[{"page":"1983-2005","isi":1,"file_date_updated":"2020-07-14T12:47:17Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Wiley","publication":"Communications on Pure and Applied Mathematics","type":"journal_article","day":"08","date_updated":"2024-10-09T20:58:47Z","date_created":"2019-02-17T22:59:24Z","status":"public","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","abstract":[{"lang":"eng","text":"We give a construction allowing us to build local renormalized solutions to general quasilinear stochastic PDEs within the theory of regularity structures, thus greatly generalizing the recent results of [1, 5, 11]. Loosely speaking, our construction covers quasilinear variants of all classes of equations for which the general construction of [3, 4, 7] applies, including in particular one‐dimensional systems with KPZ‐type nonlinearities driven by space‐time white noise. In a less singular and more specific case, we furthermore show that the counterterms introduced by the renormalization procedure are given by local functionals of the solution. The main feature of our construction is that it allows exploitation of a number of existing results developed for the semilinear case, so that the number of additional arguments it requires is relatively small."}],"doi":"10.1002/cpa.21816","external_id":{"isi":["000475465000003"]},"volume":72,"department":[{"_id":"JaMa"}],"has_accepted_license":"1","ddc":["500"],"oa":1,"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"09aec427eb48c0f96a1cce9ff53f013b","file_name":"2019_Wiley_Gerencser.pdf","file_size":381350,"date_created":"2020-01-07T13:25:55Z","file_id":"7237","creator":"kschuh","date_updated":"2020-07-14T12:47:17Z","access_level":"open_access"}],"title":"A solution theory for quasilinear singular SPDEs","_id":"6028","quality_controlled":"1","intvolume":" 72","corr_author":"1","year":"2019","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","date_published":"2019-02-08T00:00:00Z","month":"02","issue":"9","citation":{"chicago":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics. Wiley, 2019. https://doi.org/10.1002/cpa.21816.","short":"M. Gerencser, M. Hairer, Communications on Pure and Applied Mathematics 72 (2019) 1983–2005.","ista":"Gerencser M, Hairer M. 2019. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 72(9), 1983–2005.","apa":"Gerencser, M., & Hairer, M. (2019). A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21816","ieee":"M. Gerencser and M. Hairer, “A solution theory for quasilinear singular SPDEs,” Communications on Pure and Applied Mathematics, vol. 72, no. 9. Wiley, pp. 1983–2005, 2019.","mla":"Gerencser, Mate, and Martin Hairer. “A Solution Theory for Quasilinear Singular SPDEs.” Communications on Pure and Applied Mathematics, vol. 72, no. 9, Wiley, 2019, pp. 1983–2005, doi:10.1002/cpa.21816.","ama":"Gerencser M, Hairer M. A solution theory for quasilinear singular SPDEs. Communications on Pure and Applied Mathematics. 2019;72(9):1983-2005. doi:10.1002/cpa.21816"},"author":[{"full_name":"Gerencser, Mate","first_name":"Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hairer, Martin","last_name":"Hairer","first_name":"Martin"}]},{"date_published":"2019-04-16T00:00:00Z","publication_status":"published","oa_version":"Submitted Version","year":"2019","citation":{"ama":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. JuliaReach: A toolbox for set-based reachability. In: Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. Vol 22. ACM; 2019:39-44. doi:10.1145/3302504.3311804","apa":"Bogomolov, S., Forets, M., Frehse, G., Potomkin, K., & Schilling, C. (2019). JuliaReach: A toolbox for set-based reachability. In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control (Vol. 22, pp. 39–44). Montreal, QC, Canada: ACM. https://doi.org/10.1145/3302504.3311804","ieee":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, and C. Schilling, “JuliaReach: A toolbox for set-based reachability,” in Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, Montreal, QC, Canada, 2019, vol. 22, pp. 39–44.","mla":"Bogomolov, Sergiy, et al. “JuliaReach: A Toolbox for Set-Based Reachability.” Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, vol. 22, ACM, 2019, pp. 39–44, doi:10.1145/3302504.3311804.","short":"S. Bogomolov, M. Forets, G. Frehse, K. Potomkin, C. Schilling, in:, Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 39–44.","chicago":"Bogomolov, Sergiy, Marcelo Forets, Goran Frehse, Kostiantyn Potomkin, and Christian Schilling. “JuliaReach: A Toolbox for Set-Based Reachability.” In Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control, 22:39–44. ACM, 2019. https://doi.org/10.1145/3302504.3311804.","ista":"Bogomolov S, Forets M, Frehse G, Potomkin K, Schilling C. 2019. JuliaReach: A toolbox for set-based reachability. Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control vol. 22, 39–44."},"month":"04","keyword":["reachability analysis","hybrid systems","lazy computation"],"author":[{"orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"full_name":"Potomkin, Kostiantyn","first_name":"Kostiantyn","last_name":"Potomkin"},{"orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"}],"department":[{"_id":"ToHe"}],"conference":{"location":"Montreal, QC, Canada","name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2019-04-18","start_date":"2019-04-16"},"oa":1,"ddc":["000"],"has_accepted_license":"1","_id":"6035","title":"JuliaReach: A toolbox for set-based reachability","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:17Z","creator":"cschilli","file_id":"6067","date_created":"2019-03-05T09:27:18Z","file_size":3784414,"file_name":"hscc19.pdf","checksum":"28ed56439aea5991c3122d4730fd828f","content_type":"application/pdf","relation":"main_file"}],"publication_identifier":{"isbn":["9781450362825"]},"intvolume":" 22","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"We present JuliaReach, a toolbox for set-based reachability analysis of dynamical systems. JuliaReach consists of two main packages: Reachability, containing implementations of reachability algorithms for continuous and hybrid systems, and LazySets, a standalone library that implements state-of-the-art algorithms for calculus with convex sets. The library offers both concrete and lazy set representations, where the latter stands for the ability to delay set computations until they are needed. The choice of the programming language Julia and the accompanying documentation of our toolbox allow researchers to easily translate set-based algorithms from mathematics to software in a platform-independent way, while achieving runtime performance that is comparable to statically compiled languages. Combining lazy operations in high dimensions and explicit computations in low dimensions, JuliaReach can be applied to solve complex, large-scale problems.","lang":"eng"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"external_id":{"arxiv":["1901.10736"],"isi":["000516713900005"]},"doi":"10.1145/3302504.3311804","volume":22,"page":"39-44","publication":"Proceedings of the 22nd International Conference on Hybrid Systems: Computation and Control","publisher":"ACM","ec_funded":1,"isi":1,"file_date_updated":"2020-07-14T12:47:17Z","arxiv":1,"date_updated":"2025-07-10T11:53:09Z","day":"16","type":"conference","date_created":"2019-02-18T14:43:28Z","status":"public"},{"file_date_updated":"2020-07-14T12:47:17Z","isi":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publisher":"Springer Nature","publication":"25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ","page":"226-243","date_created":"2019-02-18T16:44:06Z","status":"public","type":"conference","day":"04","date_updated":"2025-04-15T06:26:12Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","abstract":[{"text":"Static program analyzers are increasingly effective in checking correctness properties of programs and reporting any errors found, often in the form of error traces. However, developers still spend a significant amount of time on debugging. This involves processing long error traces in an effort to localize a bug to a relatively small part of the program and to identify its cause. In this paper, we present a technique for automated fault localization that, given a program and an error trace, efficiently narrows down the cause of the error to a few statements. These statements are then ranked in terms of their suspiciousness. Our technique relies only on the semantics of the given program and does not require any test cases or user guidance. In experiments on a set of C benchmarks, we show that our technique is effective in quickly isolating the cause of error while out-performing other state-of-the-art fault-localization techniques.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"volume":11427,"doi":"10.1007/978-3-030-17462-0_13","external_id":{"isi":["000681166500013"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"has_accepted_license":"1","ddc":["000"],"oa":1,"conference":{"end_date":"2019-04-11","start_date":"2019-04-06","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Prague, Czech Republic"},"department":[{"_id":"ToHe"}],"alternative_title":["LNCS"],"quality_controlled":"1","intvolume":" 11427","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2019_LNCS_Christakis.pdf","checksum":"9998496f6fe202c0a19124b4209154c6","file_id":"6408","date_created":"2019-05-10T14:16:05Z","file_size":773083,"creator":"dernst","date_updated":"2020-07-14T12:47:17Z","access_level":"open_access"}],"title":"Semantic fault localization and suspiciousness ranking","_id":"6042","year":"2019","oa_version":"Published Version","publication_status":"published","date_published":"2019-04-04T00:00:00Z","author":[{"full_name":"Christakis, Maria","last_name":"Christakis","first_name":"Maria"},{"full_name":"Heizmann, Matthias","last_name":"Heizmann","first_name":"Matthias"},{"last_name":"Mansur","first_name":"Muhammad Numair","full_name":"Mansur, Muhammad Numair"},{"orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","full_name":"Schilling, Christian","last_name":"Schilling","first_name":"Christian"},{"last_name":"Wüstholz","first_name":"Valentin","full_name":"Wüstholz, Valentin"}],"month":"04","citation":{"chicago":"Christakis, Maria, Matthias Heizmann, Muhammad Numair Mansur, Christian Schilling, and Valentin Wüstholz. “Semantic Fault Localization and Suspiciousness Ranking.” In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , 11427:226–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17462-0_13.","short":"M. Christakis, M. Heizmann, M.N. Mansur, C. Schilling, V. Wüstholz, in:, 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2019, pp. 226–243.","ista":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. 2019. Semantic fault localization and suspiciousness ranking. 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 11427, 226–243.","ama":"Christakis M, Heizmann M, Mansur MN, Schilling C, Wüstholz V. Semantic fault localization and suspiciousness ranking. In: 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . Vol 11427. Springer Nature; 2019:226-243. doi:10.1007/978-3-030-17462-0_13","apa":"Christakis, M., Heizmann, M., Mansur, M. N., Schilling, C., & Wüstholz, V. (2019). Semantic fault localization and suspiciousness ranking. In 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (Vol. 11427, pp. 226–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-17462-0_13","ieee":"M. Christakis, M. Heizmann, M. N. Mansur, C. Schilling, and V. Wüstholz, “Semantic fault localization and suspiciousness ranking,” in 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Prague, Czech Republic, 2019, vol. 11427, pp. 226–243.","mla":"Christakis, Maria, et al. “Semantic Fault Localization and Suspiciousness Ranking.” 25th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , vol. 11427, Springer Nature, 2019, pp. 226–43, doi:10.1007/978-3-030-17462-0_13."}},{"title":"Temporal order and precision of complex stress responses in individual bacteria","_id":"6046","intvolume":" 15","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30765425"}],"department":[{"_id":"GaTk"}],"oa":1,"month":"02","citation":{"apa":"Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2019). Temporal order and precision of complex stress responses in individual bacteria. Molecular Systems Biology. Embo Press. https://doi.org/10.15252/msb.20188470","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Temporal order and precision of complex stress responses in individual bacteria,” Molecular systems biology, vol. 15, no. 2. Embo Press, 2019.","mla":"Mitosch, Karin, et al. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology, vol. 15, no. 2, e8470, Embo Press, 2019, doi:10.15252/msb.20188470.","ama":"Mitosch K, Rieckh G, Bollenbach MT. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 2019;15(2). doi:10.15252/msb.20188470","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Molecular Systems Biology 15 (2019).","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Temporal Order and Precision of Complex Stress Responses in Individual Bacteria.” Molecular Systems Biology. Embo Press, 2019. https://doi.org/10.15252/msb.20188470.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2019. Temporal order and precision of complex stress responses in individual bacteria. Molecular systems biology. 15(2), e8470."},"issue":"2","author":[{"full_name":"Mitosch, Karin","first_name":"Karin","last_name":"Mitosch","id":"39B66846-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Georg","last_name":"Rieckh","full_name":"Rieckh, Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"date_published":"2019-02-14T00:00:00Z","year":"2019","oa_version":"Submitted Version","publication_status":"published","date_updated":"2025-04-15T08:09:37Z","type":"journal_article","day":"14","status":"public","date_created":"2019-02-24T22:59:18Z","pmid":1,"publisher":"Embo Press","publication":"Molecular systems biology","isi":1,"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"}],"doi":"10.15252/msb.20188470","external_id":{"isi":["000459628300003"],"pmid":["30765425"]},"volume":15,"language":[{"iso":"eng"}],"article_number":"e8470","scopus_import":"1","article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"text":"Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"month":"01","issue":"4","citation":{"short":"D. De Martino, Journal of Physics A: Mathematical and Theoretical 52 (2019).","chicago":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2019. https://doi.org/10.1088/1751-8121/aaf2dd.","ista":"De Martino D. 2019. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 52(4), 045002.","apa":"De Martino, D. (2019). Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/aaf2dd","ieee":"D. De Martino, “Feedback-induced self-oscillations in large interacting systems subjected to phase transitions,” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4. IOP Publishing, 2019.","mla":"De Martino, Daniele. “Feedback-Induced Self-Oscillations in Large Interacting Systems Subjected to Phase Transitions.” Journal of Physics A: Mathematical and Theoretical, vol. 52, no. 4, 045002, IOP Publishing, 2019, doi:10.1088/1751-8121/aaf2dd.","ama":"De Martino D. Feedback-induced self-oscillations in large interacting systems subjected to phase transitions. Journal of Physics A: Mathematical and Theoretical. 2019;52(4). doi:10.1088/1751-8121/aaf2dd"},"author":[{"orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","first_name":"Daniele","full_name":"De Martino, Daniele"}],"corr_author":"1","date_published":"2019-01-07T00:00:00Z","year":"2019","oa_version":"Published Version","publication_status":"published","title":"Feedback-induced self-oscillations in large interacting systems subjected to phase transitions","_id":"6049","file":[{"date_updated":"2020-07-14T12:47:17Z","access_level":"open_access","file_id":"6344","file_size":1804557,"date_created":"2019-04-19T12:18:57Z","creator":"kschuh","file_name":"2019_IOP_DeMartino.pdf","checksum":"1112304ad363a6d8afaeccece36473cf","relation":"main_file","content_type":"application/pdf"}],"intvolume":" 52","quality_controlled":"1","department":[{"_id":"GaTk"}],"oa":1,"has_accepted_license":"1","ddc":["570"],"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"doi":"10.1088/1751-8121/aaf2dd","external_id":{"isi":["000455379500001"]},"volume":52,"language":[{"iso":"eng"}],"article_number":"045002","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","abstract":[{"lang":"eng","text":"In this article it is shown that large systems with many interacting units endowing multiple phases display self-oscillations in the presence of linear feedback between the control and order parameters, where an Andronov–Hopf bifurcation takes over the phase transition. This is simply illustrated through the mean field Landau theory whose feedback dynamics turn out to be described by the Van der Pol equation and it is then validated for the fully connected Ising model following heat bath dynamics. Despite its simplicity, this theory accounts potentially for a rich range of phenomena: here it is applied to describe in a stylized way (i) excess demand-price cycles due to strong herding in a simple agent-based market model; (ii) congestion waves in queuing networks triggered by user feedback to delays in overloaded conditions; and (iii) metabolic network oscillations resulting from cell growth control in a bistable phenotypic landscape."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-04-15T06:50:24Z","type":"journal_article","day":"07","date_created":"2019-02-24T22:59:19Z","status":"public","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publisher":"IOP Publishing","publication":"Journal of Physics A: Mathematical and Theoretical","file_date_updated":"2020-07-14T12:47:17Z","isi":1},{"volume":147,"doi":"10.1090/proc/14240","external_id":{"arxiv":["1709.02562"],"isi":["000450363900008"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We answer a question of David Hilbert: given two circles it is not possible in general to construct their centers using only a straightedge. On the other hand, we give infinitely many families of pairs of circles for which such construction is possible. "}],"scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2019-02-24T22:59:19Z","status":"public","type":"journal_article","day":"01","arxiv":1,"date_updated":"2023-08-24T14:48:59Z","isi":1,"publisher":"AMS","publication":"Proceedings of the American Mathematical Society","page":"91-102","author":[{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X"},{"last_name":"Fedorov","first_name":"Roman","full_name":"Fedorov, Roman"}],"month":"01","citation":{"chicago":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14240.","short":"A. Akopyan, R. Fedorov, Proceedings of the American Mathematical Society 147 (2019) 91–102.","ista":"Akopyan A, Fedorov R. 2019. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 147, 91–102.","ieee":"A. Akopyan and R. Fedorov, “Two circles and only a straightedge,” Proceedings of the American Mathematical Society, vol. 147. AMS, pp. 91–102, 2019.","apa":"Akopyan, A., & Fedorov, R. (2019). Two circles and only a straightedge. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14240","mla":"Akopyan, Arseniy, and Roman Fedorov. “Two Circles and Only a Straightedge.” Proceedings of the American Mathematical Society, vol. 147, AMS, 2019, pp. 91–102, doi:10.1090/proc/14240.","ama":"Akopyan A, Fedorov R. Two circles and only a straightedge. Proceedings of the American Mathematical Society. 2019;147:91-102. doi:10.1090/proc/14240"},"year":"2019","oa_version":"Preprint","publication_status":"published","date_published":"2019-01-01T00:00:00Z","quality_controlled":"1","intvolume":" 147","title":"Two circles and only a straightedge","_id":"6050","oa":1,"department":[{"_id":"HeEd"}],"main_file_link":[{"url":"https://arxiv.org/abs/1709.02562","open_access":"1"}]},{"pmid":1,"page":"832–863","publication":"Nature Protocols","ec_funded":1,"publisher":"Nature Publishing Group","isi":1,"file_date_updated":"2021-06-29T14:41:46Z","date_updated":"2025-04-14T07:44:00Z","day":"01","type":"journal_article","date_created":"2019-02-24T22:59:20Z","status":"public","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Expansion microscopy is a relatively new approach to super-resolution imaging that uses expandable hydrogels to isotropically increase the physical distance between fluorophores in biological samples such as cell cultures or tissue slices. The classic gel recipe results in an expansion factor of ~4×, with a resolution of 60–80 nm. We have recently developed X10 microscopy, which uses a gel that achieves an expansion factor of ~10×, with a resolution of ~25 nm. Here, we provide a step-by-step protocol for X10 expansion microscopy. A typical experiment consists of seven sequential stages: (i) immunostaining, (ii) anchoring, (iii) polymerization, (iv) homogenization, (v) expansion, (vi) imaging, and (vii) validation. The protocol presented here includes recommendations for optimization, pitfalls and their solutions, and detailed guidelines that should increase reproducibility. Although our protocol focuses on X10 expansion microscopy, we detail which of these suggestions are also applicable to classic fourfold expansion microscopy. We exemplify our protocol using primary hippocampal neurons from rats, but our approach can be used with other primary cells or cultured cell lines of interest. This protocol will enable any researcher with basic experience in immunostainings and access to an epifluorescence microscope to perform super-resolution microscopy with X10. The procedure takes 3 d and requires ~5 h of actively handling the sample for labeling and expansion, and another ~3 h for imaging and analysis."}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"}],"external_id":{"isi":["000459890700008"],"pmid":["30778205"]},"doi":"10.1038/s41596-018-0117-3","volume":14,"department":[{"_id":"JoDa"},{"_id":"Bio"}],"oa":1,"ddc":["570"],"has_accepted_license":"1","_id":"6052","title":"A practical guide to optimization in X10 expansion microscopy","file":[{"checksum":"7efb9951e7ddf3e3dcc2fb92b859c623","file_name":"181031_Truckenbrodt_ExM_NatProtoc.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"main_file","access_level":"open_access","date_updated":"2021-06-29T14:41:46Z","creator":"kschuh","date_created":"2021-06-29T14:41:46Z","file_size":84478958,"file_id":"9619","success":1}],"intvolume":" 14","quality_controlled":"1","article_type":"original","date_published":"2019-03-01T00:00:00Z","publication_status":"published","oa_version":"Submitted Version","year":"2019","issue":"3","citation":{"ista":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. 2019. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 14(3), 832–863.","chicago":"Truckenbrodt, Sven M, Christoph M Sommer, Silvio O Rizzoli, and Johann G Danzl. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols. Nature Publishing Group, 2019. https://doi.org/10.1038/s41596-018-0117-3.","short":"S.M. Truckenbrodt, C.M. Sommer, S.O. Rizzoli, J.G. Danzl, Nature Protocols 14 (2019) 832–863.","ama":"Truckenbrodt SM, Sommer CM, Rizzoli SO, Danzl JG. A practical guide to optimization in X10 expansion microscopy. Nature Protocols. 2019;14(3):832–863. doi:10.1038/s41596-018-0117-3","mla":"Truckenbrodt, Sven M., et al. “A Practical Guide to Optimization in X10 Expansion Microscopy.” Nature Protocols, vol. 14, no. 3, Nature Publishing Group, 2019, pp. 832–863, doi:10.1038/s41596-018-0117-3.","apa":"Truckenbrodt, S. M., Sommer, C. M., Rizzoli, S. O., & Danzl, J. G. (2019). A practical guide to optimization in X10 expansion microscopy. Nature Protocols. Nature Publishing Group. https://doi.org/10.1038/s41596-018-0117-3","ieee":"S. M. Truckenbrodt, C. M. Sommer, S. O. Rizzoli, and J. G. Danzl, “A practical guide to optimization in X10 expansion microscopy,” Nature Protocols, vol. 14, no. 3. Nature Publishing Group, pp. 832–863, 2019."},"month":"03","author":[{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","first_name":"Sven M"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer"},{"full_name":"Rizzoli, Silvio O","last_name":"Rizzoli","first_name":"Silvio O"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"}]},{"publication_identifier":{"eissn":["1748-3395"],"issn":["1748-3387"]},"_id":"6053","title":"Quantum electromechanics of a hypersonic crystal","quality_controlled":"1","intvolume":" 14","department":[{"_id":"JoFi"}],"main_file_link":[{"open_access":"1","url":"https://authors.library.caltech.edu/92123/"}],"oa":1,"citation":{"ama":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 2019;14(4):334–339. doi:10.1038/s41565-019-0377-2","mla":"Kalaee, Mahmoud, et al. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology, vol. 14, no. 4, Springer Nature, 2019, pp. 334–339, doi:10.1038/s41565-019-0377-2.","ieee":"M. Kalaee, M. Mirhosseini, P. B. Dieterle, M. Peruzzo, J. M. Fink, and O. Painter, “Quantum electromechanics of a hypersonic crystal,” Nature Nanotechnology, vol. 14, no. 4. Springer Nature, pp. 334–339, 2019.","apa":"Kalaee, M., Mirhosseini, M., Dieterle, P. B., Peruzzo, M., Fink, J. M., & Painter, O. (2019). Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. Springer Nature. https://doi.org/10.1038/s41565-019-0377-2","ista":"Kalaee M, Mirhosseini M, Dieterle PB, Peruzzo M, Fink JM, Painter O. 2019. Quantum electromechanics of a hypersonic crystal. Nature Nanotechnology. 14(4), 334–339.","short":"M. Kalaee, M. Mirhosseini, P.B. Dieterle, M. Peruzzo, J.M. Fink, O. Painter, Nature Nanotechnology 14 (2019) 334–339.","chicago":"Kalaee, Mahmoud, Mohammad Mirhosseini, Paul B. Dieterle, Matilda Peruzzo, Johannes M Fink, and Oskar Painter. “Quantum Electromechanics of a Hypersonic Crystal.” Nature Nanotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41565-019-0377-2."},"issue":"4","month":"04","author":[{"full_name":"Kalaee, Mahmoud","last_name":"Kalaee","first_name":"Mahmoud"},{"full_name":"Mirhosseini, Mohammad","first_name":"Mohammad","last_name":"Mirhosseini"},{"first_name":"Paul B.","last_name":"Dieterle","full_name":"Dieterle, Paul B."},{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","first_name":"Matilda","last_name":"Peruzzo"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"}],"article_type":"original","publication_status":"published","oa_version":"Submitted Version","year":"2019","date_published":"2019-04-01T00:00:00Z","day":"01","type":"journal_article","date_updated":"2023-08-24T14:48:08Z","date_created":"2019-02-24T22:59:21Z","status":"public","page":"334–339","isi":1,"publication":"Nature Nanotechnology","publisher":"Springer Nature","external_id":{"isi":["000463195700014"]},"doi":"10.1038/s41565-019-0377-2","volume":14,"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Recent technical developments in the fields of quantum electromechanics and optomechanics have spawned nanoscale mechanical transducers with the sensitivity to measure mechanical displacements at the femtometre scale and the ability to convert electromagnetic signals at the single photon level. A key challenge in this field is obtaining strong coupling between motion and electromagnetic fields without adding additional decoherence. Here we present an electromechanical transducer that integrates a high-frequency (0.42 GHz) hypersonic phononic crystal with a superconducting microwave circuit. The use of a phononic bandgap crystal enables quantum-level transduction of hypersonic mechanical motion and concurrently eliminates decoherence caused by acoustic radiation. Devices with hypersonic mechanical frequencies provide a natural pathway for integration with Josephson junction quantum circuits, a leading quantum computing technology, and nanophotonic systems capable of optical networking and distributing quantum information."}],"article_processing_charge":"No"},{"author":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"related_material":{"record":[{"id":"6418","status":"public","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:6060","month":"02","citation":{"ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.","chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060.","short":"B. Vicoso, (2019).","ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060","mla":"Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.","ieee":"B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019.","apa":"Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060"},"year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"No","date_published":"2019-02-28T00:00:00Z","status":"public","date_created":"2019-02-28T10:55:15Z","type":"research_data","file":[{"checksum":"a338a622d728af0e3199cb07e6dd64d3","file_name":"SupData.zip","content_type":"application/zip","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:17Z","creator":"bvicoso","date_created":"2019-02-28T10:54:27Z","file_size":36646050,"file_id":"6061"}],"day":"28","title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","date_updated":"2025-04-15T07:49:47Z","_id":"6060","file_date_updated":"2020-07-14T12:47:17Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","oa":1,"department":[{"_id":"BeVi"}]},{"file_date_updated":"2020-07-14T12:47:18Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png"},"oa":1,"department":[{"_id":"JoCs"}],"date_created":"2019-03-04T14:20:58Z","status":"public","type":"research_data","file":[{"content_type":"application/zip","relation":"main_file","file_name":"Online_data.zip","checksum":"48e7b9a02939b763417733239522a236","creator":"mnardin","file_id":"6068","file_size":37002186,"date_created":"2019-03-05T09:29:37Z","access_level":"open_access","date_updated":"2020-07-14T12:47:18Z","title":"Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\""}],"day":"29","title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","date_updated":"2025-04-15T07:21:17Z","_id":"6062","year":"2019","license":"https://creativecommons.org/licenses/by-sa/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","article_processing_charge":"No","date_published":"2019-03-29T00:00:00Z","abstract":[{"text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7).","lang":"eng"}],"author":[{"orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin"}],"doi":"10.15479/AT:ISTA:6062","related_material":{"record":[{"relation":"research_paper","status":"public","id":"6194"}]},"month":"03","citation":{"ama":"Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062","ieee":"M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.","apa":"Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6062","mla":"Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal Cognitive Map Is Attracted to Goals.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6062.","short":"M. Nardin, (2019).","chicago":"Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6062.","ista":"Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6062."}},{"publication":"Nature Communications","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"publisher":"Springer Nature","file_date_updated":"2020-07-14T12:47:18Z","isi":1,"status":"public","date_created":"2019-03-05T13:18:30Z","date_updated":"2025-04-14T07:44:00Z","day":"26","type":"journal_article","abstract":[{"lang":"eng","text":"Electron transport in two-dimensional conducting materials such as graphene, with dominant electron–electron interaction, exhibits unusual vortex flow that leads to a nonlocal current-field relation (negative resistance), distinct from the classical Ohm’s law. The transport behavior of these materials is best described by low Reynolds number hydrodynamics, where the constitutive pressure–speed relation is Stoke’s law. Here we report evidence of such vortices observed in a viscous flow of Newtonian fluid in a microfluidic device consisting of a rectangular cavity—analogous to the electronic system. We extend our experimental observations to elliptic cavities of different eccentricities, and validate them by numerically solving bi-harmonic equation obtained for the viscous flow with no-slip boundary conditions. We verify the existence of a predicted threshold at which vortices appear. Strikingly, we find that a two-dimensional theoretical model captures the essential features of three-dimensional Stokes flow in experiments."}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"937","language":[{"iso":"eng"}],"scopus_import":"1","volume":10,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000459704600001"]},"doi":"10.1038/s41467-019-08916-5","oa":1,"ddc":["530","532"],"has_accepted_license":"1","department":[{"_id":"BjHo"}],"intvolume":" 10","quality_controlled":"1","_id":"6069","title":"Stokes flow analogous to viscous electron current in graphene","file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2019_NatureComm_Mayzel.pdf","checksum":"61192fc49e0d44907c2a4fe384e4b97f","file_id":"6070","date_created":"2019-03-05T13:33:04Z","file_size":2646391,"creator":"dernst","date_updated":"2020-07-14T12:47:18Z","access_level":"open_access"}],"publication_identifier":{"issn":["2041-1723"]},"date_published":"2019-02-26T00:00:00Z","publication_status":"published","oa_version":"Published Version","year":"2019","corr_author":"1","author":[{"first_name":"Jonathan","last_name":"Mayzel","full_name":"Mayzel, Jonathan"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"},{"full_name":"Varshney, Atul","first_name":"Atul","last_name":"Varshney","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ista":"Mayzel J, Steinberg V, Varshney A. 2019. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 10, 937.","chicago":"Mayzel, Jonathan, Victor Steinberg, and Atul Varshney. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-08916-5.","short":"J. Mayzel, V. Steinberg, A. Varshney, Nature Communications 10 (2019).","ama":"Mayzel J, Steinberg V, Varshney A. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 2019;10. doi:10.1038/s41467-019-08916-5","mla":"Mayzel, Jonathan, et al. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications, vol. 10, 937, Springer Nature, 2019, doi:10.1038/s41467-019-08916-5.","ieee":"J. Mayzel, V. Steinberg, and A. Varshney, “Stokes flow analogous to viscous electron current in graphene,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Mayzel, J., Steinberg, V., & Varshney, A. (2019). Stokes flow analogous to viscous electron current in graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-08916-5"},"month":"02"},{"type":"dissertation","day":"11","date_updated":"2025-09-22T07:55:44Z","status":"public","date_created":"2019-03-06T16:16:10Z","page":"189","file_date_updated":"2020-07-14T12:47:18Z","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:th6071","supervisor":[{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. "}],"publication_identifier":{"issn":["2663-337X"]},"file":[{"file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","checksum":"e60a72de35d270b31f1a23d50f224ec0","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:47:18Z","access_level":"open_access","file_id":"6072","file_size":20995465,"date_created":"2019-03-06T16:05:07Z","creator":"rprizak"},{"relation":"source_file","content_type":"application/zip","checksum":"67c2630333d05ebafef5f018863a8465","file_name":"thesis_v2_merge.zip","file_size":85705272,"date_created":"2019-03-06T16:09:39Z","file_id":"6073","creator":"rprizak","title":"Latex files","date_updated":"2020-07-14T12:47:18Z","access_level":"closed"}],"title":"Coevolution of transcription factors and their binding sites in sequence space","_id":"6071","alternative_title":["ISTA Thesis"],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"has_accepted_license":"1","ddc":["576"],"oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"955"},{"id":"1358","status":"public","relation":"part_of_dissertation"}]},"month":"03","citation":{"ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071."},"author":[{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan"}],"corr_author":"1","year":"2019","oa_version":"Published Version","publication_status":"published","degree_awarded":"PhD","date_published":"2019-03-11T00:00:00Z"},{"day":"09","file":[{"date_created":"2019-03-07T13:37:19Z","file_size":33202743,"file_id":"6084","creator":"dernst","date_updated":"2020-07-14T12:47:18Z","access_level":"open_access","relation":"supplementary_material","content_type":"application/zip","checksum":"bc1b285edca9e98a2c63d153c79bb75b","file_name":"Setd5_paper.zip"}],"type":"research_data","_id":"6074","title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","date_updated":"2025-04-15T07:50:27Z","status":"public","date_created":"2019-03-07T13:32:35Z","department":[{"_id":"GaNo"}],"ddc":["570"],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:18Z","oa":1,"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:6074","related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"citation":{"ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","mla":"Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074.","chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074.","short":"C. Dotter, G. Novarino, (2019).","ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074."},"month":"01","author":[{"orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","year":"2019","date_published":"2019-01-09T00:00:00Z","abstract":[{"lang":"eng","text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS."}],"article_processing_charge":"No"},{"publication_status":"published","oa_version":"Preprint","year":"2019","date_published":"2019-04-01T00:00:00Z","citation":{"ama":"Sadel C, Xu D. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 2019;39(4):1082-1098. doi:10.1017/etds.2017.52","apa":"Sadel, C., & Xu, D. (2019). Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2017.52","ieee":"C. Sadel and D. Xu, “Singular analytic linear cocycles with negative infinite Lyapunov exponents,” Ergodic Theory and Dynamical Systems, vol. 39, no. 4. Cambridge University Press, pp. 1082–1098, 2019.","mla":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems, vol. 39, no. 4, Cambridge University Press, 2019, pp. 1082–98, doi:10.1017/etds.2017.52.","short":"C. Sadel, D. Xu, Ergodic Theory and Dynamical Systems 39 (2019) 1082–1098.","chicago":"Sadel, Christian, and Disheng Xu. “Singular Analytic Linear Cocycles with Negative Infinite Lyapunov Exponents.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2019. https://doi.org/10.1017/etds.2017.52.","ista":"Sadel C, Xu D. 2019. Singular analytic linear cocycles with negative infinite Lyapunov exponents. Ergodic Theory and Dynamical Systems. 39(4), 1082–1098."},"issue":"4","month":"04","author":[{"first_name":"Christian","last_name":"Sadel","full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xu, Disheng","last_name":"Xu","first_name":"Disheng"}],"department":[{"_id":"LaEr"}],"main_file_link":[{"url":"https://arxiv.org/abs/1601.06118","open_access":"1"}],"oa":1,"_id":"6086","title":"Singular analytic linear cocycles with negative infinite Lyapunov exponents","quality_controlled":"1","intvolume":" 39","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"We show that linear analytic cocycles where all Lyapunov exponents are negative infinite are nilpotent. For such one-frequency cocycles we show that they can be analytically conjugated to an upper triangular cocycle or a Jordan normal form. As a consequence, an arbitrarily small analytic perturbation leads to distinct Lyapunov exponents. Moreover, in the one-frequency case where the th Lyapunov exponent is finite and the st negative infinite, we obtain a simple criterion for domination in which case there is a splitting into a nilpotent part and an invertible part."}],"article_processing_charge":"No","external_id":{"arxiv":["1601.06118"],"isi":["000459725600012"]},"doi":"10.1017/etds.2017.52","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"volume":39,"page":"1082-1098","isi":1,"publication":"Ergodic Theory and Dynamical Systems","ec_funded":1,"publisher":"Cambridge University Press","day":"01","type":"journal_article","date_updated":"2025-04-15T06:50:24Z","arxiv":1,"status":"public","date_created":"2019-03-10T22:59:18Z"},{"pmid":1,"acknowledgement":"We thank Roland Dosch, Makoto Furutani-Seiki, Brian Link, Mary Mullins, and Masazumi Tada for providing transgenic and/or mutant zebrafish lines; Alexandra Schauer, Shayan Shami-Pour, and the rest of the Heisenberg lab for technical assistance and feedback on the manuscript; and the Bioimaging, Electron Microscopy, and Zebrafish facilities of IST Austria for continuous support. This work was supported by an ERC advanced grant ( MECSPEC to C.-P.H.).","page":"1379-1392.e14","publication":"Cell","ec_funded":1,"publisher":"Elsevier","isi":1,"date_updated":"2025-04-14T07:46:59Z","day":"07","type":"journal_article","date_created":"2019-03-10T22:59:19Z","status":"public","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Cell fate specification by lateral inhibition typically involves contact signaling through the Delta-Notch signaling pathway. However, whether this is the only signaling mode mediating lateral inhibition remains unclear. Here we show that in zebrafish oogenesis, a group of cells within the granulosa cell layer at the oocyte animal pole acquire elevated levels of the transcriptional coactivator TAZ in their nuclei. One of these cells, the future micropyle precursor cell (MPC), accumulates increasingly high levels of nuclear TAZ and grows faster than its surrounding cells, mechanically compressing those cells, which ultimately lose TAZ from their nuclei. Strikingly, relieving neighbor-cell compression by MPC ablation or aspiration restores nuclear TAZ accumulation in neighboring cells, eventually leading to MPC re-specification from these cells. Conversely, MPC specification is defective in taz−/− follicles. These findings uncover a novel mode of lateral inhibition in cell fate specification based on mechanical signals controlling TAZ activity."}],"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"LifeSc"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"external_id":{"isi":["000460509600013"],"pmid":["30773315"]},"doi":"10.1016/j.cell.2019.01.019","volume":176,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.01.019"}],"department":[{"_id":"CaHe"},{"_id":"EM-Fac"}],"oa":1,"_id":"6087","title":"Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity","intvolume":" 176","quality_controlled":"1","article_type":"original","date_published":"2019-03-07T00:00:00Z","publication_status":"published","oa_version":"Published Version","year":"2019","citation":{"ama":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 2019;176(6):1379-1392.e14. doi:10.1016/j.cell.2019.01.019","mla":"Xia, Peng, et al. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell, vol. 176, no. 6, Elsevier, 2019, p. 1379–1392.e14, doi:10.1016/j.cell.2019.01.019.","ieee":"P. Xia, D. J. Gütl, V. Zheden, and C.-P. J. Heisenberg, “Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity,” Cell, vol. 176, no. 6. Elsevier, p. 1379–1392.e14, 2019.","apa":"Xia, P., Gütl, D. J., Zheden, V., & Heisenberg, C.-P. J. (2019). Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.01.019","ista":"Xia P, Gütl DJ, Zheden V, Heisenberg C-PJ. 2019. Lateral inhibition in cell specification mediated by mechanical signals modulating TAZ activity. Cell. 176(6), 1379–1392.e14.","short":"P. Xia, D.J. Gütl, V. Zheden, C.-P.J. Heisenberg, Cell 176 (2019) 1379–1392.e14.","chicago":"Xia, Peng, Daniel J Gütl, Vanessa Zheden, and Carl-Philipp J Heisenberg. “Lateral Inhibition in Cell Specification Mediated by Mechanical Signals Modulating TAZ Activity.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.01.019."},"issue":"6","month":"03","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/in-zebrafish-eggs-most-rapidly-growing-cell-inhibits-its-neighbours-through-mechanical-signals/"}]},"author":[{"last_name":"Xia","first_name":"Peng","full_name":"Xia, Peng","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5419-7756"},{"first_name":"Daniel J","last_name":"Gütl","full_name":"Gütl, Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","abstract":[{"lang":"eng","text":"P-Glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) are two efflux transporters at the blood–brain barrier (BBB), which effectively restrict brain distribution of diverse drugs, such as tyrosine kinase inhibitors. There is a crucial need for pharmacological ABCB1 and ABCG2 inhibition protocols for a more effective treatment of brain diseases. In the present study, seven marketed drugs (osimertinib, erlotinib, nilotinib, imatinib, lapatinib, pazopanib, and cyclosporine A) and one nonmarketed drug (tariquidar), with known in vitro ABCB1/ABCG2 inhibitory properties, were screened for their inhibitory potency at the BBB in vivo. Positron emission tomography (PET) using the model ABCB1/ABCG2 substrate [11C]erlotinib was performed in mice. Tested inhibitors were administered as i.v. bolus injections at 30 min before the start of the PET scan, followed by a continuous i.v. infusion for the duration of the PET scan. Five of the tested drugs increased total distribution volume of [11C]erlotinib in the brain (VT,brain) compared to vehicle-treated animals (tariquidar, + 69%; erlotinib, + 19% and +23% for the 21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 22%; lapatinib, + 25%; and cyclosporine A, + 49%). For all drugs, increases in [11C]erlotinib brain distribution were lower than in Abcb1a/b(−/−)Abcg2(−/−) mice (+149%), which suggested that only partial ABCB1/ABCG2 inhibition was reached at the mouse BBB. The plasma concentrations of the tested drugs at the time of the PET scan were higher than clinically achievable plasma concentrations. Some of the tested drugs led to significant increases in blood radioactivity concentrations measured at the end of the PET scan (erlotinib, + 103% and +113% for the 21.5 mg/kg and the 43 mg/kg dose, respectively; imatinib, + 125%; and cyclosporine A, + 101%), which was most likely caused by decreased hepatobiliary excretion of radioactivity. Taken together, our data suggest that some marketed tyrosine kinase inhibitors may be repurposed to inhibit ABCB1 and ABCG2 at the BBB. From a clinical perspective, moderate increases in brain delivery despite the administration of high i.v. doses as well as peripheral drug–drug interactions due to transporter inhibition in clearance organs question the translatability of this concept."}],"scopus_import":"1","language":[{"iso":"eng"}],"volume":16,"doi":"10.1021/acs.molpharmaceut.8b01217","external_id":{"pmid":["30694684"],"isi":["000460600400031"]},"isi":1,"publisher":"American Chemical Society","publication":"Molecular Pharmaceutics","page":"1282-1293","pmid":1,"status":"public","date_created":"2019-03-10T22:59:19Z","type":"journal_article","day":"04","date_updated":"2023-08-25T08:02:51Z","year":"2019","publication_status":"published","oa_version":"None","date_published":"2019-03-04T00:00:00Z","author":[{"full_name":"Traxl, Alexander","last_name":"Traxl","first_name":"Alexander"},{"first_name":"Severin","last_name":"Mairinger","full_name":"Mairinger, Severin"},{"first_name":"Thomas","last_name":"Filip","full_name":"Filip, Thomas"},{"first_name":"Michael","last_name":"Sauberer","full_name":"Sauberer, Michael"},{"last_name":"Stanek","first_name":"Johann","full_name":"Stanek, Johann"},{"last_name":"Poschner","first_name":"Stefan","full_name":"Poschner, Stefan"},{"last_name":"Jäger","first_name":"Walter","full_name":"Jäger, Walter"},{"last_name":"Zoufal","first_name":"Viktoria","full_name":"Zoufal, Viktoria"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"},{"first_name":"Nicolas","last_name":"Tournier","full_name":"Tournier, Nicolas"},{"last_name":"Bauer","first_name":"Martin","full_name":"Bauer, Martin"},{"full_name":"Wanek, Thomas","first_name":"Thomas","last_name":"Wanek"},{"last_name":"Langer","first_name":"Oliver","full_name":"Langer, Oliver"}],"month":"03","citation":{"ama":"Traxl A, Mairinger S, Filip T, et al. Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. 2019;16(3):1282-1293. doi:10.1021/acs.molpharmaceut.8b01217","apa":"Traxl, A., Mairinger, S., Filip, T., Sauberer, M., Stanek, J., Poschner, S., … Langer, O. (2019). Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. American Chemical Society. https://doi.org/10.1021/acs.molpharmaceut.8b01217","ieee":"A. Traxl et al., “Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” Molecular Pharmaceutics, vol. 16, no. 3. American Chemical Society, pp. 1282–1293, 2019.","mla":"Traxl, Alexander, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Molecular Pharmaceutics, vol. 16, no. 3, American Chemical Society, 2019, pp. 1282–93, doi:10.1021/acs.molpharmaceut.8b01217.","short":"A. Traxl, S. Mairinger, T. Filip, M. Sauberer, J. Stanek, S. Poschner, W. Jäger, V. Zoufal, G. Novarino, N. Tournier, M. Bauer, T. Wanek, O. Langer, Molecular Pharmaceutics 16 (2019) 1282–1293.","chicago":"Traxl, Alexander, Severin Mairinger, Thomas Filip, Michael Sauberer, Johann Stanek, Stefan Poschner, Walter Jäger, et al. “Inhibition of ABCB1 and ABCG2 at the Mouse Blood-Brain Barrier with Marketed Drugs to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Molecular Pharmaceutics. American Chemical Society, 2019. https://doi.org/10.1021/acs.molpharmaceut.8b01217.","ista":"Traxl A, Mairinger S, Filip T, Sauberer M, Stanek J, Poschner S, Jäger W, Zoufal V, Novarino G, Tournier N, Bauer M, Wanek T, Langer O. 2019. Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Molecular Pharmaceutics. 16(3), 1282–1293."},"issue":"3","department":[{"_id":"GaNo"}],"quality_controlled":"1","intvolume":" 16","title":"Inhibition of ABCB1 and ABCG2 at the mouse blood-brain barrier with marketed drugs to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib","_id":"6088"},{"_id":"6089","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"intvolume":" 36","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa":1,"citation":{"short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246."},"issue":"3","month":"03","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5757"}]},"author":[{"last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","first_name":"Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"date_published":"2019-03-01T00:00:00Z","publication_status":"published","oa_version":"Submitted Version","year":"2019","date_updated":"2025-04-15T08:18:38Z","day":"01","type":"journal_article","date_created":"2019-03-10T22:59:19Z","status":"public","pmid":1,"page":"500-515","publication":"Molecular biology and evolution","publisher":"Oxford University Press","isi":1,"project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"doi":"10.1093/molbev/msy246","volume":36,"language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general."}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"isi":1,"publication":"Physical Review E","publisher":"American Physical Society","day":"26","type":"journal_article","date_updated":"2024-02-28T13:12:06Z","status":"public","date_created":"2019-03-10T22:59:20Z","scopus_import":"1","article_number":"022423","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"article_processing_charge":"No","external_id":{"isi":["000459916500007"]},"doi":"10.1103/PhysRevE.99.022423","volume":99,"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"oa":1,"_id":"6090","title":"Receptor crosstalk improves concentration sensing of multiple ligands","quality_controlled":"1","intvolume":" 99","oa_version":"Preprint","publication_status":"published","year":"2019","date_published":"2019-02-26T00:00:00Z","citation":{"ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423."},"issue":"2","month":"02","author":[{"first_name":"Martín","last_name":"Carballo-Pacheco","full_name":"Carballo-Pacheco, Martín"},{"full_name":"Desponds, Jonathan","first_name":"Jonathan","last_name":"Desponds"},{"full_name":"Gavrilchenko, Tatyana","first_name":"Tatyana","last_name":"Gavrilchenko"},{"first_name":"Andreas","last_name":"Mayer","full_name":"Mayer, Andreas"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan"},{"first_name":"Gautam","last_name":"Reddy","full_name":"Reddy, Gautam"},{"full_name":"Nemenman, Ilya","first_name":"Ilya","last_name":"Nemenman"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"}]},{"article_number":"e41563","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"Cortical networks are characterized by sparse connectivity, with synapses found at only a subset of axo-dendritic contacts. Yet within these networks, neurons can exhibit high connection probabilities, suggesting that cell-intrinsic factors, not proximity, determine connectivity. Here, we identify ephrin-B3 (eB3) as a factor that determines synapse density by mediating a cell-cell competition that requires ephrin-B-EphB signaling. In a microisland culture system designed to isolate cell-cell competition, we find that eB3 determines winning and losing neurons in a contest for synapses. In a Mosaic Analysis with Double Markers (MADM) genetic mouse model system in vivo the relative levels of eB3 control spine density in layer 5 and 6 neurons. MADM cortical neurons in vitro reveal that eB3 controls synapse density independently of action potential-driven activity. Our findings illustrate a new class of competitive mechanism mediated by trans-synaptic organizing proteins which control the number of synapses neurons receive relative to neighboring neurons."}],"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["30789343"],"isi":["000459380600001"]},"doi":"10.7554/eLife.41563","volume":8,"pmid":1,"publication":"eLife","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"eLife Sciences Publications","isi":1,"file_date_updated":"2020-07-14T12:47:19Z","date_updated":"2023-08-24T14:50:50Z","day":"21","type":"journal_article","status":"public","date_created":"2019-03-10T22:59:20Z","date_published":"2019-02-21T00:00:00Z","oa_version":"Published Version","publication_status":"published","year":"2019","citation":{"ama":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 2019;8. doi:10.7554/eLife.41563","mla":"Henderson, Nathan T., et al. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife, vol. 8, e41563, eLife Sciences Publications, 2019, doi:10.7554/eLife.41563.","ieee":"N. T. Henderson, S. J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, and M. B. Dalva, “Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Henderson, N. T., Le Marchand, S. J., Hruska, M., Hippenmeyer, S., Luo, L., & Dalva, M. B. (2019). Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.41563","ista":"Henderson NT, Le Marchand SJ, Hruska M, Hippenmeyer S, Luo L, Dalva MB. 2019. Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs. eLife. 8, e41563.","chicago":"Henderson, Nathan T., Sylvain J. Le Marchand, Martin Hruska, Simon Hippenmeyer, Liqun Luo, and Matthew B. Dalva. “Ephrin-B3 Controls Excitatory Synapse Density through Cell-Cell Competition for EphBs.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.41563.","short":"N.T. Henderson, S.J. Le Marchand, M. Hruska, S. Hippenmeyer, L. Luo, M.B. Dalva, ELife 8 (2019)."},"month":"02","author":[{"last_name":"Henderson","first_name":"Nathan T.","full_name":"Henderson, Nathan T."},{"first_name":"Sylvain J.","last_name":"Le Marchand","full_name":"Le Marchand, Sylvain J."},{"first_name":"Martin","last_name":"Hruska","full_name":"Hruska, Martin"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"},{"last_name":"Dalva","first_name":"Matthew B.","full_name":"Dalva, Matthew B."}],"department":[{"_id":"SiHi"}],"oa":1,"ddc":["570"],"has_accepted_license":"1","_id":"6091","title":"Ephrin-B3 controls excitatory synapse density through cell-cell competition for EphBs","file":[{"date_updated":"2020-07-14T12:47:19Z","access_level":"open_access","file_id":"6098","file_size":7260753,"date_created":"2019-03-11T16:15:37Z","creator":"dernst","file_name":"2019_eLife_Henderson.pdf","checksum":"7b0800d003f14cd06b1802dea0c52941","relation":"main_file","content_type":"application/pdf"}],"intvolume":" 8","quality_controlled":"1"},{"volume":99,"project":[{"call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"external_id":{"isi":["000459223400004"],"arxiv":["1802.01638"]},"doi":"10.1103/PhysRevB.99.064428","abstract":[{"lang":"eng","text":"In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization of a magnetic material results in mechanical rotation and vice versa. At the microscopic level, this effect governs the transfer between electron spin and orbital angular momentum, and lattice degrees of freedom, understanding which is key for molecular magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now, the timescales of electron-to-lattice angular momentum transfer remain unclear, since modeling this process on a microscopic level requires the addition of an infinite amount of quantum angular momenta. We show that this problem can be solved by reformulating it in terms of the recently discovered angulon quasiparticles, which results in a rotationally invariant quantum many-body theory. In particular, we demonstrate that nonperturbative effects take place even if the electron-phonon coupling is weak and give rise to angular momentum transfer on femtosecond timescales."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"064428","language":[{"iso":"eng"}],"scopus_import":"1","status":"public","date_created":"2019-03-10T22:59:20Z","arxiv":1,"date_updated":"2025-04-15T07:59:29Z","day":"01","type":"journal_article","publication":"Physical Review B","publisher":"American Physical Society","isi":1,"author":[{"full_name":"Mentink, Johann H","first_name":"Johann H","last_name":"Mentink"},{"full_name":"Katsnelson, Mikhail","last_name":"Katsnelson","first_name":"Mikhail"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"}],"issue":"6","citation":{"mla":"Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B, vol. 99, no. 6, 064428, American Physical Society, 2019, doi:10.1103/PhysRevB.99.064428.","apa":"Mentink, J. H., Katsnelson, M., & Lemeshko, M. (2019). Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.99.064428","ieee":"J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics of the Einstein-de Haas effect,” Physical Review B, vol. 99, no. 6. American Physical Society, 2019.","ama":"Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 2019;99(6). doi:10.1103/PhysRevB.99.064428","ista":"Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 99(6), 064428.","short":"J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).","chicago":"Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.99.064428."},"month":"02","date_published":"2019-02-01T00:00:00Z","publication_status":"published","oa_version":"Preprint","year":"2019","intvolume":" 99","quality_controlled":"1","_id":"6092","title":"Quantum many-body dynamics of the Einstein-de Haas effect","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1802.01638","open_access":"1"}],"department":[{"_id":"MiLe"}]}]