[{"publication_identifier":{"eissn":["1611-3349"],"isbn":["9-783-0308-8493-2"],"issn":["0302-9743"],"eisbn":["978-3-030-88494-9"]},"article_processing_charge":"No","oa":1,"title":"Into the unknown: active monitoring of neural networks","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"ToHe"}],"keyword":["monitoring","neural networks","novelty detection"],"day":"06","_id":"10206","date_published":"2021-10-06T00:00:00Z","quality_controlled":"1","conference":{"name":"RV: Runtime Verification","end_date":"2021-10-14","start_date":"2021-10-11","location":"Virtual"},"publisher":"Springer Nature","isi":1,"acknowledgement":"We thank Christoph Lampert and Alex Greengold for fruitful discussions. This research was supported in part by the Simons Institute for the Theory of Computing, the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","place":"Cham","doi":"10.1007/978-3-030-88494-9_3","author":[{"first_name":"Anna","last_name":"Lukina","full_name":"Lukina, Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425"},{"full_name":"Schilling, Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","first_name":"Christian","last_name":"Schilling"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"alternative_title":["LNCS"],"page":"42-61","publication_status":"published","year":"2021","month":"10","related_material":{"record":[{"status":"public","id":"13234","relation":"extended_version"}]},"volume":"12974 ","abstract":[{"text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. The typical approach is to detect inputs from novel classes and retrain the classifier on an augmented dataset. However, not only the classifier but also the detection mechanism needs to adapt in order to distinguish between newly learned and yet unknown input classes. To address this challenge, we introduce an algorithmic framework for active monitoring of a neural network. A monitor wrapped in our framework operates in parallel with the neural network and interacts with a human user via a series of interpretable labeling queries for incremental adaptation. In addition, we propose an adaptive quantitative monitor to improve precision. An experimental evaluation on a diverse set of benchmarks with varying numbers of classes confirms the benefits of our active monitoring framework in dynamic scenarios.","lang":"eng"}],"external_id":{"isi":["000719383800003"],"arxiv":["2009.06429"]},"status":"public","oa_version":"Preprint","publication":"21st International Conference on Runtime Verification","date_created":"2021-10-31T23:01:31Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2009.06429"}],"type":"conference","corr_author":"1","ec_funded":1,"citation":{"ieee":"A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring of neural networks,” in <i>21st International Conference on Runtime Verification</i>, Virtual, 2021, vol. 12974, pp. 42–61.","ista":"Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring of neural networks. 21st International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 42–61.","ama":"Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural networks. In: <i>21st International Conference on Runtime Verification</i>. Vol 12974. Cham: Springer Nature; 2021:42-61. doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">10.1007/978-3-030-88494-9_3</a>","apa":"Lukina, A., Schilling, C., &#38; Henzinger, T. A. (2021). Into the unknown: active monitoring of neural networks. In <i>21st International Conference on Runtime Verification</i> (Vol. 12974, pp. 42–61). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">https://doi.org/10.1007/978-3-030-88494-9_3</a>","short":"A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.","mla":"Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.” <i>21st International Conference on Runtime Verification</i>, vol. 12974, Springer Nature, 2021, pp. 42–61, doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">10.1007/978-3-030-88494-9_3</a>.","chicago":"Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks.” In <i>21st International Conference on Runtime Verification</i>, 12974:42–61. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">https://doi.org/10.1007/978-3-030-88494-9_3</a>."},"language":[{"iso":"eng"}],"date_updated":"2025-04-15T06:26:14Z","arxiv":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}]},{"doi":"10.4230/LIPIcs.DISC.2021.52","file":[{"file_name":"2021_LIPIcsDISC_BChatterjee.pdf","file_id":"10276","date_updated":"2021-11-12T09:23:22Z","checksum":"76546df112a0ba1166c864d33d7834e2","success":1,"file_size":795860,"content_type":"application/pdf","date_created":"2021-11-12T09:23:22Z","access_level":"open_access","creator":"cchlebak","relation":"main_file"}],"acknowledgement":"This work was partially funded by National Supercomputing Mission, Govt. of India under the project “Concurrent and Distributed Programming primitives and algorithms for Temporal Graphs”(DST/NSM/R&D_Exascale/2021/16).\r\n","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"name":"DISC: Distributed Computing","end_date":"2021-10-08","location":"Freiburg, Germany","start_date":"2021-10-04"},"quality_controlled":"1","_id":"10216","date_published":"2021-10-04T00:00:00Z","article_number":"52","day":"04","department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds","article_processing_charge":"No","publication_identifier":{"isbn":["9-783-9597-7210-5"],"issn":["1868-8969"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"       209","date_updated":"2025-05-14T10:54:39Z","ddc":["000"],"arxiv":1,"citation":{"chicago":"Chatterjee, Bapi, Sathya Peri, and Muktikanta Sa. “Brief Announcement: Non-Blocking Dynamic Unbounded Graphs with Worst-Case Amortized Bounds.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">https://doi.org/10.4230/LIPIcs.DISC.2021.52</a>.","short":"B. Chatterjee, S. Peri, M. Sa, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","mla":"Chatterjee, Bapi, et al. “Brief Announcement: Non-Blocking Dynamic Unbounded Graphs with Worst-Case Amortized Bounds.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 52, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">10.4230/LIPIcs.DISC.2021.52</a>.","ieee":"B. Chatterjee, S. Peri, and M. Sa, “Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","ista":"Chatterjee B, Peri S, Sa M. 2021. Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds. 35th International Symposium on Distributed Computing. DISC: Distributed Computing, LIPIcs, vol. 209, 52.","ama":"Chatterjee B, Peri S, Sa M. Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">10.4230/LIPIcs.DISC.2021.52</a>","apa":"Chatterjee, B., Peri, S., &#38; Sa, M. (2021). Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">https://doi.org/10.4230/LIPIcs.DISC.2021.52</a>"},"language":[{"iso":"eng"}],"date_created":"2021-11-07T23:01:23Z","oa_version":"Published Version","publication":"35th International Symposium on Distributed Computing","scopus_import":"1","type":"conference","abstract":[{"lang":"eng","text":"This paper reports a new concurrent graph data structure that supports updates of both edges and vertices and queries: Breadth-first search, Single-source shortest-path, and Betweenness centrality. The operations are provably linearizable and non-blocking."}],"status":"public","external_id":{"arxiv":["2003.01697"]},"has_accepted_license":"1","volume":209,"month":"10","year":"2021","file_date_updated":"2021-11-12T09:23:22Z","publication_status":"published","alternative_title":["LIPIcs"],"author":[{"orcid":"0000-0002-2742-4028","first_name":"Bapi","last_name":"Chatterjee","full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sathya","last_name":"Peri","full_name":"Peri, Sathya"},{"full_name":"Sa, Muktikanta","last_name":"Sa","first_name":"Muktikanta"}]},{"project":[{"grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"intvolume":"       209","date_updated":"2025-05-14T10:54:30Z","ddc":["000"],"ec_funded":1,"citation":{"chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Giorgi Nadiradze. “Lower Bounds for Shared-Memory Leader Election under Bounded Write Contention.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">https://doi.org/10.4230/LIPIcs.DISC.2021.4</a>.","ista":"Alistarh D-A, Gelashvili R, Nadiradze G. 2021. Lower bounds for shared-memory leader election under bounded write contention. 35th International Symposium on Distributed Computing. DISC: Distributed Computing, LIPIcs, vol. 209, 4.","ieee":"D.-A. Alistarh, R. Gelashvili, and G. Nadiradze, “Lower bounds for shared-memory leader election under bounded write contention,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","ama":"Alistarh D-A, Gelashvili R, Nadiradze G. Lower bounds for shared-memory leader election under bounded write contention. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">10.4230/LIPIcs.DISC.2021.4</a>","apa":"Alistarh, D.-A., Gelashvili, R., &#38; Nadiradze, G. (2021). Lower bounds for shared-memory leader election under bounded write contention. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">https://doi.org/10.4230/LIPIcs.DISC.2021.4</a>","short":"D.-A. Alistarh, R. Gelashvili, G. Nadiradze, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","mla":"Alistarh, Dan-Adrian, et al. “Lower Bounds for Shared-Memory Leader Election under Bounded Write Contention.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 4, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">10.4230/LIPIcs.DISC.2021.4</a>."},"language":[{"iso":"eng"}],"date_created":"2021-11-07T23:01:23Z","scopus_import":"1","publication":"35th International Symposium on Distributed Computing","oa_version":"Published Version","type":"conference","abstract":[{"text":"This paper gives tight logarithmic lower bounds on the solo step complexity of leader election in an asynchronous shared-memory model with single-writer multi-reader (SWMR) registers, for both deterministic and randomized obstruction-free algorithms. The approach extends to lower bounds for deterministic and randomized obstruction-free algorithms using multi-writer registers under bounded write concurrency, showing a trade-off between the solo step complexity of a leader election algorithm, and the worst-case number of stalls incurred by a processor in an execution.","lang":"eng"}],"has_accepted_license":"1","status":"public","volume":209,"month":"10","year":"2021","file_date_updated":"2021-11-12T09:33:26Z","publication_status":"published","alternative_title":["LIPIcs"],"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"full_name":"Nadiradze, Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze","orcid":"0000-0001-5634-0731","first_name":"Giorgi"}],"doi":"10.4230/LIPIcs.DISC.2021.4","acknowledgement":"Dan Alistarh: Supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Giorgi Nadiradze: Supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). The authors would like to thank the DISC anonymous reviewers for their useful\r\nfeedback and comments.","file":[{"file_name":"2021_LIPIcsDISC_Alistarh.pdf","file_id":"10277","date_updated":"2021-11-12T09:33:26Z","success":1,"checksum":"b4cdc6668c899a601c5e6a96b8ca54d9","file_size":706791,"content_type":"application/pdf","date_created":"2021-11-12T09:33:26Z","access_level":"open_access","creator":"cchlebak","relation":"main_file"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"location":"Freiburg, Germany","start_date":"2021-10-04","end_date":"2021-10-08","name":"DISC: Distributed Computing"},"_id":"10217","date_published":"2021-10-04T00:00:00Z","quality_controlled":"1","article_number":"4","day":"04","department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Lower bounds for shared-memory leader election under bounded write contention","article_processing_charge":"No","publication_identifier":{"isbn":["9-783-9597-7210-5"],"issn":["1868-8969"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"article_number":"43","_id":"10218","quality_controlled":"1","date_published":"2021-10-04T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 840605.","file":[{"access_level":"open_access","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","date_created":"2021-11-12T08:16:44Z","file_size":534219,"date_updated":"2021-11-12T08:16:44Z","file_id":"10274","file_name":"2021_LIPIcsDISC_Alistarh.pdf","checksum":"fd2a690f6856d21247e9aa952b0e2885","success":1}],"doi":"10.4230/LIPIcs.DISC.2021.43","conference":{"location":"Freiburg, Germany","start_date":"2021-10-04","end_date":"2021-10-08","name":"DISC: Distributed Computing "},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["1868-8969"],"isbn":["9-783-9597-7210-5"]},"article_processing_charge":"No","department":[{"_id":"DaAl"}],"day":"04","title":"Brief announcement: Fast graphical population protocols","oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"ec_funded":1,"citation":{"chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Brief Announcement: Fast Graphical Population Protocols.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">https://doi.org/10.4230/LIPIcs.DISC.2021.43</a>.","ieee":"D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Brief announcement: Fast graphical population protocols,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","ista":"Alistarh D-A, Gelashvili R, Rybicki J. 2021. Brief announcement: Fast graphical population protocols. 35th International Symposium on Distributed Computing. DISC: Distributed Computing , LIPIcs, vol. 209, 43.","ama":"Alistarh D-A, Gelashvili R, Rybicki J. Brief announcement: Fast graphical population protocols. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">10.4230/LIPIcs.DISC.2021.43</a>","apa":"Alistarh, D.-A., Gelashvili, R., &#38; Rybicki, J. (2021). Brief announcement: Fast graphical population protocols. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">https://doi.org/10.4230/LIPIcs.DISC.2021.43</a>","short":"D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","mla":"Alistarh, Dan-Adrian, et al. “Brief Announcement: Fast Graphical Population Protocols.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 43, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">10.4230/LIPIcs.DISC.2021.43</a>."},"external_id":{"arxiv":["2102.08808"]},"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"Let G be a graph on n nodes. In the stochastic population protocol model, a collection of n indistinguishable, resource-limited nodes collectively solve tasks via pairwise interactions. In each interaction, two randomly chosen neighbors first read each other’s states, and then update their local states. A rich line of research has established tight upper and lower bounds on the complexity of fundamental tasks, such as majority and leader election, in this model, when G is a clique. Specifically, in the clique, these tasks can be solved fast, i.e., in n polylog n pairwise interactions, with high probability, using at most polylog n states per node. In this work, we consider the more general setting where G is an arbitrary graph, and present a technique for simulating protocols designed for fully-connected networks in any connected regular graph. Our main result is a simulation that is efficient on many interesting graph families: roughly, the simulation overhead is polylogarithmic in the number of nodes, and quadratic in the conductance of the graph. As an example, this implies that, in any regular graph with conductance φ, both leader election and exact majority can be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability, using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast and space-efficient population protocols for leader election and exact majority on graphs with good expansion properties."}],"type":"conference","scopus_import":"1","oa_version":"Published Version","date_created":"2021-11-07T23:01:24Z","publication":"35th International Symposium on Distributed Computing","project":[{"name":"Coordination in constrained and natural distributed systems","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"840605"}],"ddc":["000"],"arxiv":1,"date_updated":"2025-04-14T07:50:55Z","intvolume":"       209","author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","orcid":"0000-0002-6432-6646","first_name":"Joel"}],"alternative_title":["LIPIcs"],"month":"10","volume":209,"file_date_updated":"2021-11-12T08:16:44Z","publication_status":"published","year":"2021"},{"date_published":"2021-10-04T00:00:00Z","_id":"10219","quality_controlled":"1","article_number":"58","conference":{"end_date":"2021-10-08","location":"Freiburg, Germany","start_date":"2021-10-04","name":"DISC: Distributed Computing "},"file":[{"file_id":"10275","file_name":"2021_LIPIcsDISC_Korhonen.pdf","date_updated":"2021-11-12T08:27:42Z","checksum":"c43188dc2070bbd2bf5fd6fdaf9ce36d","success":1,"file_size":474242,"date_created":"2021-11-12T08:27:42Z","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","relation":"main_file"}],"acknowledgement":"Janne H. Korhonen: Project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Ami Paz: We acknowledge the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N. Stefan Schmid: Research supported by the Austrian Science Fund (FWF) project ADVISE, I 4800-N, 2020-2023.\r\n","doi":"10.4230/LIPIcs.DISC.2021.58","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"No","publication_identifier":{"issn":["1868-8969"],"isbn":["9-783-9597-7210-5"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Brief announcement: Sinkless orientation is hard also in the supported LOCAL model","day":"04","department":[{"_id":"DaAl"}],"scopus_import":"1","oa_version":"Published Version","publication":"35th International Symposium on Distributed Computing","date_created":"2021-11-07T23:01:24Z","type":"conference","abstract":[{"lang":"eng","text":"We show that any algorithm that solves the sinkless orientation problem in the supported LOCAL model requires Ω(log n) rounds, and this is tight. The supported LOCAL is at least as strong as the usual LOCAL model, and as a corollary this also gives a new, short and elementary proof that shows that the round complexity of the sinkless orientation problem in the deterministic LOCAL model is Ω(log n)."}],"status":"public","external_id":{"arxiv":["2108.02655"]},"has_accepted_license":"1","citation":{"ista":"Korhonen J, Paz A, Rybicki J, Schmid S, Suomela J. 2021. Brief announcement: Sinkless orientation is hard also in the supported LOCAL model. 35th International Symposium on Distributed Computing. DISC: Distributed Computing , LIPIcs, vol. 209, 58.","ieee":"J. Korhonen, A. Paz, J. Rybicki, S. Schmid, and J. Suomela, “Brief announcement: Sinkless orientation is hard also in the supported LOCAL model,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","ama":"Korhonen J, Paz A, Rybicki J, Schmid S, Suomela J. Brief announcement: Sinkless orientation is hard also in the supported LOCAL model. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">10.4230/LIPIcs.DISC.2021.58</a>","apa":"Korhonen, J., Paz, A., Rybicki, J., Schmid, S., &#38; Suomela, J. (2021). Brief announcement: Sinkless orientation is hard also in the supported LOCAL model. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">https://doi.org/10.4230/LIPIcs.DISC.2021.58</a>","short":"J. Korhonen, A. Paz, J. Rybicki, S. Schmid, J. Suomela, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","mla":"Korhonen, Janne, et al. “Brief Announcement: Sinkless Orientation Is Hard Also in the Supported LOCAL Model.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 58, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">10.4230/LIPIcs.DISC.2021.58</a>.","chicago":"Korhonen, Janne, Ami Paz, Joel Rybicki, Stefan Schmid, and Jukka Suomela. “Brief Announcement: Sinkless Orientation Is Hard Also in the Supported LOCAL Model.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">https://doi.org/10.4230/LIPIcs.DISC.2021.58</a>."},"ec_funded":1,"language":[{"iso":"eng"}],"intvolume":"       209","date_updated":"2025-05-14T10:54:13Z","ddc":["000"],"arxiv":1,"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"alternative_title":["LIPIcs"],"author":[{"id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne","first_name":"Janne","last_name":"Korhonen"},{"full_name":"Paz, Ami","first_name":"Ami","last_name":"Paz"},{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","orcid":"0000-0002-6432-6646","first_name":"Joel"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"}],"year":"2021","file_date_updated":"2021-11-12T08:27:42Z","publication_status":"published","volume":209,"month":"10"},{"month":"10","related_material":{"record":[{"relation":"earlier_version","id":"9308","status":"public"},{"relation":"earlier_version","id":"8183","status":"public"}]},"volume":245,"publication_status":"published","year":"2021","page":"501–534 ","author":[{"last_name":"Avvakumov","orcid":"0000-0002-7840-5062","first_name":"Sergey","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Isaac","last_name":"Mabillard","full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Skopenkov, Arkadiy B.","last_name":"Skopenkov","first_name":"Arkadiy B."},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"project":[{"call_identifier":"FWF","_id":"26611F5C-B435-11E9-9278-68D0E5697425","name":"Algorithms for Embeddings and Homotopy Theory","grant_number":"P31312"}],"date_updated":"2025-07-02T10:54:52Z","arxiv":1,"intvolume":"       245","article_type":"original","citation":{"ista":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534.","ieee":"S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections. III. Codimension 2,” <i>Israel Journal of Mathematics</i>, vol. 245. Springer Nature, pp. 501–534, 2021.","ama":"Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity intersections. III. Codimension 2. <i>Israel Journal of Mathematics</i>. 2021;245:501–534. doi:<a href=\"https://doi.org/10.1007/s11856-021-2216-z\">10.1007/s11856-021-2216-z</a>","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A. B., &#38; Wagner, U. (2021). Eliminating higher-multiplicity intersections. III. Codimension 2. <i>Israel Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11856-021-2216-z\">https://doi.org/10.1007/s11856-021-2216-z</a>","short":"S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 501–534.","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” <i>Israel Journal of Mathematics</i>, vol. 245, Springer Nature, 2021, pp. 501–534, doi:<a href=\"https://doi.org/10.1007/s11856-021-2216-z\">10.1007/s11856-021-2216-z</a>.","chicago":"Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” <i>Israel Journal of Mathematics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11856-021-2216-z\">https://doi.org/10.1007/s11856-021-2216-z</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"We study conditions under which a finite simplicial complex K can be mapped to ℝd without higher-multiplicity intersections. An almost r-embedding is a map f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on previous constructions of counterexamples (for d ≥ 3r) based on a series of papers by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite 2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection number of the f-images of any r pairwise disjoint simplices of K is zero. This result can be restated in terms of a cohomological obstruction and extends an analogous codimension 3 criterion by the second and fourth authors. As another application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for r = 2 is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample.","lang":"eng"}],"external_id":{"arxiv":["1511.03501"],"isi":["000712942100013"]},"status":"public","scopus_import":"1","oa_version":"Preprint","publication":"Israel Journal of Mathematics","date_created":"2021-11-07T23:01:24Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"type":"journal_article","corr_author":"1","department":[{"_id":"UlWa"}],"day":"30","oa":1,"title":"Eliminating higher-multiplicity intersections. III. Codimension 2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0021-2172"],"eissn":["1565-8511"]},"article_processing_charge":"No","publisher":"Springer Nature","doi":"10.1007/s11856-021-2216-z","acknowledgement":"Research supported by the Swiss National Science Foundation (Project SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169), by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful comments and discussions.","isi":1,"_id":"10220","date_published":"2021-10-30T00:00:00Z","quality_controlled":"1"},{"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"intvolume":"       388","date_updated":"2025-04-15T06:53:08Z","arxiv":1,"ddc":["510"],"citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00220-021-04239-z\">https://doi.org/10.1007/s00220-021-04239-z</a>.","mla":"Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” <i>Communications in Mathematical Physics</i>, vol. 388, no. 2, Springer Nature, 2021, pp. 1005–1048, doi:<a href=\"https://doi.org/10.1007/s00220-021-04239-z\">10.1007/s00220-021-04239-z</a>.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Eigenstate thermalization hypothesis for Wigner matrices. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-021-04239-z\">https://doi.org/10.1007/s00220-021-04239-z</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis for Wigner matrices,” <i>Communications in Mathematical Physics</i>, vol. 388, no. 2. Springer Nature, pp. 1005–1048, 2021.","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048.","ama":"Cipolloni G, Erdös L, Schröder DJ. Eigenstate thermalization hypothesis for Wigner matrices. <i>Communications in Mathematical Physics</i>. 2021;388(2):1005–1048. doi:<a href=\"https://doi.org/10.1007/s00220-021-04239-z\">10.1007/s00220-021-04239-z</a>"},"article_type":"original","language":[{"iso":"eng"}],"publication":"Communications in Mathematical Physics","oa_version":"Published Version","date_created":"2021-11-07T23:01:25Z","scopus_import":"1","type":"journal_article","corr_author":"1","abstract":[{"lang":"eng","text":"We prove that any deterministic matrix is approximately the identity in the eigenbasis of a large random Wigner matrix with very high probability and with an optimal error inversely proportional to the square root of the dimension. Our theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch (Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity (QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278, 2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020)."}],"status":"public","has_accepted_license":"1","external_id":{"isi":["000712232700001"],"arxiv":["2012.13215"]},"issue":"2","volume":388,"month":"10","year":"2021","publication_status":"published","file_date_updated":"2022-02-02T10:19:55Z","page":"1005–1048","author":[{"last_name":"Cipolloni","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","full_name":"Cipolloni, Giorgio"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","first_name":"László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"last_name":"Schröder","orcid":"0000-0002-2904-1856","first_name":"Dominik J","full_name":"Schröder, Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_created":"2022-02-02T10:19:55Z","content_type":"application/pdf","relation":"main_file","creator":"cchlebak","access_level":"open_access","checksum":"a2c7b6f5d23b5453cd70d1261272283b","success":1,"date_updated":"2022-02-02T10:19:55Z","file_id":"10715","file_name":"2021_CommunMathPhys_Cipolloni.pdf","file_size":841426}],"isi":1,"doi":"10.1007/s00220-021-04239-z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).","publisher":"Springer Nature","date_published":"2021-10-29T00:00:00Z","_id":"10221","quality_controlled":"1","day":"29","department":[{"_id":"LaEr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"title":"Eigenstate thermalization hypothesis for Wigner matrices","article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"publication_status":"published","year":"2021","month":"11","issue":"7884","related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/stop-and-grow/"}],"record":[{"id":"10095","status":"public","relation":"earlier_version"}]},"volume":599,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"author":[{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin","last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"first_name":"Koji","last_name":"Takahashi","full_name":"Takahashi, Koji"},{"full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","first_name":"Lesia","last_name":"Rodriguez Solovey"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"first_name":"Jian","last_name":"Chen","full_name":"Chen, Jian"},{"first_name":"Lana","last_name":"Shabala","full_name":"Shabala, Lana"},{"full_name":"Smet, Wouter","first_name":"Wouter","last_name":"Smet"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"full_name":"De Rybel, Bert","first_name":"Bert","last_name":"De Rybel"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"full_name":"Gray, William M.","first_name":"William M.","last_name":"Gray"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"page":"273-277","pmid":1,"date_updated":"2025-07-10T11:49:46Z","intvolume":"       599","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"grant_number":"25351","name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments."}],"external_id":{"pmid":["34707283"],"isi":["000713338100006"]},"status":"public","scopus_import":"1","oa_version":"Preprint","date_created":"2021-11-07T23:01:25Z","publication":"Nature","corr_author":"1","main_file_link":[{"url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3","open_access":"1"}],"type":"journal_article","citation":{"ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. Nature. 599(7884), 273–277.","ieee":"L. Li <i>et al.</i>, “Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth,” <i>Nature</i>, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. 2021;599(7884):273-277. doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.","mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:<a href=\"https://doi.org/10.1038/s41586-021-04037-6\">10.1038/s41586-021-04037-6</a>.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H<sup>+</sup> Fluxes in Root Growth.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-021-04037-6\">https://doi.org/10.1038/s41586-021-04037-6</a>."},"article_type":"original","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"title":"Cell surface and intracellular auxin signalling for H<sup>+</sup> fluxes in root growth","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"day":"11","keyword":["Multidisciplinary"],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"article_processing_charge":"No","publisher":"Springer Nature","acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","doi":"10.1038/s41586-021-04037-6","isi":1,"quality_controlled":"1","_id":"10223","date_published":"2021-11-11T00:00:00Z"},{"publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"RoSe"}],"day":"25","oa":1,"title":"The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10224","date_published":"2021-10-25T00:00:00Z","quality_controlled":"1","publisher":"Springer Nature","isi":1,"file":[{"content_type":"application/pdf","date_created":"2021-12-14T08:35:42Z","access_level":"open_access","creator":"alisjak","relation":"main_file","file_name":"2021_Springer_Feliciangeli.pdf","file_id":"10544","date_updated":"2021-12-14T08:35:42Z","checksum":"672e9c21b20f1a50854b7c821edbb92f","success":1,"file_size":990529}],"acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.7.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","doi":"10.1007/s00205-021-01715-7","page":"1835–1906","author":[{"first_name":"Dario","orcid":"0000-0003-0754-8530","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","full_name":"Feliciangeli, Dario"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"month":"10","issue":"3","related_material":{"record":[{"status":"public","id":"9787","relation":"earlier_version"}]},"volume":242,"publication_status":"published","file_date_updated":"2021-12-14T08:35:42Z","year":"2021","ec_funded":1,"article_type":"original","citation":{"apa":"Feliciangeli, D., &#38; Seiringer, R. (2021). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-021-01715-7\">https://doi.org/10.1007/s00205-021-01715-7</a>","ieee":"D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.","ista":"Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 242(3), 1835–1906.","ama":"Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. <i>Archive for Rational Mechanics and Analysis</i>. 2021;242(3):1835–1906. doi:<a href=\"https://doi.org/10.1007/s00205-021-01715-7\">10.1007/s00205-021-01715-7</a>","mla":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906, doi:<a href=\"https://doi.org/10.1007/s00205-021-01715-7\">10.1007/s00205-021-01715-7</a>.","short":"D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00205-021-01715-7\">https://doi.org/10.1007/s00205-021-01715-7</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.","lang":"eng"}],"status":"public","external_id":{"isi":["000710850600001"],"arxiv":["2101.12566"]},"has_accepted_license":"1","oa_version":"Published Version","publication":"Archive for Rational Mechanics and Analysis","scopus_import":"1","date_created":"2021-11-07T23:01:26Z","type":"journal_article","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"date_updated":"2025-04-14T09:11:09Z","ddc":["530"],"arxiv":1,"intvolume":"       242"},{"publisher":"Springer Nature","doi":"10.1007/978-1-0716-1677-2_2","acknowledgement":"The Ceratopteris richardii spores were obtained from the lab of Jo Ann Banks at Purdue University. This work was supported by funding from the European Union’s Horizon 2020 research and innovation program (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), IST Fellow program and DOC Fellowship of the Austrian Academy of Sciences.","quality_controlled":"1","_id":"10267","date_published":"2021-10-14T00:00:00Z","department":[{"_id":"JiFr"}],"editor":[{"full_name":"Blancaflor, Elison B","first_name":"Elison B","last_name":"Blancaflor"}],"day":"14","title":"Evaluation of gravitropism in non-seed plants","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eisbn":["978-1-0716-1677-2"],"isbn":["978-1-0716-1676-5"]},"article_processing_charge":"No","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03630"}],"date_updated":"2025-04-14T07:45:00Z","intvolume":"      2368","language":[{"iso":"eng"}],"ec_funded":1,"citation":{"mla":"Zhang, Yuzhou, et al. “Evaluation of Gravitropism in Non-Seed Plants.” <i>Plant Gravitropism</i>, edited by Elison B Blancaflor, vol. 2368, Springer Nature, 2021, pp. 43–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">10.1007/978-1-0716-1677-2_2</a>.","short":"Y. Zhang, L. Li, J. Friml, in:, E.B. Blancaflor (Ed.), Plant Gravitropism, Springer Nature, 2021, pp. 43–51.","apa":"Zhang, Y., Li, L., &#38; Friml, J. (2021). Evaluation of gravitropism in non-seed plants. In E. B. Blancaflor (Ed.), <i>Plant Gravitropism</i> (Vol. 2368, pp. 43–51). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">https://doi.org/10.1007/978-1-0716-1677-2_2</a>","ista":"Zhang Y, Li L, Friml J. 2021.Evaluation of gravitropism in non-seed plants. In: Plant Gravitropism. Methods in Molecular Biology, vol. 2368, 43–51.","ama":"Zhang Y, Li L, Friml J. Evaluation of gravitropism in non-seed plants. In: Blancaflor EB, ed. <i>Plant Gravitropism</i>. Vol 2368. MIMB. Springer Nature; 2021:43-51. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">10.1007/978-1-0716-1677-2_2</a>","ieee":"Y. Zhang, L. Li, and J. Friml, “Evaluation of gravitropism in non-seed plants,” in <i>Plant Gravitropism</i>, vol. 2368, E. B. Blancaflor, Ed. Springer Nature, 2021, pp. 43–51.","chicago":"Zhang, Yuzhou, Lanxin Li, and Jiří Friml. “Evaluation of Gravitropism in Non-Seed Plants.” In <i>Plant Gravitropism</i>, edited by Elison B Blancaflor, 2368:43–51. MIMB. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1677-2_2\">https://doi.org/10.1007/978-1-0716-1677-2_2</a>."},"external_id":{"pmid":["34647246"]},"status":"public","abstract":[{"lang":"eng","text":"Tropisms are among the most important growth responses for plant adaptation to the surrounding environment. One of the most common tropisms is root gravitropism. Root gravitropism enables the plant to anchor securely to the soil enabling the absorption of water and nutrients. Most of the knowledge related to the plant gravitropism has been acquired from the flowering plants, due to limited research in non-seed plants. Limited research on non-seed plants is due in large part to the lack of standard research methods. Here, we describe the experimental methods to evaluate gravitropism in representative non-seed plant species, including the non-vascular plant moss Physcomitrium patens, the early diverging extant vascular plant lycophyte Selaginella moellendorffii and fern Ceratopteris richardii. In addition, we introduce the methods used for statistical analysis of the root gravitropism in non-seed plant species."}],"type":"book_chapter","corr_author":"1","oa_version":"None","date_created":"2021-11-11T09:26:10Z","scopus_import":"1","publication":"Plant Gravitropism","series_title":"MIMB","month":"10","volume":2368,"publication_status":"published","year":"2021","page":"43-51","pmid":1,"author":[{"id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou","orcid":"0000-0003-2627-6956"},{"full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","last_name":"Li","orcid":"0000-0002-5607-272X","first_name":"Lanxin"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"}],"alternative_title":["Methods in Molecular Biology"]},{"date_published":"2021-10-28T00:00:00Z","_id":"10268","quality_controlled":"1","publisher":"Humana Press","doi":"10.1007/978-1-0716-1744-1_6","acknowledgement":"We thank B. De Rybel for allowing M.G. to work on this manuscript during a postdoc in his laboratory, and EMBO for supporting M.G. with a Long-Term fellowship (ALTF 1005-2019) during this time. We acknowledge the service and support by the Bioimaging Facility at IST Austria, and finally, we thank A. Mally for proofreading and correcting the manuscript.","publication_identifier":{"issn":["1064-3745"],"eisbn":["978-1-0716-1744-1"],"eissn":["1940-6029"],"isbn":["978-1-0716-1743-4"]},"article_processing_charge":"No","title":"Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"day":"28","abstract":[{"text":"The analysis of dynamic cellular processes such as plant cytokinesis stands and falls with live-cell time-lapse confocal imaging. Conventional approaches to time-lapse imaging of cell division in Arabidopsis root tips are tedious and have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous imaging of multiple root tips on a vertical-stage confocal microscope with automated root tracking. We also provide modifications of the basic protocol to implement this imaging method in the analysis of genetic, pharmacological or laser ablation wounding-mediated experimental manipulations. Our method dramatically improves the efficiency of cell division time-lapse imaging by increasing the throughput, while reducing the person-hour requirements of such experiments.","lang":"eng"}],"status":"public","external_id":{"pmid":["34705235"]},"scopus_import":"1","date_created":"2021-11-11T10:03:30Z","publication":"Plant Cell Division","oa_version":"None","type":"book_chapter","citation":{"short":"L. Hörmayer, J. Friml, M. Glanc, in:, Plant Cell Division, Humana Press, 2021, pp. 105–114.","mla":"Hörmayer, Lukas, et al. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–14, doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>.","ista":"Hörmayer L, Friml J, Glanc M. 2021.Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: Plant Cell Division. Methods in Molecular Biology, vol. 2382, 105–114.","ieee":"L. Hörmayer, J. Friml, and M. Glanc, “Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy,” in <i>Plant Cell Division</i>, vol. 2382, Humana Press, 2021, pp. 105–114.","ama":"Hörmayer L, Friml J, Glanc M. Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In: <i>Plant Cell Division</i>. Vol 2382. MIMB. Humana Press; 2021:105-114. doi:<a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">10.1007/978-1-0716-1744-1_6</a>","apa":"Hörmayer, L., Friml, J., &#38; Glanc, M. (2021). Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy. In <i>Plant Cell Division</i> (Vol. 2382, pp. 105–114). Humana Press. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>","chicago":"Hörmayer, Lukas, Jiří Friml, and Matous Glanc. “Automated Time-Lapse Imaging and Manipulation of Cell Divisions in Arabidopsis Roots by Vertical-Stage Confocal Microscopy.” In <i>Plant Cell Division</i>, 2382:105–14. MIMB. Humana Press, 2021. <a href=\"https://doi.org/10.1007/978-1-0716-1744-1_6\">https://doi.org/10.1007/978-1-0716-1744-1_6</a>."},"language":[{"iso":"eng"}],"date_updated":"2022-06-03T06:47:06Z","intvolume":"      2382","acknowledged_ssus":[{"_id":"Bio"}],"author":[{"first_name":"Lukas","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","orcid":"0000-0003-0619-7783","first_name":"Matous"}],"alternative_title":["Methods in Molecular Biology"],"page":"105-114","pmid":1,"publication_status":"published","year":"2021","series_title":"MIMB","month":"10","volume":2382},{"date_updated":"2023-08-14T11:49:23Z","ddc":["570"],"intvolume":"        10","article_type":"original","citation":{"mla":"Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>, vol. 10, 72132, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>.","short":"M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021).","apa":"Marconi, M., Gallemi, M., Benková, E., &#38; Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>","ama":"Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72132\">10.7554/elife.72132</a>","ista":"Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132.","ieee":"M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","chicago":"Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72132\">https://doi.org/10.7554/elife.72132</a>."},"language":[{"iso":"eng"}],"abstract":[{"text":"Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.","lang":"eng"}],"status":"public","external_id":{"isi":["000734671200001"],"pmid":["34723798"]},"has_accepted_license":"1","scopus_import":"1","publication":"eLife","date_created":"2021-11-11T10:05:18Z","oa_version":"Published Version","type":"journal_article","month":"11","volume":10,"file_date_updated":"2022-05-13T09:00:29Z","publication_status":"published","year":"2021","pmid":1,"author":[{"full_name":"Marconi, Marco","first_name":"Marco","last_name":"Marconi"},{"first_name":"Marçal","orcid":"0000-0003-4675-6893","last_name":"Gallemi","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"full_name":"Wabnik, Krzysztof","last_name":"Wabnik","first_name":"Krzysztof"}],"publisher":"eLife Sciences Publications","acknowledgement":"e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).","doi":"10.7554/elife.72132","isi":1,"file":[{"file_size":14137503,"success":1,"checksum":"fad13c509b53bb7a2bef9c946a7ca60a","date_updated":"2022-05-13T09:00:29Z","file_name":"2021_eLife_Marconi.pdf","file_id":"11372","relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2022-05-13T09:00:29Z","content_type":"application/pdf"}],"article_number":"72132","quality_controlled":"1","_id":"10270","date_published":"2021-11-01T00:00:00Z","department":[{"_id":"EvBe"}],"day":"01","oa":1,"title":"A coupled mechano-biochemical model for cell polarity guided anisotropic root growth","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["2050-084X"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes"},{"author":[{"id":"3B22D412-F248-11E8-B48F-1D18A9856A87","full_name":"Qi, Qin","last_name":"Qi","first_name":"Qin","orcid":"0000-0002-6148-2416"},{"full_name":"Angermayr, S. Andreas","first_name":"S. Andreas","last_name":"Angermayr"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"}],"pmid":1,"file_date_updated":"2021-11-11T10:54:40Z","publication_status":"published","year":"2021","month":"10","volume":12,"abstract":[{"lang":"eng","text":"Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions."}],"status":"public","has_accepted_license":"1","external_id":{"isi":["000715997300001"],"pmid":["34745067"]},"scopus_import":"1","date_created":"2021-11-11T10:39:37Z","oa_version":"Published Version","publication":"Frontiers in Microbiology","type":"journal_article","ec_funded":1,"citation":{"mla":"Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” <i>Frontiers in Microbiology</i>, vol. 12, 760017, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fmicb.2021.760017\">10.3389/fmicb.2021.760017</a>.","short":"Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021).","apa":"Qi, Q., Angermayr, S. A., &#38; Bollenbach, M. T. (2021). Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. <i>Frontiers in Microbiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fmicb.2021.760017\">https://doi.org/10.3389/fmicb.2021.760017</a>","ieee":"Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli,” <i>Frontiers in Microbiology</i>, vol. 12. Frontiers, 2021.","ista":"Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 12, 760017.","ama":"Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. <i>Frontiers in Microbiology</i>. 2021;12. doi:<a href=\"https://doi.org/10.3389/fmicb.2021.760017\">10.3389/fmicb.2021.760017</a>","chicago":"Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” <i>Frontiers in Microbiology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fmicb.2021.760017\">https://doi.org/10.3389/fmicb.2021.760017</a>."},"article_type":"original","language":[{"iso":"eng"}],"date_updated":"2025-04-14T09:40:44Z","ddc":["610"],"intvolume":"        12","project":[{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_identifier":{"eissn":["1664-302X"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","oa":1,"title":"Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["microbiology"],"day":"20","article_number":"760017","_id":"10271","quality_controlled":"1","date_published":"2021-10-20T00:00:00Z","publisher":"Frontiers","acknowledgement":"High-throughput sequencing data were generated by the Vienna BioCenter Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and Nadine Kraupner for their constructive feedback. The authors would also like to thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando for technical support.","isi":1,"doi":"10.3389/fmicb.2021.760017","file":[{"file_size":2397203,"file_name":"2021_FrontiersMicrob_Qi.pdf","file_id":"10272","date_updated":"2021-11-11T10:54:40Z","success":1,"checksum":"d41321748e9588dd3cf03e9a7222127f","access_level":"open_access","creator":"cchlebak","relation":"main_file","date_created":"2021-11-11T10:54:40Z","content_type":"application/pdf"}]},{"pmid":1,"author":[{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"},{"id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","full_name":"Martinet, Quentin","last_name":"Martinet","first_name":"Quentin","orcid":"0000-0002-2916-6632"},{"first_name":"Jérémie A","orcid":"0000-0002-7253-9465","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"}],"month":"11","issue":"1","volume":12,"publication_status":"published","file_date_updated":"2021-11-15T13:25:52Z","year":"2021","article_type":"original","citation":{"apa":"Aubret, A., Martinet, Q., &#38; Palacci, J. A. (2021). Metamachines of pluripotent colloids. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26699-6\">https://doi.org/10.1038/s41467-021-26699-6</a>","ieee":"A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26699-6\">10.1038/s41467-021-26699-6</a>","ista":"Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398.","mla":"Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” <i>Nature Communications</i>, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26699-6\">10.1038/s41467-021-26699-6</a>.","short":"A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021).","chicago":"Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26699-6\">https://doi.org/10.1038/s41467-021-26699-6</a>."},"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials."}],"status":"public","external_id":{"isi":["000714754400010"],"pmid":["34737315"]},"has_accepted_license":"1","publication":"Nature Communications","scopus_import":"1","oa_version":"Published Version","date_created":"2021-11-14T23:01:23Z","type":"journal_article","date_updated":"2023-08-14T11:48:37Z","ddc":["530"],"intvolume":"        12","publication_identifier":{"eissn":["2041-1723"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes","department":[{"_id":"JePa"}],"day":"04","oa":1,"title":"Metamachines of pluripotent colloids","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"6398","quality_controlled":"1","_id":"10280","date_published":"2021-11-04T00:00:00Z","publisher":"Springer Nature","acknowledgement":"The authors thank R. Jazzar for useful advice regarding the synthesis of heterodimers. We thank S. Sacanna for critical reading. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1554724 and Department of Army Research under grant W911NF-20-1-0112.","doi":"10.1038/s41467-021-26699-6","isi":1,"file":[{"date_created":"2021-11-15T13:25:52Z","content_type":"application/pdf","access_level":"open_access","creator":"cchlebak","relation":"main_file","file_id":"10292","file_name":"2021_NatComm_Aubret.pdf","date_updated":"2021-11-15T13:25:52Z","success":1,"checksum":"1c392b12b9b7b615d422d9fabe19cdb9","file_size":6282703}]},{"_id":"10281","quality_controlled":"1","date_published":"2021-10-30T00:00:00Z","article_number":"1746","file":[{"file_size":1335308,"file_name":"2021_Genes_Vasic.pdf","file_id":"11380","date_updated":"2022-05-16T07:02:27Z","checksum":"256cb832a9c3051c7dc741f6423b8cbd","success":1,"access_level":"open_access","creator":"dernst","relation":"main_file","content_type":"application/pdf","date_created":"2022-05-16T07:02:27Z"}],"doi":"10.3390/genes12111746","acknowledgement":"This review was funded by the IMI2 Initiative under the grant AIMS-2-TRIALS No 777394, by the Hessian Ministry for Science and Arts; State of Hesse Ministry for Science and Arts: LOEWE-Grant to the CePTER-Consortium (www.uni-frankfurt.de/67689811); Research (BMBF) under the grant RAISE-genic No 779282 all to AGC. This work was also supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM) and by the Austrian Science Fund (FWF) (DK W1232-B24) both to G.N. and both BMBF GeNeRARe 01GM1519A and CRC 1080, project B10, of the German Research Foundation (DFG) to M.J.S, respectively. We want to thank R. Waltes for her support in preparing this manuscript.","isi":1,"publisher":"MDPI","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["2073-4425"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment","oa":1,"day":"30","department":[{"_id":"GaNo"}],"type":"journal_article","scopus_import":"1","publication":"Genes","date_created":"2021-11-14T23:01:24Z","oa_version":"Published Version","external_id":{"isi":["000834044200002"]},"status":"public","has_accepted_license":"1","abstract":[{"text":"Mutations affecting mTOR or RAS signaling underlie defined syndromes (the so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder (ASD). These syndromes show a broad variety of somatic phenotypes including cancers, skin abnormalities, heart disease and facial dysmorphisms. Less well studied are the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these signalopathies in ASD reviewing genetic, human cell model, rodent studies and clinical trials. We conclude that signalopathies have an increased liability for ASD and that, in particular, ASD individuals with dysmorphic features and intellectual disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related genes. Studies on rodent and human cell models confirm aberrant neuronal development as the underlying pathology. Human studies further suggest that multiple hits are necessary to induce the respective phenotypes. Recent clinical trials do only report improvements for comorbid conditions such as epilepsy or cancer but not for behavioral aspects. Animal models show that treatment during early development can rescue behavioral phenotypes. Taken together, we suggest investigating the differential roles of mTOR and RAS signaling in both human and rodent models, and to test drug treatment both during and after neuronal development in the available model systems","lang":"eng"}],"language":[{"iso":"eng"}],"ec_funded":1,"article_type":"original","citation":{"chicago":"Vasic, Verica, Mattson S.O. Jones, Denise Haslinger, Lisa Knaus, Michael J. Schmeisser, Gaia Novarino, and Andreas G. Chiocchetti. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12111746\">https://doi.org/10.3390/genes12111746</a>.","apa":"Vasic, V., Jones, M. S. O., Haslinger, D., Knaus, L., Schmeisser, M. J., Novarino, G., &#38; Chiocchetti, A. G. (2021). Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12111746\">https://doi.org/10.3390/genes12111746</a>","ista":"Vasic V, Jones MSO, Haslinger D, Knaus L, Schmeisser MJ, Novarino G, Chiocchetti AG. 2021. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 12(11), 1746.","ama":"Vasic V, Jones MSO, Haslinger D, et al. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. <i>Genes</i>. 2021;12(11). doi:<a href=\"https://doi.org/10.3390/genes12111746\">10.3390/genes12111746</a>","ieee":"V. Vasic <i>et al.</i>, “Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment,” <i>Genes</i>, vol. 12, no. 11. MDPI, 2021.","mla":"Vasic, Verica, et al. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” <i>Genes</i>, vol. 12, no. 11, 1746, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12111746\">10.3390/genes12111746</a>.","short":"V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021)."},"intvolume":"        12","ddc":["570"],"date_updated":"2025-04-15T07:29:28Z","project":[{"name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715508"},{"grant_number":"W1232","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"alternative_title":["Special Issue \"From Genes to Therapy in Autism Spectrum Disorder\""],"author":[{"full_name":"Vasic, Verica","first_name":"Verica","last_name":"Vasic"},{"first_name":"Mattson S.O.","last_name":"Jones","full_name":"Jones, Mattson S.O."},{"full_name":"Haslinger, Denise","id":"76922BDA-3D3B-11EA-90BD-A44F3DDC885E","first_name":"Denise","last_name":"Haslinger"},{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","full_name":"Knaus, Lisa","last_name":"Knaus","first_name":"Lisa"},{"full_name":"Schmeisser, Michael J.","last_name":"Schmeisser","first_name":"Michael J."},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"},{"full_name":"Chiocchetti, Andreas G.","first_name":"Andreas G.","last_name":"Chiocchetti"}],"year":"2021","file_date_updated":"2022-05-16T07:02:27Z","publication_status":"published","volume":12,"issue":"11","month":"10"},{"file_date_updated":"2022-05-16T07:07:41Z","publication_status":"published","year":"2021","month":"11","volume":22,"author":[{"full_name":"Restivo, Leonardo","first_name":"Leonardo","last_name":"Restivo"},{"full_name":"Gerlach, Björn","last_name":"Gerlach","first_name":"Björn"},{"last_name":"Tsoory","first_name":"Michael","full_name":"Tsoory, Michael"},{"last_name":"Bikovski","first_name":"Lior","full_name":"Bikovski, Lior"},{"full_name":"Badurek, Sylvia","last_name":"Badurek","first_name":"Sylvia"},{"full_name":"Pitzer, Claudia","last_name":"Pitzer","first_name":"Claudia"},{"full_name":"Kos-Braun, Isabelle C.","first_name":"Isabelle C.","last_name":"Kos-Braun"},{"full_name":"Mausset-Bonnefont, Anne Laure Mj","last_name":"Mausset-Bonnefont","first_name":"Anne Laure Mj"},{"full_name":"Ward, Jonathan","first_name":"Jonathan","last_name":"Ward"},{"full_name":"Schunn, Michael","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300","first_name":"Michael","last_name":"Schunn"},{"full_name":"Noldus, Lucas P.J.J.","first_name":"Lucas P.J.J.","last_name":"Noldus"},{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"full_name":"Voikar, Vootele","first_name":"Vootele","last_name":"Voikar"}],"date_updated":"2023-08-14T11:47:35Z","ddc":["570"],"intvolume":"        22","abstract":[{"lang":"eng","text":"During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research."}],"status":"public","has_accepted_license":"1","external_id":{"isi":["000714350000001"]},"publication":"EMBO Reports","scopus_import":"1","date_created":"2021-11-14T23:01:24Z","oa_version":"Published Version","type":"journal_article","citation":{"chicago":"Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” <i>EMBO Reports</i>. EMBO Press, 2021. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>.","apa":"Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. <i>EMBO Reports</i>. EMBO Press. <a href=\"https://doi.org/10.15252/embr.202153824\">https://doi.org/10.15252/embr.202153824</a>","ieee":"L. Restivo <i>et al.</i>, “Towards best practices in research: Role of academic core facilities,” <i>EMBO Reports</i>, vol. 22. EMBO Press, 2021.","ista":"Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.","ama":"Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. <i>EMBO Reports</i>. 2021;22. doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>","mla":"Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” <i>EMBO Reports</i>, vol. 22, e53824, EMBO Press, 2021, doi:<a href=\"https://doi.org/10.15252/embr.202153824\">10.15252/embr.202153824</a>.","short":"L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021)."},"article_type":"original","language":[{"iso":"eng"}],"oa":1,"title":"Towards best practices in research: Role of academic core facilities","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"PreCl"}],"day":"04","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_processing_charge":"Yes (in subscription journal)","publisher":"EMBO Press","isi":1,"acknowledgement":"This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback.","doi":"10.15252/embr.202153824","file":[{"content_type":"application/pdf","date_created":"2022-05-16T07:07:41Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"74743baa6ef431ef60c3de3bc4da045a","success":1,"file_id":"11381","file_name":"2021_EmboReports_Restivo.pdf","date_updated":"2022-05-16T07:07:41Z","file_size":488583}],"article_number":"e53824","_id":"10283","date_published":"2021-11-04T00:00:00Z","quality_controlled":"1"},{"article_processing_charge":"No","publication_identifier":{"eissn":["1083-6489"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"28","department":[{"_id":"LaEr"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"title":"On eigenvector statistics in the spherical and truncated unitary ensembles","quality_controlled":"1","_id":"10285","date_published":"2021-09-28T00:00:00Z","article_number":"124","acknowledgement":"We acknowledge partial support from the grants NSF DMS-1812114 of P. Bourgade (PI) and NSF CAREER DMS-1653602 of L.-P. Arguin (PI). This project has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We would like to thank Paul Bourgade and László Erdős for many helpful comments.","file":[{"creator":"cchlebak","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_created":"2021-11-15T10:10:17Z","file_size":735940,"checksum":"1c975afb31460277ce4d22b93538e5f9","success":1,"file_name":"2021_ElecJournalProb_Dubach.pdf","file_id":"10288","date_updated":"2021-11-15T10:10:17Z"}],"doi":"10.1214/21-EJP686","publisher":"Institute of Mathematical Statistics","author":[{"full_name":"Dubach, Guillaume","id":"D5C6A458-10C4-11EA-ABF4-A4B43DDC885E","orcid":"0000-0001-6892-8137","first_name":"Guillaume","last_name":"Dubach"}],"volume":26,"month":"09","year":"2021","publication_status":"published","file_date_updated":"2021-11-15T10:10:17Z","article_type":"original","citation":{"mla":"Dubach, Guillaume. “On Eigenvector Statistics in the Spherical and Truncated Unitary Ensembles.” <i>Electronic Journal of Probability</i>, vol. 26, 124, Institute of Mathematical Statistics, 2021, doi:<a href=\"https://doi.org/10.1214/21-EJP686\">10.1214/21-EJP686</a>.","short":"G. Dubach, Electronic Journal of Probability 26 (2021).","apa":"Dubach, G. (2021). On eigenvector statistics in the spherical and truncated unitary ensembles. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-EJP686\">https://doi.org/10.1214/21-EJP686</a>","ieee":"G. Dubach, “On eigenvector statistics in the spherical and truncated unitary ensembles,” <i>Electronic Journal of Probability</i>, vol. 26. Institute of Mathematical Statistics, 2021.","ista":"Dubach G. 2021. On eigenvector statistics in the spherical and truncated unitary ensembles. Electronic Journal of Probability. 26, 124.","ama":"Dubach G. On eigenvector statistics in the spherical and truncated unitary ensembles. <i>Electronic Journal of Probability</i>. 2021;26. doi:<a href=\"https://doi.org/10.1214/21-EJP686\">10.1214/21-EJP686</a>","chicago":"Dubach, Guillaume. “On Eigenvector Statistics in the Spherical and Truncated Unitary Ensembles.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2021. <a href=\"https://doi.org/10.1214/21-EJP686\">https://doi.org/10.1214/21-EJP686</a>."},"ec_funded":1,"language":[{"iso":"eng"}],"publication":"Electronic Journal of Probability","scopus_import":"1","oa_version":"Published Version","date_created":"2021-11-14T23:01:25Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study the overlaps between right and left eigenvectors for random matrices of the spherical ensemble, as well as truncated unitary ensembles in the regime where half of the matrix at least is truncated. These two integrable models exhibit a form of duality, and the essential steps of our investigation can therefore be performed in parallel. In every case, conditionally on all eigenvalues, diagonal overlaps are shown to be distributed as a product of independent random variables with explicit distributions. This enables us to prove that the scaled diagonal overlaps, conditionally on one eigenvalue, converge in distribution to a heavy-tail limit, namely, the inverse of a γ2 distribution. We also provide formulae for the conditional expectation of diagonal and off-diagonal overlaps, either with respect to one eigenvalue, or with respect to the whole spectrum. These results, analogous to what is known for the complex Ginibre ensemble, can be obtained in these cases thanks to integration techniques inspired from a previous work by Forrester & Krishnapur."}],"status":"public","has_accepted_license":"1","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"intvolume":"        26","date_updated":"2025-04-14T07:43:47Z","ddc":["519"]},{"intvolume":"        10","ddc":["570"],"date_updated":"2024-10-21T06:02:05Z","type":"journal_article","scopus_import":"1","oa_version":"Published Version","publication":"eLife","date_created":"2021-11-18T06:59:45Z","external_id":{"isi":["000720945900001"]},"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","text":"De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement."}],"language":[{"iso":"eng"}],"citation":{"ama":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>","ista":"Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575.","ieee":"M. J. Conde-Dusman <i>et al.</i>, “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","apa":"Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>","short":"M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021).","mla":"Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” <i>ELife</i>, vol. 10, e71575, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.71575\">10.7554/elife.71575</a>.","chicago":"Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.71575\">https://doi.org/10.7554/elife.71575</a>."},"article_type":"original","year":"2021","file_date_updated":"2021-11-18T07:02:02Z","publication_status":"published","volume":10,"month":"11","author":[{"first_name":"María J","last_name":"Conde-Dusman","full_name":"Conde-Dusman, María J"},{"full_name":"Dey, Partha N","first_name":"Partha N","last_name":"Dey"},{"first_name":"Óscar","last_name":"Elía-Zudaire","full_name":"Elía-Zudaire, Óscar"},{"full_name":"Garcia Rabaneda, Luis E","id":"33D1B084-F248-11E8-B48F-1D18A9856A87","first_name":"Luis E","last_name":"Garcia Rabaneda"},{"first_name":"Carmen","last_name":"García-Lira","full_name":"García-Lira, Carmen"},{"full_name":"Grand, Teddy","first_name":"Teddy","last_name":"Grand"},{"full_name":"Briz, Victor","first_name":"Victor","last_name":"Briz"},{"first_name":"Eric R","last_name":"Velasco","full_name":"Velasco, Eric R"},{"full_name":"Andero Galí, Raül","first_name":"Raül","last_name":"Andero Galí"},{"full_name":"Niñerola, Sergio","first_name":"Sergio","last_name":"Niñerola"},{"first_name":"Angel","last_name":"Barco","full_name":"Barco, Angel"},{"last_name":"Paoletti","first_name":"Pierre","full_name":"Paoletti, Pierre"},{"first_name":"John F","last_name":"Wesseling","full_name":"Wesseling, John F"},{"full_name":"Gardoni, Fabrizio","last_name":"Gardoni","first_name":"Fabrizio"},{"full_name":"Tavalin, Steven J","last_name":"Tavalin","first_name":"Steven J"},{"full_name":"Perez-Otaño, Isabel","first_name":"Isabel","last_name":"Perez-Otaño"}],"isi":1,"doi":"10.7554/elife.71575","file":[{"date_created":"2021-11-18T07:02:02Z","content_type":"application/pdf","creator":"lgarciar","relation":"main_file","access_level":"open_access","checksum":"59318e9e41507cec83c2f4070e6ad540","success":1,"file_id":"10302","file_name":"elife-71575-v1.pdf","date_updated":"2021-11-18T07:02:02Z","file_size":2477302}],"acknowledgement":"We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723).","publisher":"eLife Sciences Publications","_id":"10301","quality_controlled":"1","date_published":"2021-11-17T00:00:00Z","article_number":"e71575","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly","oa":1,"keyword":["general immunology and microbiology","general biochemistry","genetics and molecular biology","general medicine","general neuroscience"],"day":"17","department":[{"_id":"GaNo"}],"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"issn":["2050-084X"]}},{"oa":1,"title":"Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"LeSa"}],"keyword":["general agricultural and biological Sciences","general biochemistry","genetics and molecular biology","medicine (miscellaneous)"],"day":"08","publication_identifier":{"issn":["2399-3642"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"Springer ","acknowledgement":"We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K.","doi":"10.1038/s42003-021-01808-9","file":[{"content_type":"application/pdf","date_created":"2021-11-19T15:09:18Z","creator":"cchlebak","relation":"main_file","access_level":"open_access","checksum":"8ffd39f2bba7152a2441802ff313bf0b","success":1,"file_name":"2021_CommBio_Çoruh.pdf","file_id":"10318","date_updated":"2021-11-19T15:09:18Z","file_size":6030261}],"isi":1,"article_number":"304","quality_controlled":"1","_id":"10310","date_published":"2021-03-08T00:00:00Z","publication_status":"published","file_date_updated":"2021-11-19T15:09:18Z","year":"2021","month":"03","issue":"1","volume":4,"author":[{"last_name":"Çoruh","orcid":"0000-0002-3219-2022","first_name":"Mehmet Orkun","full_name":"Çoruh, Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef"},{"last_name":"Frank","first_name":"Anna","full_name":"Frank, Anna"},{"full_name":"Tanaka, Hideaki","first_name":"Hideaki","last_name":"Tanaka"},{"last_name":"Kawamoto","first_name":"Akihiro","full_name":"Kawamoto, Akihiro"},{"last_name":"El-Mohsnawy","first_name":"Eithar","full_name":"El-Mohsnawy, Eithar"},{"first_name":"Takayuki","last_name":"Kato","full_name":"Kato, Takayuki"},{"full_name":"Namba, Keiichi","first_name":"Keiichi","last_name":"Namba"},{"full_name":"Gerle, Christoph","first_name":"Christoph","last_name":"Gerle"},{"full_name":"Nowaczyk, Marc M.","first_name":"Marc M.","last_name":"Nowaczyk"},{"first_name":"Genji","last_name":"Kurisu","full_name":"Kurisu, Genji"}],"pmid":1,"date_updated":"2023-08-14T11:51:19Z","ddc":["570"],"intvolume":"         4","abstract":[{"text":"A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700.","lang":"eng"}],"status":"public","external_id":{"isi":["000627440700001"],"pmid":["33686186"]},"has_accepted_license":"1","date_created":"2021-11-19T11:37:29Z","publication":"Communications Biology","scopus_import":"1","oa_version":"Published Version","type":"journal_article","citation":{"chicago":"Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” <i>Communications Biology</i>. Springer , 2021. <a href=\"https://doi.org/10.1038/s42003-021-01808-9\">https://doi.org/10.1038/s42003-021-01808-9</a>.","mla":"Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” <i>Communications Biology</i>, vol. 4, no. 1, 304, Springer , 2021, doi:<a href=\"https://doi.org/10.1038/s42003-021-01808-9\">10.1038/s42003-021-01808-9</a>.","short":"M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021).","apa":"Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. <i>Communications Biology</i>. Springer . <a href=\"https://doi.org/10.1038/s42003-021-01808-9\">https://doi.org/10.1038/s42003-021-01808-9</a>","ieee":"M. O. Çoruh <i>et al.</i>, “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” <i>Communications Biology</i>, vol. 4, no. 1. Springer , 2021.","ista":"Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304.","ama":"Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. <i>Communications Biology</i>. 2021;4(1). doi:<a href=\"https://doi.org/10.1038/s42003-021-01808-9\">10.1038/s42003-021-01808-9</a>"},"article_type":"original","language":[{"iso":"eng"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","day":"10","department":[{"_id":"SiHi"}],"article_processing_charge":"Yes","publication_identifier":{"eissn":["2666-1667"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1016/j.xpro.2021.100939","file":[{"file_size":7309464,"file_name":"2021_STARProtocols_Amberg.pdf","file_id":"10329","date_updated":"2021-11-22T08:23:58Z","checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","success":1,"access_level":"open_access","creator":"cchlebak","relation":"main_file","date_created":"2021-11-22T08:23:58Z","content_type":"application/pdf"}],"acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","publisher":"Cell Press","date_published":"2021-11-10T00:00:00Z","_id":"10321","quality_controlled":"1","article_number":"100939","year":"2021","publication_status":"published","file_date_updated":"2021-11-22T08:23:58Z","issue":"4","volume":2,"month":"11","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"author":[{"full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","orcid":"0000-0002-3183-8207","first_name":"Nicole"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"         2","date_updated":"2025-04-15T08:23:07Z","ddc":["573"],"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression","grant_number":"T01031"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","grant_number":"F7805"}],"date_created":"2021-11-21T23:01:28Z","publication":"STAR Protocols","scopus_import":"1","oa_version":"Published Version","corr_author":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021)."}],"status":"public","has_accepted_license":"1","article_type":"original","ec_funded":1,"citation":{"chicago":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">https://doi.org/10.1016/j.xpro.2021.100939</a>.","mla":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” <i>STAR Protocols</i>, vol. 2, no. 4, 100939, Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">10.1016/j.xpro.2021.100939</a>.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).","apa":"Amberg, N., &#38; Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">https://doi.org/10.1016/j.xpro.2021.100939</a>","ista":"Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.","ieee":"N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” <i>STAR Protocols</i>, vol. 2, no. 4. Cell Press, 2021.","ama":"Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. <i>STAR Protocols</i>. 2021;2(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.100939\">10.1016/j.xpro.2021.100939</a>"},"language":[{"iso":"eng"}]}]