33Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 293","date_published":"2024-06-01T00:00:00Z","citation":{"ista":"Edelsbrunner H, Pach J. 2024. Maximum Betti numbers of Čech complexes. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 53.","mla":"Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” 40th International Symposium on Computational Geometry, vol. 293, 53, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.SoCG.2024.53.","short":"H. Edelsbrunner, J. Pach, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” In 40th International Symposium on Computational Geometry, Vol. 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.SoCG.2024.53.","ama":"Edelsbrunner H, Pach J. Maximum Betti numbers of Čech complexes. In: 40th International Symposium on Computational Geometry. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.SoCG.2024.53","apa":"Edelsbrunner, H., & Pach, J. (2024). Maximum Betti numbers of Čech complexes. In 40th International Symposium on Computational Geometry (Vol. 293). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2024.53","ieee":"H. Edelsbrunner and J. Pach, “Maximum Betti numbers of Čech complexes,” in 40th International Symposium on Computational Geometry, Athens, Greece, 2024, vol. 293."},"alternative_title":["LIPIcs"],"article_number":"53","arxiv":1,"ec_funded":1,"status":"public","type":"conference","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","conference":{"location":"Athens, Greece","name":"SoCG: Symposium on Computational Geometry","end_date":"2024-06-14","start_date":"2024-06-11"},"related_material":{"record":[{"relation":"later_version","id":"20657","status":"public"}]},"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"Mathematics, Computer Science","call_identifier":"FWF","grant_number":"Z00342"}],"scopus_import":"1","date_updated":"2025-12-01T15:19:20Z","volume":293,"date_created":"2024-06-16T22:01:06Z","quality_controlled":"1","month":"06","_id":"17146","oa_version":"Published Version","doi":"10.4230/LIPIcs.SoCG.2024.53"},{"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331"}],"scopus_import":"1","quality_controlled":"1","date_updated":"2026-04-07T13:02:12Z","date_created":"2024-06-21T09:31:17Z","volume":27,"_id":"17154","oa_version":"Published Version","month":"06","doi":"10.1007/s11040-024-09483-y","type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17164"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 27","citation":{"ama":"Reker J. Fluctuation moments for regular functions of Wigner Matrices. Mathematical Physics, Analysis and Geometry. 2024;27(3). doi:10.1007/s11040-024-09483-y","apa":"Reker, J. (2024). Fluctuation moments for regular functions of Wigner Matrices. Mathematical Physics, Analysis and Geometry. Springer Nature. https://doi.org/10.1007/s11040-024-09483-y","ieee":"J. Reker, “Fluctuation moments for regular functions of Wigner Matrices,” Mathematical Physics, Analysis and Geometry, vol. 27, no. 3. Springer Nature, 2024.","ista":"Reker J. 2024. Fluctuation moments for regular functions of Wigner Matrices. Mathematical Physics, Analysis and Geometry. 27(3), 10.","mla":"Reker, Jana. “Fluctuation Moments for Regular Functions of Wigner Matrices.” Mathematical Physics, Analysis and Geometry, vol. 27, no. 3, 10, Springer Nature, 2024, doi:10.1007/s11040-024-09483-y.","short":"J. Reker, Mathematical Physics, Analysis and Geometry 27 (2024).","chicago":"Reker, Jana. “Fluctuation Moments for Regular Functions of Wigner Matrices.” Mathematical Physics, Analysis and Geometry. Springer Nature, 2024. https://doi.org/10.1007/s11040-024-09483-y."},"date_published":"2024-06-20T00:00:00Z","article_number":"10","arxiv":1,"ec_funded":1,"status":"public","department":[{"_id":"LaEr"}],"file_date_updated":"2024-06-26T11:26:42Z","publisher":"Springer Nature","title":"Fluctuation moments for regular functions of Wigner Matrices","abstract":[{"lang":"eng","text":"We compute the deterministic approximation for mixed fluctuation moments of products of deterministic matrices and general Sobolev functions of Wigner matrices. Restricting to polynomials, our formulas reproduce recent results of Male et al. (Random Matrices Theory Appl. 11(2):2250015, 2022), showing that the underlying combinatorics of non-crossing partitions and annular non-crossing permutations continue to stay valid beyond the setting of second-order free probability theory. The formulas obtained further characterize the variance in the functional central limit theorem given in the recent companion paper (Reker in Preprint, arXiv:2204.03419, 2023). and thus allow identifying the fluctuation around the thermal value in certain thermalization problems."}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","oa":1,"day":"20","ddc":["519"],"author":[{"full_name":"Reker, Jana","first_name":"Jana","last_name":"Reker","id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9"}],"issue":"3","language":[{"iso":"eng"}],"external_id":{"arxiv":["2307.11029"],"isi":["001251464300001"]},"article_type":"original","year":"2024","publication":"Mathematical Physics, Analysis and Geometry","isi":1,"file":[{"file_name":"2024_MathPhysAnaGeo_Reker.pdf","relation":"main_file","file_id":"17175","checksum":"7d04318d66f765621bdcb648378d458e","success":1,"creator":"cchlebak","date_updated":"2024-06-26T11:26:42Z","file_size":1327596,"date_created":"2024-06-26T11:26:42Z","access_level":"open_access","content_type":"application/pdf"}],"publication_identifier":{"eissn":["1572-9656"],"issn":["1385-0172"]}},{"year":"2024","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"file":[{"access_level":"closed","content_type":"application/zip","creator":"krychlew","date_created":"2024-06-26T20:56:27Z","file_size":2761814,"date_updated":"2024-06-26T21:00:14Z","checksum":"1610063569f5452f8a5acef728c2fc26","file_name":"thesis.zip","relation":"source_file","file_id":"17179"},{"file_name":"thesis.pdf","file_id":"17180","relation":"main_file","checksum":"7bbadb1fbc9ed2a1ecf54597f88af99c","creator":"krychlew","date_updated":"2024-06-26T20:58:24Z","date_created":"2024-06-26T20:58:24Z","file_size":3695952,"content_type":"application/pdf","access_level":"open_access"}],"page":"117","publication_status":"published","abstract":[{"lang":"eng","text":"This dissertation is the summary of the author’s work, concerning the relations between\r\ncohomology rings of algebraic varieties and rings of functions on zero schemes and fixed\r\npoint schemes. For most of the thesis, the focus is on smooth complex varieties with\r\nan action of a principally paired group, e.g. a parabolic subgroup of a reductive group.\r\nThe fundamental theorem 5.2.11 from co-authored article [66] says that if the principal\r\nnilpotent has a unique zero, then the zero scheme over the Kostant section is isomorphic\r\nto the spectrum of the equivariant cohomology ring, remembering the grading in terms of\r\na C^* action. A similar statement is proved also for the G-invariant functions on the total\r\nzero scheme over the whole Lie algebra. Additionally, we are able to prove an analogous\r\nresult for the GKM spaces, which poses the question on a joint generalisation.\r\nWe also tackle the situation of a singular variety. As long as it is embedded in a smooth\r\nvariety with regular action, we are able to study its cohomology as well by means of\r\nthe zero scheme. In case of e.g. Schubert varieties this determines the cohomology ring\r\ncompletely. In largest generality, this allows us to see a significant part of the cohomology\r\nring.\r\nWe also show (Theorem 6.2.1) that the cohomology ring of spherical varieties appears as\r\nthe ring of functions on the zero scheme. The computational aspect is not easy, but one\r\ncan hope that this can bring some concrete information about such cohomology rings.\r\nLastly, the K-theory conjecture 6.3.1 is studied, with some results attained for GKM\r\nspaces.\r\nThe thesis includes also an introduction to group actions on algebraic varieties. In\r\nparticular, the vector fields associated to the actions are extensively studied. We also\r\nprovide a version of the Kostant section for arbitrary principally paired group, which\r\nparametrises the regular orbits in the Lie algebra of an algebraic group. Before proving\r\nthe main theorem, we also include a historical overview of the field. In particular we bring\r\ntogether the results of Akyildiz, Carrell and Lieberman on non-equivariant cohomology\r\nrings."}],"title":"Equivariant cohomology and rings of functions","supervisor":[{"first_name":"Tamás","full_name":"Hausel, Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","orcid":"0000-0002-9582-2634"}],"day":"25","ddc":["516"],"author":[{"first_name":"Kamil P","full_name":"Rychlewicz, Kamil P","last_name":"Rychlewicz","id":"85A07246-A8BF-11E9-B4FA-D9E3E5697425"}],"oa":1,"OA_place":"publisher","degree_awarded":"PhD","article_processing_charge":"No","status":"public","corr_author":"1","alternative_title":["ISTA Thesis"],"citation":{"ieee":"K. P. Rychlewicz, “Equivariant cohomology and rings of functions,” Institute of Science and Technology Austria, 2024.","apa":"Rychlewicz, K. P. (2024). Equivariant cohomology and rings of functions. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17156","ama":"Rychlewicz KP. Equivariant cohomology and rings of functions. 2024. doi:10.15479/at:ista:17156","short":"K.P. Rychlewicz, Equivariant Cohomology and Rings of Functions, Institute of Science and Technology Austria, 2024.","chicago":"Rychlewicz, Kamil P. “Equivariant Cohomology and Rings of Functions.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17156.","mla":"Rychlewicz, Kamil P. Equivariant Cohomology and Rings of Functions. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17156.","ista":"Rychlewicz KP. 2024. Equivariant cohomology and rings of functions. Institute of Science and Technology Austria."},"date_published":"2024-06-25T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","department":[{"_id":"TaHa"},{"_id":"GradSch"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2024-06-26T21:00:14Z","doi":"10.15479/at:ista:17156","date_created":"2024-06-23T15:07:06Z","date_updated":"2026-04-07T12:55:46Z","month":"06","_id":"17156","oa_version":"Published Version","project":[{"name":"Topology of open smooth varieties with a torus action","_id":"34cd0f74-11ca-11ed-8bc3-bf0492a14a24","grant_number":"26525"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17157"}]},"keyword":["equivariant cohomology","zero schemes","algebraic groups","Lie algebras"],"tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"has_accepted_license":"1","type":"dissertation"},{"publisher":"Copernicus Publications","department":[{"_id":"PaSc"}],"file_date_updated":"2024-06-27T06:42:55Z","status":"public","date_published":"2024-06-11T00:00:00Z","citation":{"ama":"Aebischer K, Becker LM, Schanda P, Ernst M. Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR. Magnetic Resonance. 2024;5(1):69-86. doi:10.5194/mr-5-69-2024","apa":"Aebischer, K., Becker, L. M., Schanda, P., & Ernst, M. (2024). Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR. Magnetic Resonance. Copernicus Publications. https://doi.org/10.5194/mr-5-69-2024","ieee":"K. Aebischer, L. M. Becker, P. Schanda, and M. Ernst, “Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR,” Magnetic Resonance, vol. 5, no. 1. Copernicus Publications, pp. 69–86, 2024.","ista":"Aebischer K, Becker LM, Schanda P, Ernst M. 2024. Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR. Magnetic Resonance. 5(1), 69–86.","mla":"Aebischer, Kathrin, et al. “Evaluating the Motional Timescales Contributing to Averaged Anisotropic Interactions in MAS Solid-State NMR.” Magnetic Resonance, vol. 5, no. 1, Copernicus Publications, 2024, pp. 69–86, doi:10.5194/mr-5-69-2024.","chicago":"Aebischer, Kathrin, Lea Marie Becker, Paul Schanda, and Matthias Ernst. “Evaluating the Motional Timescales Contributing to Averaged Anisotropic Interactions in MAS Solid-State NMR.” Magnetic Resonance. Copernicus Publications, 2024. https://doi.org/10.5194/mr-5-69-2024.","short":"K. Aebischer, L.M. Becker, P. Schanda, M. Ernst, Magnetic Resonance 5 (2024) 69–86."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","doi":"10.5194/mr-5-69-2024","quality_controlled":"1","date_updated":"2025-06-11T13:26:12Z","volume":5,"date_created":"2024-06-23T22:01:02Z","oa_version":"Published Version","_id":"17161","month":"06","project":[{"grant_number":"26777","_id":"7be609c4-9f16-11ee-852c-85015ce2b9b0","name":"Exploring protein dynamics by solid-state MAS NMR through specific labeling approaches"}],"scopus_import":"1","publication_identifier":{"eissn":["2699-0016"]},"file":[{"checksum":"d01074f6919387fcaf8c9ebed320ccae","file_name":"2024_MagneticResonance_Aebischer.pdf","relation":"main_file","file_id":"17181","access_level":"open_access","content_type":"application/pdf","creator":"dernst","success":1,"file_size":6736194,"date_updated":"2024-06-27T06:42:55Z","date_created":"2024-06-27T06:42:55Z"}],"publication":"Magnetic Resonance","article_type":"original","year":"2024","language":[{"iso":"eng"}],"pmid":1,"external_id":{"pmid":["40384772"]},"issue":"1","day":"11","ddc":["530"],"author":[{"last_name":"Aebischer","full_name":"Aebischer, Kathrin","first_name":"Kathrin"},{"full_name":"Becker, Lea Marie","first_name":"Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul"},{"first_name":"Matthias","full_name":"Ernst, Matthias","last_name":"Ernst"}],"oa":1,"article_processing_charge":"Yes","page":"69-86","publication_status":"published","acknowledgement":"We would like to thank Kay Saalwächter for pointing out important aspects of the intermediate regime during the open review process. Lea Marie Becker is recipient of a DOC fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria.\r\nThis research has been supported by the Österreichischen Akademie der Wissenschaften (grant no. PR10660EAW01) and the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (grant nos. 200020_188988 and 200020_219375).","abstract":[{"text":"Dynamic processes in molecules can occur on a wide range of timescales, and it is important to understand which timescales of motion contribute to different parameters used in dynamics measurements. For spin relaxation, this can easily be understood from the sampling frequencies of the spectral-density function by different relaxation-rate constants. In addition to data from relaxation measurements, determining dynamically averaged anisotropic interactions in magic-angle spinning (MAS) solid-state NMR allows for better quantification of the amplitude of molecular motion. For partially averaged anisotropic interactions, the relevant timescales of motion are not so clearly defined. Whether the averaging depends on the experimental methods (e.g., pulse sequences) or conditions (e.g., MAS frequency, magnitude of anisotropic interaction, radio-frequency field amplitudes) is not fully understood. To investigate these questions, we performed numerical simulations of dynamic systems based on the stochastic Liouville equation using several experiments for recoupling the dipolar coupling, chemical-shift anisotropy or quadrupolar coupling. As described in the literature, the transition between slow motion, where parameters characterizing the anisotropic interaction are not averaged, and fast motion, where the tensors are averaged leading to a scaled anisotropic quantity, occurs over a window of motional rate constants that depends mainly on the strength of the interaction. This transition region can span 2 orders of magnitude in exchange-rate constants (typically in the microsecond range) but depends only marginally on the employed recoupling scheme or sample spinning frequency. The transition region often coincides with a fast relaxation of coherences, making precise quantitative measurements difficult. Residual couplings in off-magic-angle experiments, however, average over longer timescales of motion. While in principle one may gain information on the timescales of motion from the transition area, extracting such information is hampered by low signal-to-noise ratio in experimental spectra due to fast relaxation that occurs in the same region.","lang":"eng"}],"title":"Evaluating the motional timescales contributing to averaged anisotropic interactions in MAS solid-state NMR"},{"project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"scopus_import":"1","date_created":"2024-06-23T22:01:02Z","quality_controlled":"1","date_updated":"2025-04-14T07:52:47Z","volume":8,"month":"04","_id":"17162","oa_version":"Published Version","doi":"10.1145/3649824","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","citation":{"apa":"Chatterjee, K., Goharshady, A. K., Meggendorfer, T., & Zikelic, D. (2024). Quantitative bounds on resource usage of probabilistic programs. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3649824","ieee":"K. Chatterjee, A. K. Goharshady, T. Meggendorfer, and D. Zikelic, “Quantitative bounds on resource usage of probabilistic programs,” Proceedings of the ACM on Programming Languages, vol. 8, no. OOPSLA1. Association for Computing Machinery, 2024.","ama":"Chatterjee K, Goharshady AK, Meggendorfer T, Zikelic D. Quantitative bounds on resource usage of probabilistic programs. Proceedings of the ACM on Programming Languages. 2024;8(OOPSLA1). doi:10.1145/3649824","mla":"Chatterjee, Krishnendu, et al. “Quantitative Bounds on Resource Usage of Probabilistic Programs.” Proceedings of the ACM on Programming Languages, vol. 8, no. OOPSLA1, 107, Association for Computing Machinery, 2024, doi:10.1145/3649824.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Tobias Meggendorfer, and Dorde Zikelic. “Quantitative Bounds on Resource Usage of Probabilistic Programs.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2024. https://doi.org/10.1145/3649824.","short":"K. Chatterjee, A.K. Goharshady, T. Meggendorfer, D. Zikelic, Proceedings of the ACM on Programming Languages 8 (2024).","ista":"Chatterjee K, Goharshady AK, Meggendorfer T, Zikelic D. 2024. Quantitative bounds on resource usage of probabilistic programs. Proceedings of the ACM on Programming Languages. 8(OOPSLA1), 107."},"date_published":"2024-04-29T00:00:00Z","article_number":"107","ec_funded":1,"status":"public","department":[{"_id":"KrCh"}],"file_date_updated":"2024-06-27T07:48:16Z","publisher":"Association for Computing Machinery","title":"Quantitative bounds on resource usage of probabilistic programs","abstract":[{"text":"Cost analysis, also known as resource usage analysis, is the task of finding bounds on the total cost of a program and is a well-studied problem in static analysis. In this work, we consider two classical quantitative problems in cost analysis for probabilistic programs. The first problem is to find a bound on the expected total cost of the program. This is a natural measure for the resource usage of the program and can also be directly applied to average-case runtime analysis. The second problem asks for a tail bound, i.e. given a threshold t the goal is to find a probability bound p such that ℙ[total cost ≥ t] ≤ p. Intuitively, given a threshold t on the resource, the problem is to find the likelihood that the total cost exceeds this threshold.\r\nFirst, for expectation bounds, a major obstacle in previous works on cost analysis is that they can handle only non-negative costs or bounded variable updates. In contrast, we provide a new variant of the standard notion of cost martingales, that allows us to find expectation bounds for a class of programs with general positive or negative costs and no restriction on the variable updates. More specifically, our approach is applicable as long as there is a lower bound on the total cost incurred along every path.\r\nSecond, for tail bounds, all previous methods are limited to programs in which the expected total cost is finite. In contrast, we present a novel approach, based on a combination of our martingale-based method for expectation bounds with a quantitative safety analysis, to obtain a solution to the tail bound problem that is applicable even to programs with infinite expected cost. Specifically, this allows us to obtain runtime tail bounds for programs that do not terminate almost-surely.\r\nIn summary, we provide a novel combination of martingale-based cost analysis and quantitative safety analysis that is able to find expectation and tail cost bounds for probabilistic programs, without the restrictions of non-negative costs, bounded updates, or finiteness of the expected total cost. Finally, we provide experimental results showcasing that our approach can solve instances that were beyond the reach of previous methods.","lang":"eng"}],"acknowledgement":"This work was supported in part by the European Research Council (ERC) under Grant No. 863818\r\n(ForM-SMArt) and the Hong Kong Research Grants Council under ECS Project No. 26208122.","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","oa":1,"day":"29","ddc":["000"],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar"},{"orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","first_name":"Tobias"},{"first_name":"Dorde","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic"}],"issue":"OOPSLA1","language":[{"iso":"eng"}],"article_type":"original","year":"2024","publication":"Proceedings of the ACM on Programming Languages","file":[{"success":1,"creator":"dernst","date_updated":"2024-06-27T07:48:16Z","date_created":"2024-06-27T07:48:16Z","file_size":413096,"access_level":"open_access","content_type":"application/pdf","file_name":"2024_ProcACMProgLanguage_Chatterjee.pdf","relation":"main_file","file_id":"17182","checksum":"9243ded966f71df1572be5466019be5c"}],"publication_identifier":{"eissn":["2475-1421"]}},{"file_date_updated":"2024-06-26T12:44:53Z","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Reker J. 2024. Central limit theorems for random matrices: From resolvents to free probability. Institute of Science and Technology Austria.","short":"J. Reker, Central Limit Theorems for Random Matrices: From Resolvents to Free Probability, Institute of Science and Technology Austria, 2024.","chicago":"Reker, Jana. “Central Limit Theorems for Random Matrices: From Resolvents to Free Probability.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17164.","mla":"Reker, Jana. Central Limit Theorems for Random Matrices: From Resolvents to Free Probability. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17164.","ama":"Reker J. Central limit theorems for random matrices: From resolvents to free probability. 2024. doi:10.15479/at:ista:17164","ieee":"J. Reker, “Central limit theorems for random matrices: From resolvents to free probability,” Institute of Science and Technology Austria, 2024.","apa":"Reker, J. (2024). Central limit theorems for random matrices: From resolvents to free probability. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17164"},"date_published":"2024-06-26T00:00:00Z","alternative_title":["ISTA Thesis"],"corr_author":"1","status":"public","ec_funded":1,"type":"dissertation","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"has_accepted_license":"1","keyword":["Random Matrices","Spectrum","Central Limit Theorem","Resolvent","Free Probability"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17173"},{"relation":"part_of_dissertation","id":"11135","status":"public"},{"relation":"part_of_dissertation","id":"17047","status":"public"},{"id":"17154","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"17174"}]},"project":[{"_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331"}],"oa_version":"Published Version","_id":"17164","month":"06","date_created":"2024-06-24T11:23:29Z","date_updated":"2026-04-07T13:02:13Z","doi":"10.15479/at:ista:17164","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2024-06-26T12:39:36Z","file_size":2783027,"date_updated":"2024-06-26T12:44:53Z","creator":"jreker","checksum":"fb16d86e1f2753dc3a9e14d2bdfd84cd","relation":"main_file","file_id":"17176","file_name":"ISTA_Thesis_JReker.pdf"},{"content_type":"application/zip","access_level":"closed","file_size":3054878,"date_created":"2024-06-26T12:39:42Z","date_updated":"2024-06-26T12:44:53Z","creator":"jreker","checksum":"cb1e54009d47c1dcf5b866c4566fa27f","file_id":"17177","relation":"source_file","file_name":"ISTA_Thesis_JReker_SourceFiles.zip"}],"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"year":"2024","article_processing_charge":"No","degree_awarded":"PhD","oa":1,"OA_place":"publisher","author":[{"id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9","last_name":"Reker","full_name":"Reker, Jana","first_name":"Jana"}],"day":"26","ddc":["519"],"supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László"}],"title":"Central limit theorems for random matrices: From resolvents to free probability","abstract":[{"lang":"eng","text":"This thesis is structured into two parts. In the first part, we consider the random\r\nvariable X := Tr(f1(W)A1 . . . fk(W)Ak) where W is an N × N Hermitian Wigner matrix, k ∈ N, and we choose (possibly N-dependent) regular functions f1, . . . , fk as well as\r\nbounded deterministic matrices A1, . . . , Ak. In this context, we prove a functional central\r\nlimit theorem on macroscopic and mesoscopic scales, showing that the fluctuations of X\r\naround its expectation are Gaussian and that the limiting covariance structure is given\r\nby a deterministic recursion. We further give explicit error bounds in terms of the scaling\r\nof f1, . . . , fk and the number of traceless matrices among A1, . . . , Ak, thus extending\r\nthe results of Cipolloni, Erdős and Schröder [40] to products of arbitrary length k ≥ 2.\r\nAnalyzing the underlying combinatorics leads to a non-recursive formula for the variance\r\nof X as well as the covariance of X and Y := Tr(fk+1(W)Ak+1 . . . fk+ℓ(W)Ak+ℓ) of similar\r\nbuild. When restricted to polynomials, these formulas reproduce recent results of Male,\r\nMingo, Peché, and Speicher [107], showing that the underlying combinatorics of noncrossing partitions and annular non-crossing permutations continue to stay valid beyond\r\nthe setting of second-order free probability theory. As an application, we consider the\r\nfluctuation of Tr(eitW A1e\r\n−itW A2)/N around its thermal value Tr(A1) Tr(A2)/N2 when t\r\nis large and give an explicit formula for the variance.\r\nThe second part of the thesis collects three smaller projects focusing on different random\r\nmatrix models. In the first project, we show that a class of weakly perturbed Hamiltonians\r\nof the form Hλ = H0 + λW, where W is a Wigner matrix, exhibits prethermalization.\r\nThat is, the time evolution generated by Hλ relaxes to its ultimate thermal state via an\r\nintermediate prethermal state with a lifetime of order λ\r\n−2\r\n. As the main result, we obtain\r\na general relaxation formula, expressing the perturbed dynamics via the unperturbed\r\ndynamics and the ultimate thermal state. The proof relies on a two-resolvent global law\r\nfor the deformed Wigner matrix Hλ.\r\nThe second project focuses on correlated random matrices, more precisely on a correlated N × N Hermitian random matrix with a polynomially decaying metric correlation\r\nstructure. A trivial a priori bound shows that the operator norm of this model is stochastically dominated by √\r\nN. However, by calculating the trace of the moments of the matrix\r\nand using the summable decay of the cumulants, the norm estimate can be improved to a\r\nbound of order one.\r\nIn the third project, we consider a multiplicative perturbation of the form UA(t) where U\r\nis a unitary random matrix and A = diag(t, 1, ..., 1). This so-called UA model was\r\nfirst introduced by Fyodorov [73] for its applications in scattering theory. We give a\r\ngeneral description of the eigenvalue trajectories obtained by varying the parameter t and\r\nintroduce a flow of deterministic domains that separates the outlier resulting from the\r\nrank-one perturbation from the typical eigenvalues for all sub-critical timescales. The\r\nresults are obtained under generic assumptions on U that hold for various unitary random\r\nmatrices, including the circular unitary ensemble (CUE) in the original formulation of\r\nthe model."}],"publication_status":"published","page":"206"},{"project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"scopus_import":"1","volume":293,"date_created":"2024-06-25T11:45:58Z","date_updated":"2025-04-15T07:16:57Z","quality_controlled":"1","_id":"17170","oa_version":"Published Version","month":"06","doi":"10.4230/LIPIcs.SoCG.2024.11","type":"conference","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","conference":{"end_date":"2024-06-14","location":"Athens, Greece","name":"SoCG: Symposium on Computational Geometry","start_date":"2024-06-11"},"intvolume":" 293","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-06-06T00:00:00Z","citation":{"ieee":"D. Attali et al., “Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds,” in 40th International Symposium on Computational Geometry, Athens, Greece, 2024, vol. 293, p. 11:1-11:19.","apa":"Attali, D., Kourimska, H., Fillmore, C. D., Ghosh, I., Lieutier, A., Stephenson, E. R., & Wintraecken, M. (2024). Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In 40th International Symposium on Computational Geometry (Vol. 293, p. 11:1-11:19). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2024.11","ama":"Attali D, Kourimska H, Fillmore CD, et al. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. In: 40th International Symposium on Computational Geometry. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:11:1-11:19. doi:10.4230/LIPIcs.SoCG.2024.11","chicago":"Attali, Dominique, Hana Kourimska, Christopher D Fillmore, Ishika Ghosh, André Lieutier, Elizabeth R Stephenson, and Mathijs Wintraecken. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” In 40th International Symposium on Computational Geometry, 293:11:1-11:19. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.SoCG.2024.11.","short":"D. Attali, H. Kourimska, C.D. Fillmore, I. Ghosh, A. Lieutier, E.R. Stephenson, M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19.","mla":"Attali, Dominique, et al. “Tight Bounds for the Learning of Homotopy à La Niyogi, Smale, and Weinberger for Subsets of Euclidean Spaces and of Riemannian Manifolds.” 40th International Symposium on Computational Geometry, vol. 293, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 11:1-11:19, doi:10.4230/LIPIcs.SoCG.2024.11.","ista":"Attali D, Kourimska H, Fillmore CD, Ghosh I, Lieutier A, Stephenson ER, Wintraecken M. 2024. Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 11:1-11:19."},"alternative_title":["LIPIcs"],"arxiv":1,"ec_funded":1,"status":"public","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"file_date_updated":"2024-06-25T11:47:26Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds","abstract":[{"lang":"eng","text":"In this article we extend and strengthen the seminal work by Niyogi, Smale, and Weinberger on the learning of the homotopy type from a sample of an underlying space. In their work, Niyogi, Smale, and Weinberger studied samples of C² manifolds with positive reach embedded in ℝ^d. We extend their results in the following ways: - As the ambient space we consider both ℝ^d and Riemannian manifolds with lower bounded sectional curvature. - In both types of ambient spaces, we study sets of positive reach - a significantly more general setting than C² manifolds - as well as general manifolds of positive reach. - The sample P of a set (or a manifold) 𝒮 of positive reach may be noisy. We work with two one-sided Hausdorff distances - ε and δ - between P and 𝒮. We provide tight bounds in terms of ε and δ, that guarantee that there exists a parameter r such that the union of balls of radius r centred at the sample P deformation-retracts to 𝒮. We exhibit their tightness by an explicit construction. We carefully distinguish the roles of δ and ε. This is not only essential to achieve tight bounds, but also sensible in practical situations, since it allows one to adapt the bound according to sample density and the amount of noise present in the sample separately."}],"acknowledgement":"This research has been supported by the European Research Council (ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant No. I 02979-N35.\r\nWintraecken, Mathijs: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant No. M-3073, and the welcome package from IDEX of the Université Côte d'Azur.","page":"11:1-11:19","publication_status":"published","article_processing_charge":"No","oa":1,"ddc":["516"],"day":"06","author":[{"full_name":"Attali, Dominique","first_name":"Dominique","last_name":"Attali"},{"first_name":"Hana","full_name":"Kourimska, Hana","last_name":"Kourimska","id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","orcid":"0000-0001-7841-0091"},{"first_name":"Christopher D","full_name":"Fillmore, Christopher D","last_name":"Fillmore","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425"},{"last_name":"Ghosh","id":"ee449b28-344d-11ef-a6d5-9ca430e9e9ff","first_name":"Ishika","full_name":"Ghosh, Ishika"},{"full_name":"Lieutier, André","first_name":"André","last_name":"Lieutier"},{"full_name":"Stephenson, Elizabeth R","first_name":"Elizabeth R","last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-208X"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","first_name":"Mathijs","full_name":"Wintraecken, Mathijs"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["2206.10485"]},"year":"2024","publication":"40th International Symposium on Computational Geometry","file":[{"content_type":"application/pdf","access_level":"open_access","success":1,"creator":"cfillmor","date_updated":"2024-06-25T11:47:26Z","file_size":20886142,"date_created":"2024-06-25T11:47:26Z","checksum":"6a2ddc8b51aa58f197a8b294750f1f8d","file_name":"LIPIcs.SoCG.2024.11.pdf","file_id":"17171","relation":"main_file"}],"publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959773164"]}},{"citation":{"mla":"Cheung, Giselle T., et al. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols, vol. 5, no. 3, 103157, Elsevier, 2024, doi:10.1016/j.xpro.2024.103157.","short":"G.T. Cheung, C. Streicher, S. Hippenmeyer, STAR Protocols 5 (2024).","chicago":"Cheung, Giselle T, Carmen Streicher, and Simon Hippenmeyer. “Protocol for Quantitative Reconstruction of Cell Lineage Using Mosaic Analysis with Double Markers in Mice.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103157.","ista":"Cheung GT, Streicher C, Hippenmeyer S. 2024. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 5(3), 103157.","apa":"Cheung, G. T., Streicher, C., & Hippenmeyer, S. (2024). Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103157","ieee":"G. T. Cheung, C. Streicher, and S. Hippenmeyer, “Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice,” STAR Protocols, vol. 5, no. 3. Elsevier, 2024.","ama":"Cheung GT, Streicher C, Hippenmeyer S. Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice. STAR Protocols. 2024;5(3). doi:10.1016/j.xpro.2024.103157"},"date_published":"2024-09-20T00:00:00Z","intvolume":" 5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"status":"public","corr_author":"1","article_number":"103157","department":[{"_id":"SiHi"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2025-01-09T12:12:40Z","publisher":"Elsevier","date_updated":"2025-12-30T10:54:11Z","date_created":"2024-06-30T22:01:04Z","volume":5,"quality_controlled":"1","oa_version":"Published Version","_id":"17187","month":"09","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"F7805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"scopus_import":"1","doi":"10.1016/j.xpro.2024.103157","has_accepted_license":"1","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"},"type":"journal_article","language":[{"iso":"eng"}],"external_id":{"pmid":["38935508"]},"pmid":1,"article_type":"original","year":"2024","publication":"STAR Protocols","publication_identifier":{"eissn":["2666-1667"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"file":[{"checksum":"d8a8cdba82a394e731aa699ace1ae433","file_id":"18809","relation":"main_file","file_name":"2024_STARProtoc_Cheung.pdf","content_type":"application/pdf","access_level":"open_access","file_size":5186071,"date_updated":"2025-01-09T12:12:40Z","date_created":"2025-01-09T12:12:40Z","creator":"dernst","success":1}],"abstract":[{"lang":"eng","text":"The generation of diverse cell types during development is fundamental to brain\r\nfunctions. We outline a protocol to quantitatively assess the clonal output of individual neural progenitors using mosaic analysis with double markers (MADM) in\r\nmice. We first describe steps to acquire and reconstruct adult MADM clones in\r\nthe superior colliculus. Then we detail analysis pipelines to determine clonal\r\ncomposition and architecture. This protocol enables the buildup of quantitative\r\nframeworks of lineage progression with precise spatial resolution in the brain.\r\nFor complete details on the use and execution of this protocol, please refer to\r\nCheung et al.1"}],"APC_amount":"804 EUR","title":"Protocol for quantitative reconstruction of cell lineage using mosaic analysis with double markers in mice","publication_status":"published","acknowledgement":"We thank A. Heger for mouse breeding support. This work was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging & Optics and Preclinical facilities. G.C. received funding from the European Commission (IST plus postdoctoral fellowship); S.H. was funded by ISTA institutional funds and the Austrian Science Fund Special Research Programmes (FWF SFB-F78 Neuro Stem Modulation).","oa":1,"OA_place":"publisher","article_processing_charge":"Yes","OA_type":"gold","issue":"3","ddc":["570"],"day":"20","author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","last_name":"Cheung","orcid":"0000-0001-8457-2572","first_name":"Giselle T","full_name":"Cheung, Giselle T"},{"full_name":"Streicher, Carmen","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher"},{"first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}]},{"doi":"10.1016/j.artint.2024.104171","oa_version":"Published Version","_id":"17188","month":"09","volume":334,"date_updated":"2025-09-08T08:00:42Z","date_created":"2024-06-30T22:01:05Z","quality_controlled":"1","scopus_import":"1","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","corr_author":"1","status":"public","arxiv":1,"article_number":"104171","date_published":"2024-09-01T00:00:00Z","citation":{"chicago":"Braun, Pirmin, Niklas Hahn, Martin Hoefer, and Conrad Schecker. “Delegated Online Search.” Artificial Intelligence. Elsevier, 2024. https://doi.org/10.1016/j.artint.2024.104171.","short":"P. Braun, N. Hahn, M. Hoefer, C. Schecker, Artificial Intelligence 334 (2024).","mla":"Braun, Pirmin, et al. “Delegated Online Search.” Artificial Intelligence, vol. 334, 104171, Elsevier, 2024, doi:10.1016/j.artint.2024.104171.","ista":"Braun P, Hahn N, Hoefer M, Schecker C. 2024. Delegated online search. Artificial Intelligence. 334, 104171.","ieee":"P. Braun, N. Hahn, M. Hoefer, and C. Schecker, “Delegated online search,” Artificial Intelligence, vol. 334. Elsevier, 2024.","apa":"Braun, P., Hahn, N., Hoefer, M., & Schecker, C. (2024). Delegated online search. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2024.104171","ama":"Braun P, Hahn N, Hoefer M, Schecker C. Delegated online search. Artificial Intelligence. 2024;334. doi:10.1016/j.artint.2024.104171"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 334","publisher":"Elsevier","file_date_updated":"2025-01-09T10:45:24Z","department":[{"_id":"MoHe"}],"publication_status":"published","acknowledgement":"Hahn gratefully acknowledges the support of GIF grant I-1419-118.4/2017. Hoefer gratefully acknowledges the support of GIF grant I-1419-118.4/2017, DFG Research Unit ADYN (project number 411362735), and DFG grant Ho 3831/9-1 (project number 514505843).","abstract":[{"lang":"eng","text":"In a delegation problem, a principal P with commitment power tries to pick one out of 𝑛 options.\r\nEach option is drawn independently from a known distribution. Instead of inspecting the options\r\nherself, P delegates the information acquisition to a rational and self-interested agent A. After\r\ninspection, A proposes one of the options, and P can accept or reject.\r\nDelegation is a classic setting in economic information design with many prominent applications,\r\nbut the computational problems are only poorly understood. In this paper, we study a natural\r\nonline variant of delegation, in which the agent searches through the options in an online fashion.\r\nFor each option, he has to irrevocably decide if he wants to propose the current option or discard\r\nit, before seeing information on the next option(s). How can we design algorithms for P that\r\napproximate the utility of her best option in hindsight?\r\nWe show that in general P can obtain a Θ(1∕𝑛)-approximation and extend this result to ratios\r\nof Θ(𝑘∕𝑛) in case (1) A has a lookahead of 𝑘 rounds, or (2) A can propose up to 𝑘 different\r\noptions. We provide fine-grained bounds independent of 𝑛 based on three parameters. If the ratio\r\nof maximum and minimum utility for A is bounded by a factor 𝛼, we obtain an Ω(loglog 𝛼∕ log 𝛼)-\r\napproximation algorithm, and we show that this is best possible. Additionally, if P cannot\r\ndistinguish options with the same value for herself, we show that ratios polynomial in 1∕𝛼 cannot\r\nbe avoided. If there are at most 𝛽 different utility values for A, we show a Θ(1∕𝛽)-approximation.\r\nIf the utilities of P and A for each option are related by a factor 𝛾, we obtain an Ω(1∕ log 𝛾)-\r\napproximation, where 𝑂(log log 𝛾∕ log 𝛾) is best possible."}],"title":"Delegated online search","author":[{"last_name":"Braun","full_name":"Braun, Pirmin","first_name":"Pirmin"},{"first_name":"Niklas","full_name":"Hahn, Niklas","id":"0a01c7b2-b823-11ed-9928-cc3f874f9ffd","last_name":"Hahn"},{"last_name":"Hoefer","first_name":"Martin","full_name":"Hoefer, Martin"},{"last_name":"Schecker","first_name":"Conrad","full_name":"Schecker, Conrad"}],"day":"01","ddc":["000"],"oa":1,"OA_place":"publisher","OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","year":"2024","article_type":"original","external_id":{"isi":["001260448100001"],"arxiv":["2203.01084"]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0004-3702"]},"file":[{"file_id":"18806","relation":"main_file","file_name":"2024_ArtificialIntelligence_Braun.pdf","checksum":"f02a56bc7ea88f41fcc68968e4ceddf3","date_updated":"2025-01-09T10:45:24Z","file_size":772226,"date_created":"2025-01-09T10:45:24Z","creator":"dernst","success":1,"content_type":"application/pdf","access_level":"open_access"}],"isi":1,"publication":"Artificial Intelligence"},{"language":[{"iso":"eng"}],"external_id":{"isi":["001254181700001"]},"article_type":"original","year":"2024","publication":"Nature Astronomy","publication_identifier":{"eissn":["2397-3366"]},"isi":1,"abstract":[{"lang":"eng","text":"Supergranules, which are solar flow features with a lateral scale of 30,000–40,000 km and a lifetime of ~24 h, form a prominent component of the Sun’s convective spectrum. However, their internal flows, which can be probed only by helioseismology, are not well understood. We analyse dopplergrams recorded by the Solar Dynamics Observatory satellite to identify and characterize ~23,000 supergranules. We find that the vertical flows peak at a depth of ~10,000 km, and remain invariant over the full range of lateral supergranular scales, contrary to numerical predictions. We also infer that, within the local seismic resolution (≳5,000 km), downflows are ~40% weaker than upflows, indicating an apparent mass-flux imbalance. This may imply that the descending flows also comprise plumes, which maintain the mass balance but are simply too small to be detected by seismic waves. These results challenge the widely used mixing-length description of solar convection."}],"title":"Supergranular-scale solar convection not explained by mixing-length theory","page":"1088-1101","publication_status":"published","acknowledgement":"We thank F. J. Simons for the codes for computing Slepian functions,\r\nM. Rempel and R. Cameron for their insights into solar convection, J.\r\nW. Lord for the numerical simulations and J. Naranjo for his help with\r\nthe NYUAD NetDRMS system. This research was carried out with the\r\nHigh Performance Computing resources at NYUAD. The datasets were\r\nprepared in the data centre at the Center for Space Science of NYUAD.\r\nThis research is based upon work supported by Tamkeen under the\r\nNYUAD Research Institute (Grant Nos G1502 and CASS to C.S.H,\r\nS.H. and K.R.S.). S.H. acknowledges funding from the Department\r\nof Atomic Energy, India. K.R.S. and S.H. acknowledge support from\r\nthe Ofice of Sponsored Research of King Abdullah University of\r\nScience and Technology (Award No. OSR-CRG2020-4342). S.B.D.\r\nacknowledges funding from the Elisabeth H. and F. A. Dahlen Award\r\n2022 by the Department of Geosciences, Princeton University. S.B.D.\r\nalso acknowledges funding from the European Union’s Horizon 2020\r\nresearch and innovation programme under a Marie Skłodowska-Curie\r\ngrant (Grant Agreement No. 101034413). Some data products were\r\nprocessed and downloaded from the German Data Center for SDO,\r\nwhich is funded by the German Aerospace Center (DLR Grant No.\r\n500L1701).","article_processing_charge":"No","OA_type":"closed access","day":"01","author":[{"full_name":"Hanson, Chris S.","first_name":"Chris S.","last_name":"Hanson"},{"full_name":"Das, Srijan B","first_name":"Srijan B","id":"9ce7c423-dacf-11ed-8942-e09c6cb27149","last_name":"Das","orcid":"0000-0003-0896-7972"},{"last_name":"Mani","first_name":"Prasad","full_name":"Mani, Prasad"},{"last_name":"Hanasoge","first_name":"Shravan","full_name":"Hanasoge, Shravan"},{"full_name":"Sreenivasan, Katepalli R.","first_name":"Katepalli R.","last_name":"Sreenivasan"}],"date_published":"2024-09-01T00:00:00Z","citation":{"apa":"Hanson, C. S., Das, S. B., Mani, P., Hanasoge, S., & Sreenivasan, K. R. (2024). Supergranular-scale solar convection not explained by mixing-length theory. Nature Astronomy. Springer Nature. https://doi.org/10.1038/s41550-024-02304-w","ieee":"C. S. Hanson, S. B. Das, P. Mani, S. Hanasoge, and K. R. Sreenivasan, “Supergranular-scale solar convection not explained by mixing-length theory,” Nature Astronomy, vol. 8. Springer Nature, pp. 1088–1101, 2024.","ama":"Hanson CS, Das SB, Mani P, Hanasoge S, Sreenivasan KR. Supergranular-scale solar convection not explained by mixing-length theory. Nature Astronomy. 2024;8:1088-1101. doi:10.1038/s41550-024-02304-w","mla":"Hanson, Chris S., et al. “Supergranular-Scale Solar Convection Not Explained by Mixing-Length Theory.” Nature Astronomy, vol. 8, Springer Nature, 2024, pp. 1088–101, doi:10.1038/s41550-024-02304-w.","short":"C.S. Hanson, S.B. Das, P. Mani, S. Hanasoge, K.R. Sreenivasan, Nature Astronomy 8 (2024) 1088–1101.","chicago":"Hanson, Chris S., Srijan B Das, Prasad Mani, Shravan Hanasoge, and Katepalli R. Sreenivasan. “Supergranular-Scale Solar Convection Not Explained by Mixing-Length Theory.” Nature Astronomy. Springer Nature, 2024. https://doi.org/10.1038/s41550-024-02304-w.","ista":"Hanson CS, Das SB, Mani P, Hanasoge S, Sreenivasan KR. 2024. Supergranular-scale solar convection not explained by mixing-length theory. Nature Astronomy. 8, 1088–1101."},"intvolume":" 8","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"status":"public","department":[{"_id":"LiBu"}],"publisher":"Springer Nature","volume":8,"date_created":"2024-06-30T22:01:05Z","quality_controlled":"1","date_updated":"2025-09-08T08:04:56Z","month":"09","_id":"17189","oa_version":"None","project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"scopus_import":"1","doi":"10.1038/s41550-024-02304-w","type":"journal_article"},{"publication":"SIAM Journal on Discrete Mathematics","isi":1,"publication_identifier":{"issn":["0895-4801"]},"external_id":{"isi":["001292728600001"],"arxiv":["2204.01077"]},"language":[{"iso":"eng"}],"year":"2024","article_type":"original","article_processing_charge":"No","oa":1,"author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"last_name":"Garber","full_name":"Garber, Alexey","first_name":"Alexey"},{"full_name":"Ghafaris, Mohadese","first_name":"Mohadese","last_name":"Ghafaris"},{"last_name":"Heiss","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa","first_name":"Teresa"},{"last_name":"Saghafiant","first_name":"Morteza","full_name":"Saghafiant, Morteza"},{"first_name":"Mathijs","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220"}],"day":"07","issue":"2","title":"Brillouin zones of integer lattices and their perturbations","abstract":[{"text":"For a locally finite set, 𝐴⊆ℝ𝑑\r\n, the 𝑘\r\nth Brillouin zone of 𝑎∈𝐴\r\n is the region of points 𝑥∈ℝ𝑑\r\n for which ‖𝑥−𝑎‖\r\n is the 𝑘\r\nth smallest among the Euclidean distances between 𝑥\r\n and the points in 𝐴\r\n. If 𝐴\r\n is a lattice, the 𝑘\r\nth Brillouin zones of the points in 𝐴\r\n are translates of each other, and together they tile space. Depending on the value of 𝑘\r\n, they express medium- or long-range order in the set. We study fundamental geometric and combinatorial properties of Brillouin zones, focusing on the integer lattice and its perturbations. Our results include the stability of a Brillouin zone under perturbations, a linear upper bound on the number of chambers in a zone for lattices in ℝ2\r\n, and the convergence of the maximum volume of a chamber to zero for the integer lattice.","lang":"eng"}],"acknowledgement":"The second author is partially supported by the Alexander von Humboldt Foundation. The sixth author is supported by the European Union's Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement 754411, and by Austrian Science Fund(FWF) grant M-3073. All other authors are supported by European Research Council (ERC) grant 788183, by the Wittgenstein Prize, by Austrian Science Fund (FWF) grant Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF) grant I 02979-N35.","publication_status":"published","page":"1784-1807","department":[{"_id":"HeEd"}],"publisher":"Society for Industrial and Applied Mathematics","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 38","date_published":"2024-06-07T00:00:00Z","citation":{"ista":"Edelsbrunner H, Garber A, Ghafaris M, Heiss T, Saghafiant M, Wintraecken M. 2024. Brillouin zones of integer lattices and their perturbations. SIAM Journal on Discrete Mathematics. 38(2), 1784–1807.","mla":"Edelsbrunner, Herbert, et al. “Brillouin Zones of Integer Lattices and Their Perturbations.” SIAM Journal on Discrete Mathematics, vol. 38, no. 2, Society for Industrial and Applied Mathematics, 2024, pp. 1784–807, doi:10.1137/22M1489071.","short":"H. Edelsbrunner, A. Garber, M. Ghafaris, T. Heiss, M. Saghafiant, M. Wintraecken, SIAM Journal on Discrete Mathematics 38 (2024) 1784–1807.","chicago":"Edelsbrunner, Herbert, Alexey Garber, Mohadese Ghafaris, Teresa Heiss, Morteza Saghafiant, and Mathijs Wintraecken. “Brillouin Zones of Integer Lattices and Their Perturbations.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/22M1489071.","ama":"Edelsbrunner H, Garber A, Ghafaris M, Heiss T, Saghafiant M, Wintraecken M. Brillouin zones of integer lattices and their perturbations. SIAM Journal on Discrete Mathematics. 2024;38(2):1784-1807. doi:10.1137/22M1489071","apa":"Edelsbrunner, H., Garber, A., Ghafaris, M., Heiss, T., Saghafiant, M., & Wintraecken, M. (2024). Brillouin zones of integer lattices and their perturbations. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/22M1489071","ieee":"H. Edelsbrunner, A. Garber, M. Ghafaris, T. Heiss, M. Saghafiant, and M. Wintraecken, “Brillouin zones of integer lattices and their perturbations,” SIAM Journal on Discrete Mathematics, vol. 38, no. 2. Society for Industrial and Applied Mathematics, pp. 1784–1807, 2024."},"arxiv":1,"status":"public","corr_author":"1","ec_funded":1,"type":"journal_article","scopus_import":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"M03073","name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"},{"grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"},{"name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF"}],"month":"06","_id":"17190","oa_version":"Preprint","volume":38,"quality_controlled":"1","date_created":"2024-06-30T22:01:05Z","date_updated":"2025-09-08T08:06:04Z","doi":"10.1137/22M1489071","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2204.01077","open_access":"1"}]},{"external_id":{"pmid":["38907047"],"isi":["001251509300001"]},"pmid":1,"language":[{"iso":"eng"}],"year":"2024","article_type":"letter_note","publication":"Nature Immunology","isi":1,"publication_identifier":{"issn":["1529-2908"],"eissn":["1529-2916"]},"title":"Nuclear squeezing wakes up dendritic cells","abstract":[{"lang":"eng","text":"Dendritic cells migrate to and from lymph nodes in response to chemokine gradients.Data now show that steady-state migration of these cells can be triggered by a mechanosensitive pathway."}],"publication_status":"published","page":"1131–1132 ","article_processing_charge":"No","author":[{"id":"d993a7b2-292f-11ed-aaac-fb045a912e31","last_name":"Lembo","orcid":"0000-0002-2253-8771","full_name":"Lembo, Sergio","first_name":"Sergio"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K"}],"day":"21","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 25","citation":{"ista":"Lembo S, Sixt MK. 2024. Nuclear squeezing wakes up dendritic cells. Nature Immunology. 25, 1131–1132.","chicago":"Lembo, Sergio, and Michael K Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” Nature Immunology. Springer Nature, 2024. https://doi.org/10.1038/s41590-024-01881-2.","short":"S. Lembo, M.K. Sixt, Nature Immunology 25 (2024) 1131–1132.","mla":"Lembo, Sergio, and Michael K. Sixt. “Nuclear Squeezing Wakes up Dendritic Cells.” Nature Immunology, vol. 25, Springer Nature, 2024, pp. 1131–1132, doi:10.1038/s41590-024-01881-2.","ama":"Lembo S, Sixt MK. Nuclear squeezing wakes up dendritic cells. Nature Immunology. 2024;25:1131–1132. doi:10.1038/s41590-024-01881-2","ieee":"S. Lembo and M. K. Sixt, “Nuclear squeezing wakes up dendritic cells,” Nature Immunology, vol. 25. Springer Nature, pp. 1131–1132, 2024.","apa":"Lembo, S., & Sixt, M. K. (2024). Nuclear squeezing wakes up dendritic cells. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-024-01881-2"},"date_published":"2024-06-21T00:00:00Z","corr_author":"1","status":"public","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","scopus_import":"1","_id":"17191","month":"06","oa_version":"None","volume":25,"date_updated":"2025-09-08T08:06:56Z","date_created":"2024-06-30T22:01:05Z","quality_controlled":"1","doi":"10.1038/s41590-024-01881-2","type":"journal_article"},{"doi":"10.15479/AT:ISTA:17196","contributor":[{"orcid":"0000-0002-2968-611X","last_name":"Crippa","id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","contributor_type":"project_member","first_name":"Alessandro"},{"last_name":"Valentini","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","contributor_type":"project_member","first_name":"Marco"},{"last_name":"Janik","id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Levon","last_name":"Baghumyan","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7"},{"id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","last_name":"Fabris","first_name":"Giorgio","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Lucky","last_name":"Kapoor","id":"84b9700b-15b2-11ec-abd3-831089e67615"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","orcid":"0000-0001-6937-5773","first_name":"Farid","contributor_type":"project_member"},{"contributor_type":"project_member","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X"},{"last_name":"Calcaterra","first_name":"Stefano","contributor_type":"project_member"},{"last_name":"Chrastina","first_name":"Daniel","contributor_type":"project_member"},{"last_name":"Isella","contributor_type":"project_member","first_name":"Giovanni"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","first_name":"Georgios","contributor_type":"supervisor"}],"project":[{"name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge","_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a"}],"month":"07","_id":"17196","oa_version":"Published Version","date_updated":"2026-04-16T12:20:39Z","date_created":"2024-07-04T10:14:34Z","related_material":{"record":[{"relation":"used_in_publication","id":"17202","status":"public"}]},"type":"research_data","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","status":"public","corr_author":"1","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","citation":{"short":"O. Sagi, (2024).","chicago":"Sagi, Oliver. “A Gate-Tunable Transmon in Planar Ge.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17196.","mla":"Sagi, Oliver. A Gate-Tunable Transmon in Planar Ge. Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17196.","ista":"Sagi O. 2024. A gate-tunable transmon in planar Ge, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17196.","ieee":"O. Sagi, “A gate-tunable transmon in planar Ge.” Institute of Science and Technology Austria, 2024.","apa":"Sagi, O. (2024). A gate-tunable transmon in planar Ge. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17196","ama":"Sagi O. A gate-tunable transmon in planar Ge. 2024. doi:10.15479/AT:ISTA:17196"},"date_published":"2024-07-04T00:00:00Z","publisher":"Institute of Science and Technology Austria","file_date_updated":"2024-07-04T10:11:40Z","department":[{"_id":"GradSch"},{"_id":"GeKa"},{"_id":"JoFi"}],"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the Nanofabrication facility. ","title":"A gate-tunable transmon in planar Ge","abstract":[{"lang":"eng","text":"This .zip File contains the data for the figures presented in the main text and supplementary material of \"A gate tunable transmon qubit in planar Ge\" by O.Sagi et al. The measurements were done using Qcodes. The description of the files and the instructions on opening the data can be found in the Readme. An additional Jupyter Notebook is attached that walks through the data analysis."}],"author":[{"first_name":"Oliver","full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","last_name":"Sagi"}],"ddc":["530"],"day":"04","article_processing_charge":"No","oa":1,"year":"2024","file":[{"content_type":"application/octet-stream","access_level":"open_access","success":1,"creator":"osagi","date_updated":"2024-07-04T10:01:51Z","date_created":"2024-07-04T10:01:51Z","file_size":1960182,"checksum":"a9f640a0b72a92171353f3ea14406f0b","file_name":"GeGatemon_DataAnalysis.ipynb","file_id":"17197","relation":"main_file"},{"checksum":"f0feec931233e8e845ade56165c1588f","file_id":"17198","relation":"main_file","file_name":"OlSa_Readme.pptx","content_type":"application/vnd.openxmlformats-officedocument.presentationml.presentation","access_level":"open_access","date_updated":"2024-07-04T10:01:50Z","file_size":34194,"date_created":"2024-07-04T10:01:50Z","success":1,"creator":"osagi"},{"access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"creator":"osagi","file_size":72939292,"date_created":"2024-07-04T10:11:16Z","date_updated":"2024-07-04T10:11:16Z","checksum":"92bb11e3a508d736d01ff0738a1172c7","file_name":"Al_Transmon.zip","relation":"main_file","file_id":"17199"},{"checksum":"871e96fe0ecc97581196e883045cd516","file_name":"Gatemon_RT_5nm_1.zip","relation":"main_file","file_id":"17200","access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"creator":"osagi","date_created":"2024-07-04T10:11:40Z","file_size":465618029,"date_updated":"2024-07-04T10:11:40Z"},{"checksum":"a3e141af90f0104b7269c8a72370848a","file_name":"Gatemon_RT_5nm_2.zip","file_id":"17201","relation":"main_file","content_type":"application/x-zip-compressed","access_level":"open_access","success":1,"creator":"osagi","date_updated":"2024-07-04T10:11:35Z","date_created":"2024-07-04T10:11:35Z","file_size":281503513}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}]},{"publication":"Nature Communications","publication_identifier":{"eissn":["2041-1723"]},"isi":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"file":[{"checksum":"2af4d6e7364329107aa94d072d594ce0","relation":"main_file","file_id":"18459","file_name":"2024_NatureComm_Pokusaeva.pdf","access_level":"open_access","content_type":"application/pdf","file_size":8276667,"date_updated":"2024-10-21T12:11:10Z","date_created":"2024-10-21T12:11:10Z","success":1,"creator":"dernst"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001336422500001"],"pmid":["39396050"]},"pmid":1,"article_type":"original","year":"2024","oa":1,"OA_place":"publisher","article_processing_charge":"Yes","OA_type":"gold","day":"12","ddc":["570"],"author":[{"full_name":"Pokusaeva, Victoria","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","orcid":"0000-0001-7660-444X"},{"id":"46046B7A-F248-11E8-B48F-1D18A9856A87","last_name":"Satapathy","orcid":"0009-0006-2974-5075","first_name":"Roshan K","full_name":"Satapathy, Roshan K"},{"full_name":"Symonova, Olga","first_name":"Olga","orcid":"0000-0003-2012-9947","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","last_name":"Symonova"},{"orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","first_name":"Maximilian A"}],"APC_amount":"6828 EUR","abstract":[{"text":"Animals rely on compensatory actions to maintain stability and navigate their environment efficiently. These actions depend on global visual motion cues known as optic-flow. While the optomotor response has been the traditional focus for studying optic-flow compensation in insects, its simplicity has been insufficient to determine the role of the intricate optic-flow processing network involved in visual course control. Here, we reveal a series of course control behaviours in Drosophila and link them to specific neural circuits. We show that bilateral electrical coupling of optic-flow-sensitive neurons in the fly’s lobula plate are required for a proper course control. This electrical interaction works alongside chemical synapses within the HS-H2 network to control the dynamics and direction of turning behaviours. Our findings reveal how insects use bilateral motion cues for navigation, assigning a new functional significance to the HS-H2 network and suggesting a previously unknown role for gap junctions in non-linear operations.","lang":"eng"}],"title":"Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies","publication_status":"published","acknowledgement":"We thank Georg Ammer and Alexander Borst for sharing anti-ShakB serum antibodies. We thank Nélia Varela and Eugenia Chiappe for the w1118;+;10XUAS-IVS-eGFPKir2.1/TM6B fly line, Augustin Hrvoje for the shakB[2] line, as well as Jesse Isaacman-Beck and Thomas R Clandinin for the gift of y1,w*;20XUAS-IVS-PhiC31;+ fly line. We also thank Armel Nicolas and Tomas Masson for the proteomic analysis, Ece Sönmez for help with fly crosses and dissections for protein analysis, and Lisa Hofer for assistance with the reconstruction experiments. We would also like to thank Laura Burnett for drawing scientific illustrations used in the figures. We are particularly grateful to members of the Siekhaus, the Kondrashov, and the Chiappe group for providing material support and technical advice. We are grateful to Daria Siekhaus, Eugenia Chiappe, Alexander Borst, Ben deBivort, and all the members of the Joesch laboratory for valuable discussions and comments on the manuscript. Stocks from the Bloomington Drosophila Stock Center (NIH P40OD018537) and the Vienna Drosophila Resource Center were used in this study. The Scientific Service Units of ISTA supported the project through resources provided by the Imaging and Optics Facility, MIBA Machine Shop, and the Lab Support Facility, as well as Vienna Drosophila Research Centre. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) as part of the SPP 2205 – 429960716 (M.J.).","department":[{"_id":"MaJö"}],"file_date_updated":"2024-10-21T12:11:10Z","publisher":"Springer Nature","citation":{"short":"V. Pokusaeva, R.K. Satapathy, O. Symonova, M.A. Jösch, Nature Communications 15 (2024).","chicago":"Pokusaeva, Victoria, Roshan K Satapathy, Olga Symonova, and Maximilian A Jösch. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53173-w.","mla":"Pokusaeva, Victoria, et al. “Bilateral Interactions of Optic-Flow Sensitive Neurons Coordinate Course Control in Flies.” Nature Communications, vol. 15, 8830, Springer Nature, 2024, doi:10.1038/s41467-024-53173-w.","ista":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. 2024. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Nature Communications. 15, 8830.","ieee":"V. Pokusaeva, R. K. Satapathy, O. Symonova, and M. A. Jösch, “Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies,” Nature Communications, vol. 15. Springer Nature, 2024.","apa":"Pokusaeva, V., Satapathy, R. K., Symonova, O., & Jösch, M. A. (2024). Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-53173-w","ama":"Pokusaeva V, Satapathy RK, Symonova O, Jösch MA. Bilateral interactions of optic-flow sensitive neurons coordinate course control in flies. Nature Communications. 2024;15. doi:10.1038/s41467-024-53173-w"},"date_published":"2024-10-12T00:00:00Z","DOAJ_listed":"1","intvolume":" 15","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","corr_author":"1","article_number":"8830","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18568"},{"relation":"research_data","id":"17488","status":"public"}]},"quality_controlled":"1","date_updated":"2026-06-10T07:58:34Z","date_created":"2024-10-20T22:02:05Z","volume":15,"_id":"18444","month":"10","oa_version":"Published Version","project":[{"name":"Evolution of Sensorimotor Transformation Across Diptera","_id":"9B767A34-BA93-11EA-9121-9846C619BF3A","grant_number":"429960716"}],"scopus_import":"1","doi":"10.1038/s41467-024-53173-w"},{"external_id":{"pmid":["39366958"],"isi":["001409493300014"]},"pmid":1,"language":[{"iso":"eng"}],"year":"2024","article_type":"original","publication":"Nature Communications","file":[{"file_id":"18460","relation":"main_file","file_name":"2024_NatureComm_Zupancic.pdf","checksum":"03d6dd1b84efa24e9e9ede748d08764d","file_size":7215329,"date_created":"2024-10-21T12:15:38Z","date_updated":"2024-10-21T12:15:38Z","success":1,"creator":"dernst","content_type":"application/pdf","access_level":"open_access"}],"isi":1,"publication_identifier":{"eissn":["2041-1723"]},"title":"Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3","abstract":[{"lang":"eng","text":"Acquisition of specialized cellular features is controlled by the ordered expression of transcription factors (TFs) along differentiation trajectories. Here, we find a member of the Onecut TF family, ONECUT3, expressed in postmitotic neurons that leave their Ascl1+/Onecut1/2+ proliferative domain in the vertebrate hypothalamus to instruct neuronal differentiation. We combined single-cell RNA-seq and gain-of-function experiments for gene network reconstruction to show that ONECUT3 affects the polarization and morphogenesis of both hypothalamic GABA-derived dopamine and thyrotropin-releasing hormone (TRH)+ glutamate neurons through neuron navigator-2 (NAV2). In vivo, siRNA-mediated knockdown of ONECUT3 in neonatal mice reduced NAV2 mRNA, as well as neurite complexity in Onecut3-containing neurons, while genetic deletion of Onecut3/ceh-48 in C. elegans impaired neurocircuit wiring, and sensory discrimination-based behaviors. Thus, ONECUT3, conserved across neuronal subtypes and many species, underpins the polarization and morphological plasticity of phenotypically distinct neurons that descend from a common pool of Ascl1+ progenitors in the hypothalamus."}],"acknowledgement":"The authors thank Z. Máté, G. Szabó, and F. Erdélyi for the custom generation of transgenic mouse lines, C. Fekete for Trh transgenic tissues (all from the Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary), A. Goudmaeker for IVF recovery of a frozen mouse line (SSS animal facility, Université catholique de Louvain), and Y. Yanagawa (Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan) for providing GAD67gfp/+ mice. We also thank S. Cloer, D. Preininger, and A. Weissenbacher (Tiergarten Schönbrunn, Vienna, Austria) for providing naked mole rats, Seba’s fruit bats, and Indian flying foxes, as well as F. Aujard (CNRS, UMR 7179 ‘Adaptive mechanisms and evolution’, France) for Microcebus tissues. I. Milenkovic and G.G. Kovács (Clinical Institute of Neurology, Medical University of Vienna, Vienna, Austria) are acknowledged for providing post-mortem human brain samples. We are indebted to S. Rehman (Medical University of Vienna), M. Kalusa (University of Leipzig, Leipzig, Germany), and W. Reimann (Paul Flechsig Institute for Brain Research, Leipzig, Germany) for their technical assistance. C. elegans strains were provided by the National Bioresource Project for the nematode, Japan, and the CGC, with the latter being funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). This work was supported by the Austrian Science Fund (FWF, P 34121-B; to E.K.), the Swedish Research Council (2023-03058, T.Ha; 2020-01688, T.Hö.), the Swedish Brain Foundation (Hjärnfonden, FO2022-0300, to T.Ha.), the Novo Nordisk Foundation (NNF23OC0084476, to T.Ha.), the European Research Council (FOODFORLIFE, ERC-2020-AdG-101021016; to T.Ha.), the Université Catholique de Louvain (‘Fonds spéciaux de recherche’-FSR, to F.C.), and Fonds de la Recherche Scientifique F.R.S.-FNRS (‘Project de recherche (PDR)’ #T.0039.21, to F.C.). S.J.E. is supported by the Simons Foundation #543069. I.L. is supported by a post-doctoral fellowship from the Human Frontiers Science Program (LT000335/2020-L). E.R. holds a PhD grant from the FRIA (F.R.S.-FNRS, Belgium). F.C. is a Research Director of the F.R.S.-FNRS (Belgium).\r\nOpen access funding provided by Karolinska Institute.","publication_status":"published","OA_type":"gold","article_processing_charge":"Yes (via OA deal)","OA_place":"publisher","oa":1,"author":[{"last_name":"Zupančič","full_name":"Zupančič, Maja","first_name":"Maja"},{"last_name":"Keimpema","full_name":"Keimpema, Erik","first_name":"Erik"},{"full_name":"Tretiakov, Evgenii O.","first_name":"Evgenii O.","last_name":"Tretiakov"},{"full_name":"Eder, Stephanie J.","first_name":"Stephanie J.","last_name":"Eder"},{"last_name":"Lev","first_name":"Itamar","full_name":"Lev, Itamar"},{"full_name":"Englmaier, Lukas","first_name":"Lukas","last_name":"Englmaier"},{"full_name":"Bhandari, Pradeep","first_name":"Pradeep","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","last_name":"Bhandari","orcid":"0000-0003-0863-4481"},{"full_name":"Fietz, Simone A.","first_name":"Simone A.","last_name":"Fietz"},{"last_name":"Härtig","first_name":"Wolfgang","full_name":"Härtig, Wolfgang"},{"first_name":"Estelle","full_name":"Renaux, Estelle","last_name":"Renaux"},{"last_name":"Villunger","full_name":"Villunger, Andreas","first_name":"Andreas"},{"first_name":"Tomas","full_name":"Hökfelt, Tomas","last_name":"Hökfelt"},{"last_name":"Zimmer","first_name":"Manuel","full_name":"Zimmer, Manuel"},{"last_name":"Clotman","full_name":"Clotman, Frédéric","first_name":"Frédéric"},{"last_name":"Harkany","first_name":"Tibor","full_name":"Harkany, Tibor"}],"day":"05","ddc":["570"],"intvolume":" 15","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","DOAJ_listed":"1","citation":{"ama":"Zupančič M, Keimpema E, Tretiakov EO, et al. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. Nature Communications. 2024;15. doi:10.1038/s41467-024-52762-z","ieee":"M. Zupančič et al., “Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3,” Nature Communications, vol. 15. Springer Nature, 2024.","apa":"Zupančič, M., Keimpema, E., Tretiakov, E. O., Eder, S. J., Lev, I., Englmaier, L., … Harkany, T. (2024). Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-52762-z","ista":"Zupančič M, Keimpema E, Tretiakov EO, Eder SJ, Lev I, Englmaier L, Bhandari P, Fietz SA, Härtig W, Renaux E, Villunger A, Hökfelt T, Zimmer M, Clotman F, Harkany T. 2024. Concerted transcriptional regulation of the morphogenesis of hypothalamic neurons by ONECUT3. Nature Communications. 15, 8631.","short":"M. Zupančič, E. Keimpema, E.O. Tretiakov, S.J. Eder, I. Lev, L. Englmaier, P. Bhandari, S.A. Fietz, W. Härtig, E. Renaux, A. Villunger, T. Hökfelt, M. Zimmer, F. Clotman, T. Harkany, Nature Communications 15 (2024).","chicago":"Zupančič, Maja, Erik Keimpema, Evgenii O. Tretiakov, Stephanie J. Eder, Itamar Lev, Lukas Englmaier, Pradeep Bhandari, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-52762-z.","mla":"Zupančič, Maja, et al. “Concerted Transcriptional Regulation of the Morphogenesis of Hypothalamic Neurons by ONECUT3.” Nature Communications, vol. 15, 8631, Springer Nature, 2024, doi:10.1038/s41467-024-52762-z."},"date_published":"2024-10-05T00:00:00Z","article_number":"8631","status":"public","file_date_updated":"2024-10-21T12:15:38Z","department":[{"_id":"RySh"}],"publisher":"Springer Nature","scopus_import":"1","month":"10","_id":"18445","oa_version":"Published Version","date_created":"2024-10-20T22:02:05Z","quality_controlled":"1","volume":15,"date_updated":"2025-09-08T14:25:06Z","doi":"10.1038/s41467-024-52762-z","type":"journal_article","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","PlanS_conform":"1"},{"day":"11","author":[{"first_name":"Dimitri","full_name":"Fabrèges, Dimitri","last_name":"Fabrèges"},{"last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat","first_name":"Bernat"},{"first_name":"Prachiti","full_name":"Moghe, Prachiti","last_name":"Moghe"},{"last_name":"Kickuth","first_name":"Alison","full_name":"Kickuth, Alison"},{"first_name":"Takafumi","full_name":"Ichikawa, Takafumi","last_name":"Ichikawa"},{"last_name":"Iwatani","first_name":"Chizuru","full_name":"Iwatani, Chizuru"},{"last_name":"Tsukiyama","first_name":"Tomoyuki","full_name":"Tsukiyama, Tomoyuki"},{"full_name":"Daniel, Nathalie","first_name":"Nathalie","last_name":"Daniel"},{"first_name":"Julie","full_name":"Gering, Julie","last_name":"Gering"},{"last_name":"Stokkermans","first_name":"Anniek","full_name":"Stokkermans, Anniek"},{"full_name":"Wolny, Adrian","first_name":"Adrian","last_name":"Wolny"},{"first_name":"Anna","full_name":"Kreshuk, Anna","last_name":"Kreshuk"},{"full_name":"Duranthon, Véronique","first_name":"Véronique","last_name":"Duranthon"},{"full_name":"Uhlman, Virginie","first_name":"Virginie","last_name":"Uhlman"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Hiiragi","full_name":"Hiiragi, Takashi","first_name":"Takashi"}],"issue":"6718","article_processing_charge":"No","OA_type":"green","OA_place":"repository","oa":1,"acknowledgement":"We are grateful to the members of the Hiiragi laboratory for discussions and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol; members of the Tsukiyama group for the animal care with monkeys, in particular H. Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas, France) for the animal care with rabbits; the EMBL electronic and mechanical workshops and the EMBL animal facility for their support; We thank Luxendo for the close collaboration in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD) under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research Fellowship (to T.I.); Field of excellence “Complexity of life in basic research and innovation” of the University of Graz (to B.C.M.); European Research Council, ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)","publication_status":"published","title":"Temporal variability and cell mechanics control robustness in mammalian embryogenesis","abstract":[{"lang":"eng","text":"How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning."}],"isi":1,"publication_identifier":{"eissn":["1095-9203"]},"publication":"Science","article_type":"original","year":"2024","language":[{"iso":"eng"}],"pmid":1,"external_id":{"pmid":["39388574"],"isi":["001422132300018"]},"type":"journal_article","doi":"10.1126/science.adh1145","main_file_link":[{"open_access":"1","url":"https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf"}],"scopus_import":"1","volume":386,"date_created":"2024-10-20T22:02:06Z","quality_controlled":"1","date_updated":"2025-09-08T14:22:13Z","_id":"18446","month":"10","oa_version":"Submitted Version","publisher":"AAAS","department":[{"_id":"EdHa"}],"article_number":"eadh1145","corr_author":"1","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 386","citation":{"short":"D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).","chicago":"Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science. AAAS, 2024. https://doi.org/10.1126/science.adh1145.","mla":"Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science, vol. 386, no. 6718, eadh1145, AAAS, 2024, doi:10.1126/science.adh1145.","ista":"Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145.","ieee":"D. Fabrèges et al., “Temporal variability and cell mechanics control robustness in mammalian embryogenesis,” Science, vol. 386, no. 6718. AAAS, 2024.","apa":"Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. AAAS. https://doi.org/10.1126/science.adh1145","ama":"Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 2024;386(6718). doi:10.1126/science.adh1145"},"date_published":"2024-10-11T00:00:00Z"},{"status":"public","year":"2024","date_published":"2024-09-27T00:00:00Z","citation":{"ama":"Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. Portable Raman platform for SERS droplets microfludics. In: 2024 International Conference on Optical MEMS and Nanophotonics. Institute of Electrical and Electronics Engineers; 2024. doi:10.1109/OMN61224.2024.10685279","apa":"Quintero, S., Relvas, M., Aranda, M., Nodal, F., Dieguez, L., & Abalde-Cela, S. (2024). Portable Raman platform for SERS droplets microfludics. In 2024 International Conference on Optical MEMS and Nanophotonics. San Sebastian, Spain: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/OMN61224.2024.10685279","ieee":"S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, and S. Abalde-Cela, “Portable Raman platform for SERS droplets microfludics,” in 2024 International Conference on Optical MEMS and Nanophotonics, San Sebastian, Spain, 2024.","ista":"Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. 2024. Portable Raman platform for SERS droplets microfludics. 2024 International Conference on Optical MEMS and Nanophotonics. OMN: Conference on Optical MEMS and Nanophotonics.","mla":"Quintero, Sergio, et al. “Portable Raman Platform for SERS Droplets Microfludics.” 2024 International Conference on Optical MEMS and Nanophotonics, Institute of Electrical and Electronics Engineers, 2024, doi:10.1109/OMN61224.2024.10685279.","short":"S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, S. Abalde-Cela, in:, 2024 International Conference on Optical MEMS and Nanophotonics, Institute of Electrical and Electronics Engineers, 2024.","chicago":"Quintero, Sergio, Maria Relvas, Marta Aranda, Fernando Nodal, Lorena Dieguez, and Sara Abalde-Cela. “Portable Raman Platform for SERS Droplets Microfludics.” In 2024 International Conference on Optical MEMS and Nanophotonics. Institute of Electrical and Electronics Engineers, 2024. https://doi.org/10.1109/OMN61224.2024.10685279."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001327768000060"]},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2160-5041"],"issn":["2160-5033"],"isbn":["9798350384925"]},"publisher":"Institute of Electrical and Electronics Engineers","isi":1,"publication":"2024 International Conference on Optical MEMS and Nanophotonics","department":[{"_id":"GradSch"}],"publication_status":"published","doi":"10.1109/OMN61224.2024.10685279","acknowledgement":"The authors acknowledge the financial support of the project HfPT – Health from Portugal, with the reference n.° C644937233-00000047, co-funded by Component C5 – Capitalisation and Business Innovation under the Portuguese Resilience and Recovery Plan, through the NextGenerationEU Fund.","_id":"18450","oa_version":"None","month":"09","date_updated":"2025-09-08T14:19:49Z","date_created":"2024-10-20T22:02:07Z","abstract":[{"lang":"eng","text":"In this work we present the engineering of a portable platform for sensing SERS signals in droplets microfluidics. This system comprised not only the read-out platform but also a design for the microfluidic devices optimized to enhanced the obtained SERS signals."}],"quality_controlled":"1","scopus_import":"1","title":"Portable Raman platform for SERS droplets microfludics","author":[{"first_name":"Sergio","full_name":"Quintero, Sergio","last_name":"Quintero"},{"full_name":"Relvas, Maria","first_name":"Maria","last_name":"Relvas"},{"first_name":"Marta","full_name":"Aranda, Marta","last_name":"Aranda"},{"id":"8ad43d5a-1ffe-11ee-8b67-8176f59de781","last_name":"Nodal","orcid":"0009-0006-4119-4376","full_name":"Nodal, Fernando","first_name":"Fernando"},{"last_name":"Dieguez","first_name":"Lorena","full_name":"Dieguez, Lorena"},{"last_name":"Abalde-Cela","full_name":"Abalde-Cela, Sara","first_name":"Sara"}],"day":"27","conference":{"location":"San Sebastian, Spain","name":"OMN: Conference on Optical MEMS and Nanophotonics","end_date":"2024-08-01","start_date":"2024-07-28"},"type":"conference","OA_type":"closed access","article_processing_charge":"No"},{"doi":"10.1002/advs.202408416","quality_controlled":"1","date_created":"2024-10-20T22:02:07Z","date_updated":"2025-09-08T14:20:31Z","volume":11,"oa_version":"Published Version","_id":"18451","month":"12","scopus_import":"1","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","status":"public","article_number":"2408416","date_published":"2024-12-04T00:00:00Z","citation":{"ista":"Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. 2024. Protein cage directed assembly of binary nanoparticle superlattices. Advanced Science. 11(45), 2408416.","chicago":"Zhou, Yu, Ahmed Shaukat, Jani Seitsonen, Carlo Rigoni, Jaakko V.I. Timonen, and Mauri A. Kostiainen. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” Advanced Science. Wiley, 2024. https://doi.org/10.1002/advs.202408416.","short":"Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J.V.I. Timonen, M.A. Kostiainen, Advanced Science 11 (2024).","mla":"Zhou, Yu, et al. “Protein Cage Directed Assembly of Binary Nanoparticle Superlattices.” Advanced Science, vol. 11, no. 45, 2408416, Wiley, 2024, doi:10.1002/advs.202408416.","ama":"Zhou Y, Shaukat A, Seitsonen J, Rigoni C, Timonen JVI, Kostiainen MA. Protein cage directed assembly of binary nanoparticle superlattices. Advanced Science. 2024;11(45). doi:10.1002/advs.202408416","ieee":"Y. Zhou, A. Shaukat, J. Seitsonen, C. Rigoni, J. V. I. Timonen, and M. A. Kostiainen, “Protein cage directed assembly of binary nanoparticle superlattices,” Advanced Science, vol. 11, no. 45. Wiley, 2024.","apa":"Zhou, Y., Shaukat, A., Seitsonen, J., Rigoni, C., Timonen, J. V. I., & Kostiainen, M. A. (2024). Protein cage directed assembly of binary nanoparticle superlattices. Advanced Science. Wiley. https://doi.org/10.1002/advs.202408416"},"DOAJ_listed":"1","intvolume":" 11","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Wiley","department":[{"_id":"RaKl"}],"file_date_updated":"2025-01-13T09:16:25Z","publication_status":"published","acknowledgement":"This work has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 101002258). The authors acknowledge the provision of facilities and technical support by Aalto University Bioeconomy Facilities and OtaNanoNanomicroscopy Center (Aalto-NMC). This work was carried out under the Academy of Finland's Centers of Excellence Programme, Life Inspired Hybrid Materials (LIBER) Center of Excellence (2022–2029), project number 346110 and 346112.","abstract":[{"lang":"eng","text":"Inorganic nanoparticles can be assembled into superlattices with unique optical and magnetic properties arising from collective behavior. Protein cages can be utilized to guide this assembly by encapsulating nanoparticles and promoting their assembly into ordered structures. However, creating ordered multi-component structures with different protein cage types and sizes remains a challenge. Here, the co-crystallization of two different protein cages (cowpea chlorotic mottle virus and ferritin) characterized by opposing surface charges and unequal diameter is shown. Precise tuning of the electrostatic attraction between the cages enabled the preparation of binary crystals with dimensions up to several tens of micrometers. Additionally, binary metal nanoparticle superlattices are achieved by loading gold and iron oxide nanoparticles inside the cavities of the protein cages. The resulting structure adopts an AB2FCC configuration that also impacts the dipolar coupling between the particles and hence the optical properties of the crystals, providing key insight for the future preparation of plasmonic and magnetic nanoparticle metamaterials."}],"title":"Protein cage directed assembly of binary nanoparticle superlattices","issue":"45","day":"04","ddc":["540"],"author":[{"full_name":"Zhou, Yu","first_name":"Yu","last_name":"Zhou"},{"last_name":"Shaukat","first_name":"Ahmed","full_name":"Shaukat, Ahmed"},{"last_name":"Seitsonen","full_name":"Seitsonen, Jani","first_name":"Jani"},{"id":"c5df3b62-5f9e-11ef-ba3c-b97f5b5b5ef0","last_name":"Rigoni","full_name":"Rigoni, Carlo","first_name":"Carlo"},{"last_name":"Timonen","full_name":"Timonen, Jaakko V.I.","first_name":"Jaakko V.I."},{"last_name":"Kostiainen","full_name":"Kostiainen, Mauri A.","first_name":"Mauri A."}],"OA_place":"publisher","oa":1,"article_processing_charge":"Yes","OA_type":"gold","article_type":"original","year":"2024","language":[{"iso":"eng"}],"external_id":{"isi":["001330745600001"],"pmid":["39401426"]},"pmid":1,"publication_identifier":{"eissn":["2198-3844"]},"isi":1,"file":[{"date_created":"2025-01-13T09:16:25Z","file_size":7040083,"date_updated":"2025-01-13T09:16:25Z","success":1,"creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_id":"18834","relation":"main_file","file_name":"2024_AdvancedScience_Zhou.pdf","checksum":"00451eeb2c9eecf1ff41ad243c793a51"}],"publication":"Advanced Science"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 20","citation":{"ieee":"B. Cheng, “Response matching for generating materials and molecules,” Journal of Chemical Theory and Computation, vol. 20, no. 20. American Chemical Society, pp. 9259–9266, 2024.","apa":"Cheng, B. (2024). Response matching for generating materials and molecules. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.4c00998","ama":"Cheng B. Response matching for generating materials and molecules. Journal of Chemical Theory and Computation. 2024;20(20):9259-9266. doi:10.1021/acs.jctc.4c00998","chicago":"Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.” Journal of Chemical Theory and Computation. American Chemical Society, 2024. https://doi.org/10.1021/acs.jctc.4c00998.","short":"B. Cheng, Journal of Chemical Theory and Computation 20 (2024) 9259–9266.","mla":"Cheng, Bingqing. “Response Matching for Generating Materials and Molecules.” Journal of Chemical Theory and Computation, vol. 20, no. 20, American Chemical Society, 2024, pp. 9259–66, doi:10.1021/acs.jctc.4c00998.","ista":"Cheng B. 2024. Response matching for generating materials and molecules. Journal of Chemical Theory and Computation. 20(20), 9259–9266."},"date_published":"2024-10-22T00:00:00Z","arxiv":1,"status":"public","corr_author":"1","file_date_updated":"2025-01-13T09:11:09Z","department":[{"_id":"BiCh"}],"publisher":"American Chemical Society","scopus_import":"1","_id":"18452","month":"10","oa_version":"Published Version","date_updated":"2025-09-08T14:21:30Z","quality_controlled":"1","volume":20,"date_created":"2024-10-20T22:02:07Z","doi":"10.1021/acs.jctc.4c00998","type":"journal_article","has_accepted_license":"1","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"},"related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/cace"}]},"pmid":1,"external_id":{"pmid":["39365029"],"isi":["001330001500001"],"arxiv":["2405.09057"]},"language":[{"iso":"eng"}],"year":"2024","article_type":"original","publication":"Journal of Chemical Theory and Computation","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2025-01-13T09:11:09Z","file_size":4758251,"date_updated":"2025-01-13T09:11:09Z","success":1,"creator":"dernst","checksum":"aca0011bba4846140809b5af583daa9a","relation":"main_file","file_id":"18832","file_name":"2024_JCTC_Cheng.pdf"}],"isi":1,"publication_identifier":{"issn":["1549-9618"],"eissn":["1549-9626"]},"title":"Response matching for generating materials and molecules","abstract":[{"lang":"eng","text":"Diffusion models have recently emerged as powerful tools for the generation of new molecular and material structures. The key insight is that the noise in these models is related to the response of the atoms to displacement, and the denoising step is thus analogous to the geometry relaxation of atomistic systems starting from a random structure. Building on this, we present a generative method called Response Matching (RM), which leverages the fact that each stable material or molecule exists at the minimum of its potential energy surface. Any perturbation induces a response in energy and stress, driving the structure back to equilibrium. Matching this response is closely related to score matching in diffusion models. Another important aspect of state-of-the-art diffusion models is the incorporation of physical symmetries such as translation, rotation, and periodicity. RM employs a machine learning interatomic potential and random structure search as the denoising model, inherently respecting these symmetries and exploiting the locality of atomic interactions. RM handles both molecules and bulk materials under the same framework. Its efficiency and generalization are demonstrated on three systems: a small organic molecular data set, stable crystals from the Materials Project, and one-shot learning on a single diamond configuration."}],"acknowledgement":"B.C. thanks Chris Pickard for enlightening discussions.","publication_status":"published","page":"9259-9266","OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","oa":1,"OA_place":"publisher","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","first_name":"Bingqing"}],"ddc":["540"],"day":"22","issue":"20"},{"scopus_import":"1","date_updated":"2025-09-08T14:33:17Z","date_created":"2024-10-23T08:41:27Z","volume":59,"quality_controlled":"1","month":"12","_id":"18465","oa_version":"Published Version","doi":"10.1016/j.devcel.2024.09.020","type":"journal_article","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc.png","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","short":"CC BY-NC (4.0)"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 59","date_published":"2024-12-16T00:00:00Z","citation":{"ama":"Janacek D, Kolb M, Schulz L, et al. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. 2024;59(14):S1534-5807(24)00569-0. doi:10.1016/j.devcel.2024.09.020","ieee":"D. Janacek et al., “Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport,” Developmental Cell, vol. 59, no. 14. Elsevier, pp. S1534-5807(24)00569–0, 2024.","apa":"Janacek, D., Kolb, M., Schulz, L., Mergner, J., Kuster, B., Glanc, M., … Hammes, U. (2024). Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.09.020","ista":"Janacek D, Kolb M, Schulz L, Mergner J, Kuster B, Glanc M, Friml J, Ten Tusscher K, Schwechheimer C, Hammes U. 2024. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. 59(14), S1534-5807(24)00569–0.","chicago":"Janacek, DP, M Kolb, L Schulz, J Mergner, B Kuster, Matous Glanc, Jiří Friml, K Ten Tusscher, C Schwechheimer, and UZ Hammes. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.09.020.","short":"D. Janacek, M. Kolb, L. Schulz, J. Mergner, B. Kuster, M. Glanc, J. Friml, K. Ten Tusscher, C. Schwechheimer, U. Hammes, Developmental Cell 59 (2024) S1534-5807(24)00569–0.","mla":"Janacek, DP, et al. “Transport Properties of Canonical PIN-FORMED Proteins from Arabidopsis and the Role of the Loop Domain in Auxin Transport.” Developmental Cell, vol. 59, no. 14, Elsevier, 2024, pp. S1534-5807(24)00569-0, doi:10.1016/j.devcel.2024.09.020."},"status":"public","department":[{"_id":"JiFr"}],"file_date_updated":"2025-01-13T09:20:15Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","publisher":"Elsevier","title":"Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport","abstract":[{"text":"The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN) transporters and controls virtually all growth and developmental processes. Canonical PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical PINs is activated by loop phosphorylation by certain kinases. The structure of the PIN transmembrane domains was recently determined, their transport properties remained poorly characterized, and the role of the loop in the transport process was unclear. Here, we determined the quantitative kinetic parameters of auxin transport mediated by Arabidopsis PINs to mathematically model auxin distribution in roots and to test these predictions in vivo. Using chimeras between transmembrane and loop domains of different PINs, we demonstrate a strong correlation between transport parameters and physiological output, indicating that the loop domain is not only required to activate PIN-mediated auxin transport, but it has an additional role in the transport process by a currently unknown mechanism.","lang":"eng"}],"acknowledgement":"This work was funded by DFG3468/6-1, DFG3468/6-3, and SFB924 to U.Z.H. We thank Angela Alkofer and Helene Prunkl for excellent technical assistance and Xenopus maintenance. Christian Luschnig is acknowledged for sharing unpublished results and valuable discussions.","page":"S1534-5807(24)00569-0","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","OA_type":"hybrid","OA_place":"publisher","oa":1,"ddc":["570"],"day":"16","author":[{"last_name":"Janacek","full_name":"Janacek, DP","first_name":"DP"},{"last_name":"Kolb","full_name":"Kolb, M","first_name":"M"},{"first_name":"L","full_name":"Schulz, L","last_name":"Schulz"},{"last_name":"Mergner","first_name":"J","full_name":"Mergner, J"},{"full_name":"Kuster, B","first_name":"B","last_name":"Kuster"},{"orcid":"0000-0003-0619-7783","last_name":"Glanc","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","first_name":"Matous"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří"},{"first_name":"K","full_name":"Ten Tusscher, K","last_name":"Ten Tusscher"},{"first_name":"C","full_name":"Schwechheimer, C","last_name":"Schwechheimer"},{"first_name":"UZ","full_name":"Hammes, UZ","last_name":"Hammes"}],"issue":"14","language":[{"iso":"eng"}],"external_id":{"isi":["001390774300001"],"pmid":["39413780"]},"pmid":1,"article_type":"original","year":"2024","publication":"Developmental Cell","isi":1,"file":[{"file_size":3675955,"date_updated":"2025-01-13T09:20:15Z","date_created":"2025-01-13T09:20:15Z","success":1,"creator":"dernst","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"18835","file_name":"2024_DevelopmentalCell_Janacek.pdf","checksum":"34423ee9fb4e30334f3572eddf1da2ae"}],"publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]}}]