[{"publication_identifier":{"isbn":["9781611975994"]},"date_updated":"2021-01-12T08:15:38Z","conference":{"location":"Salt Lake City, UT, United States","name":"SODA: Symposium on Discrete Algorithms","end_date":"2020-01-08","start_date":"2020-01-05"},"publication_status":"published","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"01","status":"public","type":"conference","title":"Embeddability of simplicial complexes is undecidable","article_processing_charge":"No","citation":{"ieee":"M. Filakovský, U. Wagner, and S. Y. Zhechev, “Embeddability of simplicial complexes is undecidable,” in <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Salt Lake City, UT, United States, 2020, vol. 2020–January, pp. 767–785.","ista":"Filakovský M, Wagner U, Zhechev SY. 2020. Embeddability of simplicial complexes is undecidable. Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2020–January, 767–785.","apa":"Filakovský, M., Wagner, U., &#38; Zhechev, S. Y. (2020). Embeddability of simplicial complexes is undecidable. In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2020–January, pp. 767–785). Salt Lake City, UT, United States: SIAM. <a href=\"https://doi.org/10.1137/1.9781611975994.47\">https://doi.org/10.1137/1.9781611975994.47</a>","mla":"Filakovský, Marek, et al. “Embeddability of Simplicial Complexes Is Undecidable.” <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2020–January, SIAM, 2020, pp. 767–85, doi:<a href=\"https://doi.org/10.1137/1.9781611975994.47\">10.1137/1.9781611975994.47</a>.","short":"M. Filakovský, U. Wagner, S.Y. Zhechev, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2020, pp. 767–785.","ama":"Filakovský M, Wagner U, Zhechev SY. Embeddability of simplicial complexes is undecidable. In: <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2020-January. SIAM; 2020:767-785. doi:<a href=\"https://doi.org/10.1137/1.9781611975994.47\">10.1137/1.9781611975994.47</a>","chicago":"Filakovský, Marek, Uli Wagner, and Stephan Y Zhechev. “Embeddability of Simplicial Complexes Is Undecidable.” In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2020–January:767–85. SIAM, 2020. <a href=\"https://doi.org/10.1137/1.9781611975994.47\">https://doi.org/10.1137/1.9781611975994.47</a>."},"department":[{"_id":"UlWa"}],"quality_controlled":"1","page":"767-785","_id":"7806","doi":"10.1137/1.9781611975994.47","date_published":"2020-01-01T00:00:00Z","abstract":[{"text":"We consider the following decision problem EMBEDk→d in computational topology (where k ≤ d are fixed positive integers): Given a finite simplicial complex K of dimension k, does there exist a (piecewise-linear) embedding of K into ℝd?\r\nThe special case EMBED1→2 is graph planarity, which is decidable in linear time, as shown by Hopcroft and Tarjan. In higher dimensions, EMBED2→3 and EMBED3→3 are known to be decidable (as well as NP-hard), and recent results of Čadek et al. in computational homotopy theory, in combination with the classical Haefliger–Weber theorem in geometric topology, imply that EMBEDk→d can be solved in polynomial time for any fixed pair (k, d) of dimensions in the so-called metastable range .\r\nHere, by contrast, we prove that EMBEDk→d is algorithmically undecidable for almost all pairs of dimensions outside the metastable range, namely for . This almost completely resolves the decidability vs. undecidability of EMBEDk→d in higher dimensions and establishes a sharp dichotomy between polynomial-time solvability and undecidability.\r\nOur result complements (and in a wide range of dimensions strengthens) earlier results of Matoušek, Tancer, and the second author, who showed that EMBEDk→d is undecidable for 4 ≤ k ϵ {d – 1, d}, and NP-hard for all remaining pairs (k, d) outside the metastable range and satisfying d ≥ 4.","lang":"eng"}],"volume":"2020-January","author":[{"first_name":"Marek","last_name":"Filakovský","full_name":"Filakovský, Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"},{"last_name":"Zhechev","first_name":"Stephan Y","full_name":"Zhechev, Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87"}],"year":"2020","language":[{"iso":"eng"}],"day":"01","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","scopus_import":1,"main_file_link":[{"url":"https://doi.org/10.1137/1.9781611975994.47","open_access":"1"}],"publisher":"SIAM","date_created":"2020-05-10T22:00:48Z","project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","name":"Algorithms for Embeddings and Homotopy Theory","grant_number":"P31312","call_identifier":"FWF"}]},{"oa_version":"Submitted Version","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"12129","relation":"later_version","status":"public"}]},"publication_status":"published","oa":1,"conference":{"start_date":"2020-01-05","name":"SODA: Symposium on Discrete Algorithms","end_date":"2020-01-08","location":"Salt Lake City, UT, United States"},"date_updated":"2023-08-04T08:51:07Z","publication_identifier":{"isbn":["9781611975994"]},"arxiv":1,"doi":"10.1137/1.9781611975994.172","external_id":{"arxiv":["2003.13557"]},"_id":"7807","page":"2823-2841","quality_controlled":"1","department":[{"_id":"UlWa"}],"citation":{"ieee":"U. Wagner and E. Welzl, “Connectivity of triangulation flip graphs in the plane (Part I: Edge flips),” in <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Salt Lake City, UT, United States, 2020, vol. 2020–January, pp. 2823–2841.","ista":"Wagner U, Welzl E. 2020. Connectivity of triangulation flip graphs in the plane (Part I: Edge flips). Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2020–January, 2823–2841.","mla":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane (Part I: Edge Flips).” <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2020–January, SIAM, 2020, pp. 2823–41, doi:<a href=\"https://doi.org/10.1137/1.9781611975994.172\">10.1137/1.9781611975994.172</a>.","apa":"Wagner, U., &#38; Welzl, E. (2020). Connectivity of triangulation flip graphs in the plane (Part I: Edge flips). In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2020–January, pp. 2823–2841). Salt Lake City, UT, United States: SIAM. <a href=\"https://doi.org/10.1137/1.9781611975994.172\">https://doi.org/10.1137/1.9781611975994.172</a>","ama":"Wagner U, Welzl E. Connectivity of triangulation flip graphs in the plane (Part I: Edge flips). In: <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2020-January. SIAM; 2020:2823-2841. doi:<a href=\"https://doi.org/10.1137/1.9781611975994.172\">10.1137/1.9781611975994.172</a>","short":"U. Wagner, E. Welzl, in:, Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2020, pp. 2823–2841.","chicago":"Wagner, Uli, and Emo Welzl. “Connectivity of Triangulation Flip Graphs in the Plane (Part I: Edge Flips).” In <i>Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2020–January:2823–41. SIAM, 2020. <a href=\"https://doi.org/10.1137/1.9781611975994.172\">https://doi.org/10.1137/1.9781611975994.172</a>."},"article_processing_charge":"No","title":"Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)","type":"conference","status":"public","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","year":"2020","language":[{"iso":"eng"}],"author":[{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"},{"first_name":"Emo","last_name":"Welzl","full_name":"Welzl, Emo"}],"abstract":[{"lang":"eng","text":"In a straight-line embedded triangulation of a point set P in the plane, removing an inner edge and—provided the resulting quadrilateral is convex—adding the other diagonal is called an edge flip. The (edge) flip graph has all triangulations as vertices, and a pair of triangulations is adjacent if they can be obtained from each other by an edge flip. The goal of this paper is to contribute to a better understanding of the flip graph, with an emphasis on its connectivity.\r\nFor sets in general position, it is known that every triangulation allows at least edge flips (a tight bound) which gives the minimum degree of any flip graph for n points. We show that for every point set P in general position, the flip graph is at least -vertex connected. Somewhat more strongly, we show that the vertex connectivity equals the minimum degree occurring in the flip graph, i.e. the minimum number of flippable edges in any triangulation of P, provided P is large enough. Finally, we exhibit some of the geometry of the flip graph by showing that the flip graph can be covered by 1-skeletons of polytopes of dimension (products of associahedra).\r\nA corresponding result ((n – 3)-vertex connectedness) can be shown for the bistellar flip graph of partial triangulations, i.e. the set of all triangulations of subsets of P which contain all extreme points of P. This will be treated separately in a second part."}],"volume":"2020-January","date_published":"2020-01-01T00:00:00Z","date_created":"2020-05-10T22:00:48Z","publisher":"SIAM","main_file_link":[{"url":"https://doi.org/10.1137/1.9781611975994.172","open_access":"1"}],"scopus_import":1},{"project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"}],"date_created":"2020-05-10T22:00:49Z","file":[{"creator":"dernst","date_created":"2020-05-26T12:48:15Z","checksum":"f19905a42891fe5ce93d69143fa3f6fb","relation":"main_file","file_id":"7893","file_name":"2020_TACAS_Giacobbe.pdf","file_size":2744030,"access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","content_type":"application/pdf"}],"publisher":"Springer Nature","scopus_import":1,"day":"17","year":"2020","language":[{"iso":"eng"}],"publication":"International Conference on Tools and Algorithms for the Construction and Analysis of Systems","file_date_updated":"2020-07-14T12:48:03Z","volume":12079,"abstract":[{"text":"Quantization converts neural networks into low-bit fixed-point computations which can be carried out by efficient integer-only hardware, and is standard practice for the deployment of neural networks on real-time embedded devices. However, like their real-numbered counterpart, quantized networks are not immune to malicious misclassification caused by adversarial attacks. We investigate how quantization affects a network’s robustness to adversarial attacks, which is a formal verification question. We show that neither robustness nor non-robustness are monotonic with changing the number of bits for the representation and, also, neither are preserved by quantization from a real-numbered network. For this reason, we introduce a verification method for quantized neural networks which, using SMT solving over bit-vectors, accounts for their exact, bit-precise semantics. We built a tool and analyzed the effect of quantization on a classifier for the MNIST dataset. We demonstrate that, compared to our method, existing methods for the analysis of real-numbered networks often derive false conclusions about their quantizations, both when determining robustness and when detecting attacks, and that existing methods for quantized networks often miss attacks. Furthermore, we applied our method beyond robustness, showing how the number of bits in quantization enlarges the gender bias of a predictor for students’ grades.","lang":"eng"}],"date_published":"2020-04-17T00:00:00Z","author":[{"full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco","last_name":"Giacobbe","orcid":"0000-0001-8180-0904"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"}],"_id":"7808","page":"79-97","intvolume":"     12079","doi":"10.1007/978-3-030-45237-7_5","department":[{"_id":"ToHe"}],"quality_controlled":"1","article_processing_charge":"No","citation":{"short":"M. Giacobbe, T.A. Henzinger, M. Lechner, in:, International Conference on Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2020, pp. 79–97.","chicago":"Giacobbe, Mirco, Thomas A Henzinger, and Mathias Lechner. “How Many Bits Does It Take to Quantize Your Neural Network?” In <i>International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, 12079:79–97. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-45237-7_5\">https://doi.org/10.1007/978-3-030-45237-7_5</a>.","ama":"Giacobbe M, Henzinger TA, Lechner M. How many bits does it take to quantize your neural network? In: <i>International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 12079. Springer Nature; 2020:79-97. doi:<a href=\"https://doi.org/10.1007/978-3-030-45237-7_5\">10.1007/978-3-030-45237-7_5</a>","mla":"Giacobbe, Mirco, et al. “How Many Bits Does It Take to Quantize Your Neural Network?” <i>International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 12079, Springer Nature, 2020, pp. 79–97, doi:<a href=\"https://doi.org/10.1007/978-3-030-45237-7_5\">10.1007/978-3-030-45237-7_5</a>.","apa":"Giacobbe, M., Henzinger, T. A., &#38; Lechner, M. (2020). How many bits does it take to quantize your neural network? In <i>International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 12079, pp. 79–97). Dublin, Ireland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-45237-7_5\">https://doi.org/10.1007/978-3-030-45237-7_5</a>","ieee":"M. Giacobbe, T. A. Henzinger, and M. Lechner, “How many bits does it take to quantize your neural network?,” in <i>International Conference on Tools and Algorithms for the Construction and Analysis of Systems</i>, Dublin, Ireland, 2020, vol. 12079, pp. 79–97.","ista":"Giacobbe M, Henzinger TA, Lechner M. 2020. How many bits does it take to quantize your neural network? International Conference on Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 12079, 79–97."},"status":"public","type":"conference","title":"How many bits does it take to quantize your neural network?","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","related_material":{"record":[{"id":"11362","relation":"dissertation_contains","status":"public"}]},"month":"04","oa_version":"Published Version","date_updated":"2023-06-23T07:01:11Z","ddc":["000"],"publication_identifier":{"issn":["03029743"],"isbn":["9783030452360"],"eissn":["16113349"]},"publication_status":"published","oa":1,"conference":{"location":"Dublin, Ireland","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2020-04-30","start_date":"2020-04-25"},"alternative_title":["LNCS"],"has_accepted_license":"1"},{"publisher":"Springer Nature","file":[{"file_name":"2020_LNCS_Chatterjee.pdf","access_level":"open_access","file_size":651250,"date_updated":"2020-07-14T12:48:03Z","content_type":"application/pdf","date_created":"2020-05-26T13:34:48Z","creator":"dernst","relation":"main_file","checksum":"8618b80f4cf7b39a60e61a6445ad9807","file_id":"7895"}],"scopus_import":"1","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-05-10T22:00:50Z","file_date_updated":"2020-07-14T12:48:03Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar"},{"orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2020-04-18T00:00:00Z","volume":12075,"abstract":[{"lang":"eng","text":"Interprocedural data-flow analyses form an expressive and useful paradigm of numerous static analysis applications, such as live variables analysis, alias analysis and null pointers analysis. The most widely-used framework for interprocedural data-flow analysis is IFDS, which encompasses distributive data-flow functions over a finite domain. On-demand data-flow analyses restrict the focus of the analysis on specific program locations and data facts. This setting provides a natural split between (i) an offline (or preprocessing) phase, where the program is partially analyzed and analysis summaries are created, and (ii) an online (or query) phase, where analysis queries arrive on demand and the summaries are used to speed up answering queries.\r\nIn this work, we consider on-demand IFDS analyses where the queries concern program locations of the same procedure (aka same-context queries). We exploit the fact that flow graphs of programs have low treewidth to develop faster algorithms that are space and time optimal for many common data-flow analyses, in both the preprocessing and the query phase. We also use treewidth to develop query solutions that are embarrassingly parallelizable, i.e. the total work for answering each query is split to a number of threads such that each thread performs only a constant amount of work. Finally, we implement a static analyzer based on our algorithms, and perform a series of on-demand analysis experiments on standard benchmarks. Our experimental results show a drastic speed-up of the queries after only a lightweight preprocessing phase, which significantly outperforms existing techniques."}],"publication":"European Symposium on Programming","language":[{"iso":"eng"}],"year":"2020","day":"18","article_processing_charge":"No","citation":{"mla":"Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” <i>European Symposium on Programming</i>, vol. 12075, Springer Nature, 2020, pp. 112–40, doi:<a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">10.1007/978-3-030-44914-8_5</a>.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In <i>European Symposium on Programming</i> (Vol. 12075, pp. 112–140). Dublin, Ireland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">https://doi.org/10.1007/978-3-030-44914-8_5</a>","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European Symposium on Programming, Springer Nature, 2020, pp. 112–140.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. In: <i>European Symposium on Programming</i>. Vol 12075. Springer Nature; 2020:112-140. doi:<a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">10.1007/978-3-030-44914-8_5</a>","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand Data-Flow Analysis.” In <i>European Symposium on Programming</i>, 12075:112–40. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-44914-8_5\">https://doi.org/10.1007/978-3-030-44914-8_5</a>.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal and perfectly parallel algorithms for on-demand data-flow analysis,” in <i>European Symposium on Programming</i>, Dublin, Ireland, 2020, vol. 12075, pp. 112–140."},"isi":1,"title":"Optimal and perfectly parallel algorithms for on-demand data-flow analysis","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)"},"status":"public","type":"conference","external_id":{"isi":["000681656800005"]},"doi":"10.1007/978-3-030-44914-8_5","intvolume":"     12075","_id":"7810","page":"112-140","quality_controlled":"1","department":[{"_id":"KrCh"}],"has_accepted_license":"1","alternative_title":["LNCS"],"month":"04","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","conference":{"start_date":"2020-04-25","name":"ESOP: Programming Languages and Systems","end_date":"2020-04-30","location":"Dublin, Ireland"},"publication_status":"published","oa":1,"publication_identifier":{"isbn":["9783030449131"],"eissn":["16113349"],"issn":["03029743"]},"date_updated":"2025-06-02T08:53:42Z","ddc":["000"]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"05","ddc":["570"],"date_updated":"2021-01-12T08:15:42Z","publication_identifier":{"issn":["2504-284X"]},"oa":1,"publication_status":"published","has_accepted_license":"1","article_number":"48","_id":"7814","intvolume":"         5","doi":"10.3389/feduc.2020.00048","department":[{"_id":"SiHi"}],"quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"article_processing_charge":"No","citation":{"short":"R.J. Beattie, S. Hippenmeyer, F. Pauler, Frontiers in Education 5 (2020).","ama":"Beattie RJ, Hippenmeyer S, Pauler F. SCOPES: Sparking curiosity through Open-Source platforms in education and science. <i>Frontiers in Education</i>. 2020;5. doi:<a href=\"https://doi.org/10.3389/feduc.2020.00048\">10.3389/feduc.2020.00048</a>","chicago":"Beattie, Robert J, Simon Hippenmeyer, and Florian Pauler. “SCOPES: Sparking Curiosity through Open-Source Platforms in Education and Science.” <i>Frontiers in Education</i>. Frontiers Media, 2020. <a href=\"https://doi.org/10.3389/feduc.2020.00048\">https://doi.org/10.3389/feduc.2020.00048</a>.","apa":"Beattie, R. J., Hippenmeyer, S., &#38; Pauler, F. (2020). SCOPES: Sparking curiosity through Open-Source platforms in education and science. <i>Frontiers in Education</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/feduc.2020.00048\">https://doi.org/10.3389/feduc.2020.00048</a>","mla":"Beattie, Robert J., et al. “SCOPES: Sparking Curiosity through Open-Source Platforms in Education and Science.” <i>Frontiers in Education</i>, vol. 5, 48, Frontiers Media, 2020, doi:<a href=\"https://doi.org/10.3389/feduc.2020.00048\">10.3389/feduc.2020.00048</a>.","ieee":"R. J. Beattie, S. Hippenmeyer, and F. Pauler, “SCOPES: Sparking curiosity through Open-Source platforms in education and science,” <i>Frontiers in Education</i>, vol. 5. Frontiers Media, 2020.","ista":"Beattie RJ, Hippenmeyer S, Pauler F. 2020. SCOPES: Sparking curiosity through Open-Source platforms in education and science. Frontiers in Education. 5, 48."},"type":"journal_article","status":"public","title":"SCOPES: Sparking curiosity through Open-Source platforms in education and science","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":"08","language":[{"iso":"eng"}],"year":"2020","publication":"Frontiers in Education","ec_funded":1,"file_date_updated":"2020-07-14T12:48:03Z","abstract":[{"lang":"eng","text":"Scientific research is to date largely restricted to wealthy laboratories in developed nations due to the necessity of complex and expensive equipment. This inequality limits the capacity of science to be used as a diplomatic channel. Maker movements use open-source technologies including additive manufacturing (3D printing) and laser cutting, together with low-cost computers for developing novel products. This movement is setting the groundwork for a revolution, allowing scientific equipment to be sourced at a fraction of the cost and has the potential to increase the availability of equipment for scientists around the world. Science education is increasingly recognized as another channel for science diplomacy. In this perspective, we introduce the idea that the Maker movement and open-source technologies have the potential to revolutionize science, technology, engineering and mathematics (STEM) education worldwide. We present an open-source STEM didactic tool called SCOPES (Sparking Curiosity through Open-source Platforms in Education and Science). SCOPES is self-contained, independent of local resources, and cost-effective. SCOPES can be adapted to communicate complex subjects from genetics to neurobiology, perform real-world biological experiments and explore digitized scientific samples. We envision such platforms will enhance science diplomacy by providing a means for scientists to share their findings with classrooms and for educators to incorporate didactic concepts into STEM lessons. By providing students the opportunity to design, perform, and share scientific experiments, students also experience firsthand the benefits of a multinational scientific community. We provide instructions on how to build and use SCOPES on our webpage: http://scopeseducation.org."}],"volume":5,"date_published":"2020-05-08T00:00:00Z","author":[{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753","first_name":"Robert J","last_name":"Beattie"},{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler"}],"project":[{"call_identifier":"FWF","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020"}],"date_created":"2020-05-11T08:18:48Z","article_type":"original","publisher":"Frontiers Media","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:48:03Z","access_level":"open_access","file_size":1402146,"file_name":"2020_FrontiersEduc_Beattie.pdf","file_id":"7818","relation":"main_file","checksum":"a24ec24e38d843341ae620ec76c53688","date_created":"2020-05-11T11:34:08Z","creator":"dernst"}]},{"date_created":"2020-05-11T08:31:20Z","article_type":"original","project":[{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","call_identifier":"FWF"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","grant_number":"T0101031"},{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","publisher":"MyJove Corporation","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:48:03Z","file_size":1352186,"access_level":"open_access","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf","file_id":"7816","relation":"main_file","checksum":"3154ea7f90b9fb45e084cd1c2770597d","creator":"rbeattie","date_created":"2020-05-11T08:28:38Z"}],"ec_funded":1,"year":"2020","language":[{"iso":"eng"}],"day":"08","publication":"Journal of Visual Experiments","date_published":"2020-05-08T00:00:00Z","abstract":[{"text":"Beginning from a limited pool of progenitors, the mammalian cerebral cortex forms highly organized functional neural circuits. However, the underlying cellular and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs) and eventual production of neurons and glia in the developing neuroepithelium remains unclear. Methods to trace NSC division patterns and map the lineage of clonally related cells have advanced dramatically. However, many contemporary lineage tracing techniques suffer from the lack of cellular resolution of progeny cell fate, which is essential for deciphering progenitor cell division patterns. Presented is a protocol using mosaic analysis with double markers (MADM) to perform in vivo clonal analysis. MADM concomitantly manipulates individual progenitor cells and visualizes precise division patterns and lineage progression at unprecedented single cell resolution. MADM-based interchromosomal recombination events during the G2-X phase of mitosis, together with temporally inducible CreERT2, provide exact information on the birth dates of clones and their division patterns. Thus, MADM lineage tracing provides unprecedented qualitative and quantitative optical readouts of the proliferation mode of stem cell progenitors at the single cell level. MADM also allows for examination of the mechanisms and functional requirements of candidate genes in NSC lineage progression. This method is unique in that comparative analysis of control and mutant subclones can be performed in the same tissue environment in vivo. Here, the protocol is described in detail, and experimental paradigms to employ MADM for clonal analysis and lineage tracing in the developing cerebral cortex are demonstrated. Importantly, this protocol can be adapted to perform MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver is present.","lang":"eng"}],"author":[{"orcid":"0000-0002-8483-8753","last_name":"Beattie","first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","full_name":"Beattie, Robert J"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen"},{"orcid":"0000-0002-3183-8207","last_name":"Amberg","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole"},{"first_name":"Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T"},{"last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"}],"issue":"159","file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"SiHi"}],"quality_controlled":"1","_id":"7815","external_id":{"isi":["000546406600043"]},"doi":"10.3791/61147","type":"journal_article","status":"public","title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","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)"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"isi":1,"article_processing_charge":"No","citation":{"ieee":"R. J. Beattie <i>et al.</i>, “Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM),” <i>Journal of Visual Experiments</i>, no. 159. MyJove Corporation, 2020.","ista":"Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159), e61147.","mla":"Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>, no. 159, e61147, MyJove Corporation, 2020, doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>.","apa":"Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen, A. H., &#38; Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. MyJove Corporation. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>","short":"R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen, S. Hippenmeyer, Journal of Visual Experiments (2020).","chicago":"Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” <i>Journal of Visual Experiments</i>. MyJove Corporation, 2020. <a href=\"https://doi.org/10.3791/61147\">https://doi.org/10.3791/61147</a>.","ama":"Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM). <i>Journal of Visual Experiments</i>. 2020;(159). doi:<a href=\"https://doi.org/10.3791/61147\">10.3791/61147</a>"},"publication_identifier":{"issn":["1940-087X"]},"date_updated":"2024-03-25T23:30:23Z","ddc":["570"],"oa":1,"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","id":"7902","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"05","article_number":"e61147","has_accepted_license":"1"},{"author":[{"full_name":"Bouchal, Roza","last_name":"Bouchal","first_name":"Roza"},{"full_name":"Li, Zhujie","first_name":"Zhujie","last_name":"Li"},{"full_name":"Bongu, Chandra","first_name":"Chandra","last_name":"Bongu"},{"full_name":"Le Vot, Steven","first_name":"Steven","last_name":"Le Vot"},{"full_name":"Berthelot, Romain","first_name":"Romain","last_name":"Berthelot"},{"full_name":"Rotenberg, Benjamin","last_name":"Rotenberg","first_name":"Benjamin"},{"last_name":"Favier","first_name":"Fréderic","full_name":"Favier, Fréderic"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","first_name":"Stefan Alexander"},{"full_name":"Salanne, Mathieu","last_name":"Salanne","first_name":"Mathieu"},{"full_name":"Fontaine, Olivier","last_name":"Fontaine","first_name":"Olivier"}],"volume":59,"abstract":[{"text":"Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities nearing 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of 'free' and 'bound' water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability. ","lang":"eng"}],"date_published":"2020-09-07T00:00:00Z","file_date_updated":"2020-09-17T08:57:16Z","issue":"37","publication":"Angewandte Chemie International Edition","day":"07","language":[{"iso":"eng"}],"year":"2020","scopus_import":"1","file":[{"date_updated":"2020-09-17T08:57:16Z","content_type":"application/pdf","file_name":"2020_AngChemieINT_Buchal.pdf","file_size":1966184,"access_level":"open_access","file_id":"8400","creator":"dernst","date_created":"2020-09-17T08:57:16Z","relation":"main_file","checksum":"7b6c2fc20e9b0ff4353352f7a7004e2d","success":1}],"publisher":"Wiley","pmid":1,"date_created":"2020-05-14T21:00:30Z","article_type":"original","has_accepted_license":"1","publication_status":"published","oa":1,"date_updated":"2023-09-05T16:02:53Z","ddc":["540","546"],"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"month":"09","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","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)"},"status":"public","type":"journal_article","citation":{"ista":"Bouchal R, Li Z, Bongu C, Le Vot S, Berthelot R, Rotenberg B, Favier F, Freunberger SA, Salanne M, Fontaine O. 2020. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. Angewandte Chemie International Edition. 59(37), 15913–1591.","ieee":"R. Bouchal <i>et al.</i>, “Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte,” <i>Angewandte Chemie International Edition</i>, vol. 59, no. 37. Wiley, pp. 15913–1591, 2020.","chicago":"Bouchal, Roza, Zhujie Li, Chandra Bongu, Steven Le Vot, Romain Berthelot, Benjamin Rotenberg, Fréderic Favier, Stefan Alexander Freunberger, Mathieu Salanne, and Olivier Fontaine. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” <i>Angewandte Chemie International Edition</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/anie.202005378\">https://doi.org/10.1002/anie.202005378</a>.","ama":"Bouchal R, Li Z, Bongu C, et al. Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. <i>Angewandte Chemie International Edition</i>. 2020;59(37):15913-1591. doi:<a href=\"https://doi.org/10.1002/anie.202005378\">10.1002/anie.202005378</a>","short":"R. Bouchal, Z. Li, C. Bongu, S. Le Vot, R. Berthelot, B. Rotenberg, F. Favier, S.A. Freunberger, M. Salanne, O. Fontaine, Angewandte Chemie International Edition 59 (2020) 15913–1591.","apa":"Bouchal, R., Li, Z., Bongu, C., Le Vot, S., Berthelot, R., Rotenberg, B., … Fontaine, O. (2020). Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202005378\">https://doi.org/10.1002/anie.202005378</a>","mla":"Bouchal, Roza, et al. “Competitive Salt Precipitation/Dissolution during Free‐water Reduction in Water‐in‐salt Electrolyte.” <i>Angewandte Chemie International Edition</i>, vol. 59, no. 37, Wiley, 2020, pp. 15913–1591, doi:<a href=\"https://doi.org/10.1002/anie.202005378\">10.1002/anie.202005378</a>."},"article_processing_charge":"No","isi":1,"quality_controlled":"1","department":[{"_id":"StFr"}],"doi":"10.1002/anie.202005378","external_id":{"isi":["000541488700001"],"pmid":["32390281"]},"_id":"7847","page":"15913-1591","intvolume":"        59"},{"date_created":"2020-05-17T22:00:45Z","project":[{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"article_type":"original","file":[{"success":1,"file_name":"2020_JourEllipticParabEquat_Fellner.pdf","access_level":"open_access","file_size":8408694,"date_updated":"2020-11-25T08:59:59Z","content_type":"application/pdf","creator":"dernst","date_created":"2020-11-25T08:59:59Z","relation":"main_file","checksum":"6bc6832caacddceee1471291e93dcf1d","file_id":"8802"}],"publisher":"Springer Nature","scopus_import":"1","day":"01","year":"2020","language":[{"iso":"eng"}],"publication":"Journal of Elliptic and Parabolic Equations","file_date_updated":"2020-11-25T08:59:59Z","abstract":[{"lang":"eng","text":"In this paper, we establish convergence to equilibrium for a drift–diffusion–recombination system modelling the charge transport within certain semiconductor devices. More precisely, we consider a two-level system for electrons and holes which is augmented by an intermediate energy level for electrons in so-called trapped states. The recombination dynamics use the mass action principle by taking into account this additional trap level. The main part of the paper is concerned with the derivation of an entropy–entropy production inequality, which entails exponential convergence to the equilibrium via the so-called entropy method. The novelty of our approach lies in the fact that the entropy method is applied uniformly in a fast-reaction parameter which governs the lifetime of electrons on the trap level. Thus, the resulting decay estimate for the densities of electrons and holes extends to the corresponding quasi-steady-state approximation."}],"volume":6,"date_published":"2020-12-01T00:00:00Z","author":[{"first_name":"Klemens","last_name":"Fellner","full_name":"Fellner, Klemens"},{"id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333","last_name":"Kniely","first_name":"Michael"}],"_id":"7866","page":"529-598","intvolume":"         6","doi":"10.1007/s41808-020-00068-8","department":[{"_id":"JuFi"}],"acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). The second author has been supported by the International Research Training Group IGDK 1754 “Optimization and Numerical Analysis for Partial Differential Equations with Nonsmooth Structures”, funded by the German Research Council (DFG) and the Austrian Science Fund (FWF) under grant number [W 1244-N18].","quality_controlled":"1","citation":{"ista":"Fellner K, Kniely M. 2020. Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. Journal of Elliptic and Parabolic Equations. 6, 529–598.","ieee":"K. Fellner and M. Kniely, “Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model,” <i>Journal of Elliptic and Parabolic Equations</i>, vol. 6. Springer Nature, pp. 529–598, 2020.","apa":"Fellner, K., &#38; Kniely, M. (2020). Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. <i>Journal of Elliptic and Parabolic Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41808-020-00068-8\">https://doi.org/10.1007/s41808-020-00068-8</a>","mla":"Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium for a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the Limiting Shockley–Read–Hall Model.” <i>Journal of Elliptic and Parabolic Equations</i>, vol. 6, Springer Nature, 2020, pp. 529–98, doi:<a href=\"https://doi.org/10.1007/s41808-020-00068-8\">10.1007/s41808-020-00068-8</a>.","short":"K. Fellner, M. Kniely, Journal of Elliptic and Parabolic Equations 6 (2020) 529–598.","ama":"Fellner K, Kniely M. Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. <i>Journal of Elliptic and Parabolic Equations</i>. 2020;6:529-598. doi:<a href=\"https://doi.org/10.1007/s41808-020-00068-8\">10.1007/s41808-020-00068-8</a>","chicago":"Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium for a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the Limiting Shockley–Read–Hall Model.” <i>Journal of Elliptic and Parabolic Equations</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s41808-020-00068-8\">https://doi.org/10.1007/s41808-020-00068-8</a>."},"article_processing_charge":"No","status":"public","type":"journal_article","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)"},"title":"Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","oa_version":"Published Version","date_updated":"2021-01-12T08:15:47Z","ddc":["510"],"publication_identifier":{"issn":["22969020"],"eissn":["22969039"]},"publication_status":"published","oa":1,"has_accepted_license":"1"},{"scopus_import":"1","pmid":1,"file":[{"success":1,"file_name":"2020_JCellBiol_Kopf.pdf","access_level":"open_access","file_size":7536712,"date_updated":"2020-11-24T13:25:13Z","content_type":"application/pdf","date_created":"2020-11-24T13:25:13Z","creator":"dernst","checksum":"cb0b9c77842ae1214caade7b77e4d82d","relation":"main_file","file_id":"8801"}],"publisher":"Rockefeller University Press","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","call_identifier":"FP7"},{"name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin","_id":"26018E70-B435-11E9-9278-68D0E5697425"},{"_id":"252C3B08-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","grant_number":"W 1250-B20"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"Molecular and system level view of immune cell migration","_id":"25A48D24-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1396-2014"}],"date_created":"2020-05-24T22:00:56Z","article_type":"original","date_published":"2020-06-01T00:00:00Z","volume":219,"abstract":[{"lang":"eng","text":"Cells navigating through complex tissues face a fundamental challenge: while multiple protrusions explore different paths, the cell needs to avoid entanglement. How a cell surveys and then corrects its own shape is poorly understood. Here, we demonstrate that spatially distinct microtubule dynamics regulate amoeboid cell migration by locally promoting the retraction of protrusions. In migrating dendritic cells, local microtubule depolymerization within protrusions remote from the microtubule organizing center triggers actomyosin contractility controlled by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin localization, thereby causing two effects that rate-limit locomotion: (1) impaired cell edge coordination during path finding and (2) defective adhesion resolution. Compromised shape control is particularly hindering in geometrically complex microenvironments, where it leads to entanglement and ultimately fragmentation of the cell body. We thus demonstrate that microtubules can act as a proprioceptive device: they sense cell shape and control actomyosin retraction to sustain cellular coherence."}],"author":[{"orcid":"0000-0002-2187-6656","last_name":"Kopf","first_name":"Aglaja","full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz","full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"full_name":"Girkontaite, Irute","last_name":"Girkontaite","first_name":"Irute"},{"full_name":"Tedford, Kerry","first_name":"Kerry","last_name":"Tedford"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Thorn-Seshold, Oliver","last_name":"Thorn-Seshold","first_name":"Oliver"},{"full_name":"Trauner, Dirk","id":"E8F27F48-3EBA-11E9-92A1-B709E6697425","first_name":"Dirk","last_name":"Trauner"},{"full_name":"Häcker, Hans","first_name":"Hans","last_name":"Häcker"},{"last_name":"Fischer","first_name":"Klaus Dieter","full_name":"Fischer, Klaus Dieter"},{"full_name":"Kiermaier, Eva","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Kiermaier","orcid":"0000-0001-6165-5738"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"issue":"6","file_date_updated":"2020-11-24T13:25:13Z","ec_funded":1,"language":[{"iso":"eng"}],"year":"2020","day":"01","publication":"The Journal of Cell Biology","type":"journal_article","status":"public","title":"Microtubules control cellular shape and coherence in amoeboid migrating cells","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)"},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"}],"isi":1,"citation":{"ieee":"A. Kopf <i>et al.</i>, “Microtubules control cellular shape and coherence in amoeboid migrating cells,” <i>The Journal of Cell Biology</i>, vol. 219, no. 6. Rockefeller University Press, 2020.","ista":"Kopf A, Renkawitz J, Hauschild R, Girkontaite I, Tedford K, Merrin J, Thorn-Seshold O, Trauner D, Häcker H, Fischer KD, Kiermaier E, Sixt MK. 2020. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 219(6), e201907154.","apa":"Kopf, A., Renkawitz, J., Hauschild, R., Girkontaite, I., Tedford, K., Merrin, J., … Sixt, M. K. (2020). Microtubules control cellular shape and coherence in amoeboid migrating cells. <i>The Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201907154\">https://doi.org/10.1083/jcb.201907154</a>","mla":"Kopf, Aglaja, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” <i>The Journal of Cell Biology</i>, vol. 219, no. 6, e201907154, Rockefeller University Press, 2020, doi:<a href=\"https://doi.org/10.1083/jcb.201907154\">10.1083/jcb.201907154</a>.","chicago":"Kopf, Aglaja, Jörg Renkawitz, Robert Hauschild, Irute Girkontaite, Kerry Tedford, Jack Merrin, Oliver Thorn-Seshold, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” <i>The Journal of Cell Biology</i>. Rockefeller University Press, 2020. <a href=\"https://doi.org/10.1083/jcb.201907154\">https://doi.org/10.1083/jcb.201907154</a>.","ama":"Kopf A, Renkawitz J, Hauschild R, et al. Microtubules control cellular shape and coherence in amoeboid migrating cells. <i>The Journal of Cell Biology</i>. 2020;219(6). doi:<a href=\"https://doi.org/10.1083/jcb.201907154\">10.1083/jcb.201907154</a>","short":"A. Kopf, J. Renkawitz, R. Hauschild, I. Girkontaite, K. Tedford, J. Merrin, O. Thorn-Seshold, D. Trauner, H. Häcker, K.D. Fischer, E. Kiermaier, M.K. Sixt, The Journal of Cell Biology 219 (2020)."},"article_processing_charge":"No","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"quality_controlled":"1","acknowledgement":"The authors thank the Scientific Service Units (Life Sciences, Bioimaging, Preclinical) of the Institute of Science and Technology Austria for excellent support. This work was funded by the European Research Council (ERC StG 281556 and CoG 724373), two grants from the Austrian\r\nScience Fund (FWF; P29911 and DK Nanocell W1250-B20 to M. Sixt) and by the German Research Foundation (DFG SFB1032 project B09) to O. Thorn-Seshold and D. Trauner. J. Renkawitz was supported by ISTFELLOW funding from the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under the Research Executive Agency grant agreement (291734) and a European Molecular Biology Organization long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409), E. Kiermaier by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC 2151—390873048, and H. Hacker by the American Lebanese Syrian Associated ¨Charities. K.-D. Fischer was supported by the Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes graduate school funded by the Ministry of Economics, Science, and Digitisation of the State Saxony-Anhalt and by the European Funds for Social and Regional Development.","intvolume":"       219","_id":"7875","external_id":{"isi":["000538141100020"],"pmid":["32379884"]},"doi":"10.1083/jcb.201907154","article_number":"e201907154","has_accepted_license":"1","publication_identifier":{"eissn":["1540-8140"]},"date_updated":"2023-08-21T06:28:17Z","ddc":["570"],"publication_status":"published","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"06"},{"article_type":"original","date_created":"2020-05-24T22:00:57Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://pure.mpg.de/pubman/item/item_3265599_2/component/file_3265620/Sixt%20et%20al..pdf"}],"publisher":"Elsevier","language":[{"iso":"eng"}],"year":"2020","day":"19","publication":"Immunity","date_published":"2020-05-19T00:00:00Z","volume":52,"abstract":[{"lang":"eng","text":"In contrast to lymph nodes, the lymphoid regions of the spleen—the white pulp—are located deep within the organ, yielding the trafficking paths of T cells in the white pulp largely invisible. In an intravital microscopy tour de force reported in this issue of Immunity, Chauveau et al. show that T cells perform unidirectional, perivascular migration through the enigmatic marginal zone bridging channels. "}],"author":[{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Lämmermann, Tim","last_name":"Lämmermann","first_name":"Tim"}],"issue":"5","department":[{"_id":"MiSi"}],"quality_controlled":"1","intvolume":"        52","page":"721-723","_id":"7876","external_id":{"isi":["000535371100002"]},"doi":"10.1016/j.immuni.2020.04.020","type":"journal_article","status":"public","title":"T cells: Bridge-and-channel commute to the white pulp","isi":1,"article_processing_charge":"No","citation":{"ieee":"M. K. Sixt and T. Lämmermann, “T cells: Bridge-and-channel commute to the white pulp,” <i>Immunity</i>, vol. 52, no. 5. Elsevier, pp. 721–723, 2020.","ista":"Sixt MK, Lämmermann T. 2020. T cells: Bridge-and-channel commute to the white pulp. Immunity. 52(5), 721–723.","ama":"Sixt MK, Lämmermann T. T cells: Bridge-and-channel commute to the white pulp. <i>Immunity</i>. 2020;52(5):721-723. doi:<a href=\"https://doi.org/10.1016/j.immuni.2020.04.020\">10.1016/j.immuni.2020.04.020</a>","chicago":"Sixt, Michael K, and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” <i>Immunity</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.immuni.2020.04.020\">https://doi.org/10.1016/j.immuni.2020.04.020</a>.","short":"M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723.","mla":"Sixt, Michael K., and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” <i>Immunity</i>, vol. 52, no. 5, Elsevier, 2020, pp. 721–23, doi:<a href=\"https://doi.org/10.1016/j.immuni.2020.04.020\">10.1016/j.immuni.2020.04.020</a>.","apa":"Sixt, M. K., &#38; Lämmermann, T. (2020). T cells: Bridge-and-channel commute to the white pulp. <i>Immunity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.immuni.2020.04.020\">https://doi.org/10.1016/j.immuni.2020.04.020</a>"},"publication_identifier":{"issn":["10747613"],"eissn":["10974180"]},"date_updated":"2023-08-21T06:27:18Z","publication_status":"published","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"05","oa_version":"Published Version"},{"abstract":[{"text":"The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication inNIPBL, engineered in two different cell lines,alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interactwith MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protectiveagainst out-of-frame mutations that is potentially relevant for other genetic conditions.","lang":"eng"}],"volume":31,"date_published":"2020-05-19T00:00:00Z","author":[{"full_name":"Parenti, Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","first_name":"Ilaria","last_name":"Parenti"},{"full_name":"Diab, Farah","first_name":"Farah","last_name":"Diab"},{"full_name":"Gil, Sara Ruiz","last_name":"Gil","first_name":"Sara Ruiz"},{"full_name":"Mulugeta, Eskeatnaf","last_name":"Mulugeta","first_name":"Eskeatnaf"},{"first_name":"Valentina","last_name":"Casa","full_name":"Casa, Valentina"},{"last_name":"Berutti","first_name":"Riccardo","full_name":"Berutti, Riccardo"},{"full_name":"Brouwer, Rutger W.W.","first_name":"Rutger W.W.","last_name":"Brouwer"},{"last_name":"Dupé","first_name":"Valerie","full_name":"Dupé, Valerie"},{"last_name":"Eckhold","first_name":"Juliane","full_name":"Eckhold, Juliane"},{"last_name":"Graf","first_name":"Elisabeth","full_name":"Graf, Elisabeth"},{"full_name":"Puisac, Beatriz","first_name":"Beatriz","last_name":"Puisac"},{"full_name":"Ramos, Feliciano","last_name":"Ramos","first_name":"Feliciano"},{"last_name":"Schwarzmayr","first_name":"Thomas","full_name":"Schwarzmayr, Thomas"},{"full_name":"Gines, Macarena Moronta","last_name":"Gines","first_name":"Macarena Moronta"},{"first_name":"Thomas","last_name":"Van Staveren","full_name":"Van Staveren, Thomas"},{"last_name":"Van Ijcken","first_name":"Wilfred F.J.","full_name":"Van Ijcken, Wilfred F.J."},{"last_name":"Strom","first_name":"Tim M.","full_name":"Strom, Tim M."},{"last_name":"Pié","first_name":"Juan","full_name":"Pié, Juan"},{"full_name":"Watrin, Erwan","first_name":"Erwan","last_name":"Watrin"},{"full_name":"Kaiser, Frank J.","first_name":"Frank J.","last_name":"Kaiser"},{"full_name":"Wendt, Kerstin S.","last_name":"Wendt","first_name":"Kerstin S."}],"issue":"7","file_date_updated":"2020-07-14T12:48:04Z","day":"19","language":[{"iso":"eng"}],"year":"2020","publication":"Cell Reports","scopus_import":"1","publisher":"Elsevier","file":[{"file_id":"7892","relation":"main_file","checksum":"64d8f7467731ee5c166b10b939b8310b","date_created":"2020-05-26T11:05:01Z","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:48:04Z","access_level":"open_access","file_size":4695682,"file_name":"2020_CellReports_Parenti.pdf"}],"date_created":"2020-05-24T22:00:57Z","article_type":"original","article_number":"107647","has_accepted_license":"1","ddc":["570"],"date_updated":"2023-08-21T06:27:47Z","publication_identifier":{"eissn":["22111247"]},"publication_status":"published","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"05","status":"public","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome","isi":1,"citation":{"chicago":"Parenti, Ilaria, Farah Diab, Sara Ruiz Gil, Eskeatnaf Mulugeta, Valentina Casa, Riccardo Berutti, Rutger W.W. Brouwer, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” <i>Cell Reports</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.celrep.2020.107647\">https://doi.org/10.1016/j.celrep.2020.107647</a>.","short":"I. Parenti, F. Diab, S.R. Gil, E. Mulugeta, V. Casa, R. Berutti, R.W.W. Brouwer, V. Dupé, J. Eckhold, E. Graf, B. Puisac, F. Ramos, T. Schwarzmayr, M.M. Gines, T. Van Staveren, W.F.J. Van Ijcken, T.M. Strom, J. Pié, E. Watrin, F.J. Kaiser, K.S. Wendt, Cell Reports 31 (2020).","ama":"Parenti I, Diab F, Gil SR, et al. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. <i>Cell Reports</i>. 2020;31(7). doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.107647\">10.1016/j.celrep.2020.107647</a>","apa":"Parenti, I., Diab, F., Gil, S. R., Mulugeta, E., Casa, V., Berutti, R., … Wendt, K. S. (2020). MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2020.107647\">https://doi.org/10.1016/j.celrep.2020.107647</a>","mla":"Parenti, Ilaria, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” <i>Cell Reports</i>, vol. 31, no. 7, 107647, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.107647\">10.1016/j.celrep.2020.107647</a>.","ista":"Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, Van Staveren T, Van Ijcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. 2020. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 31(7), 107647.","ieee":"I. Parenti <i>et al.</i>, “MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome,” <i>Cell Reports</i>, vol. 31, no. 7. Elsevier, 2020."},"article_processing_charge":"No","department":[{"_id":"GaNo"}],"quality_controlled":"1","_id":"7877","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","intvolume":"        31","doi":"10.1016/j.celrep.2020.107647","external_id":{"isi":["000535655200005"]}},{"external_id":{"isi":["000535191600001"],"pmid":["32401196"]},"doi":"10.7554/eLife.56839","intvolume":"         9","_id":"7878","quality_controlled":"1","department":[{"_id":"RySh"}],"citation":{"apa":"Bao, J., Graupner, M., Astorga, G., Collin, T., Jalil, A., Indriati, D. W., … Llano, I. (2020). Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.56839\">https://doi.org/10.7554/eLife.56839</a>","mla":"Bao, Jin, et al. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” <i>ELife</i>, vol. 9, e56839, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.56839\">10.7554/eLife.56839</a>.","ama":"Bao J, Graupner M, Astorga G, et al. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.56839\">10.7554/eLife.56839</a>","short":"J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley, R. Shigemoto, I. Llano, ELife 9 (2020).","chicago":"Bao, Jin, Michael Graupner, Guadalupe Astorga, Thibault Collin, Abdelali Jalil, Dwi Wahyu Indriati, Jonathan Bradley, Ryuichi Shigemoto, and Isabel Llano. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.56839\">https://doi.org/10.7554/eLife.56839</a>.","ista":"Bao J, Graupner M, Astorga G, Collin T, Jalil A, Indriati DW, Bradley J, Shigemoto R, Llano I. 2020. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife. 9, e56839.","ieee":"J. Bao <i>et al.</i>, “Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"article_processing_charge":"No","isi":1,"title":"Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo","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)"},"type":"journal_article","status":"public","oa_version":"Published Version","month":"05","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","oa":1,"publication_identifier":{"eissn":["2050084X"]},"date_updated":"2023-08-21T06:26:50Z","ddc":["570"],"has_accepted_license":"1","article_number":"e56839","date_created":"2020-05-24T22:00:58Z","article_type":"original","pmid":1,"file":[{"file_id":"7891","relation":"main_file","checksum":"8ea99bb6660cc407dbdb00c173b01683","creator":"dernst","date_created":"2020-05-26T09:34:54Z","content_type":"application/pdf","date_updated":"2020-07-14T12:48:04Z","file_size":4832050,"access_level":"open_access","file_name":"2020_eLife_Bao.pdf"}],"publisher":"eLife Sciences Publications","scopus_import":"1","publication":"eLife","year":"2020","language":[{"iso":"eng"}],"day":"13","file_date_updated":"2020-07-14T12:48:04Z","author":[{"full_name":"Bao, Jin","last_name":"Bao","first_name":"Jin"},{"full_name":"Graupner, Michael","last_name":"Graupner","first_name":"Michael"},{"full_name":"Astorga, Guadalupe","last_name":"Astorga","first_name":"Guadalupe"},{"last_name":"Collin","first_name":"Thibault","full_name":"Collin, Thibault"},{"full_name":"Jalil, Abdelali","last_name":"Jalil","first_name":"Abdelali"},{"full_name":"Indriati, Dwi Wahyu","first_name":"Dwi Wahyu","last_name":"Indriati"},{"full_name":"Bradley, Jonathan","last_name":"Bradley","first_name":"Jonathan"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Llano","first_name":"Isabel","full_name":"Llano, Isabel"}],"date_published":"2020-05-13T00:00:00Z","volume":9,"abstract":[{"lang":"eng","text":"Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal signaling. While their function is well documented in slices, requirements for their activation in vivo are poorly understood. We examine this question in adult mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons (MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases Cai rises associated with locomotion. In vitro studies and freeze-fracture electron microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by close association of the two classes of receptors. Altogether our results suggest that mGluR1s, acting in synergy with iGluRs, potently contribute to processing cerebellar neuronal signaling under physiological conditions."}]},{"publication_status":"published","oa":1,"publication_identifier":{"eissn":["1083351X"],"issn":["00219258"]},"date_updated":"2023-08-21T06:26:22Z","oa_version":"Submitted Version","month":"04","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact","type":"journal_article","status":"public","citation":{"ieee":"R. R. Fagan <i>et al.</i>, “Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact,” <i>Journal of Biological Chemistry</i>, vol. 295, no. 16. ASBMB Publications, pp. 5229–5244, 2020.","ista":"Fagan RR, Kearney PJ, Sweeney CG, Luethi D, Schoot Uiterkamp FE, Schicker K, Alejandro BS, O’Connor LC, Sitte HH, Melikian HE. 2020. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 295(16), 5229–5244.","apa":"Fagan, R. R., Kearney, P. J., Sweeney, C. G., Luethi, D., Schoot Uiterkamp, F. E., Schicker, K., … Melikian, H. E. (2020). Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. <i>Journal of Biological Chemistry</i>. ASBMB Publications. <a href=\"https://doi.org/10.1074/jbc.RA120.012628\">https://doi.org/10.1074/jbc.RA120.012628</a>","mla":"Fagan, Rita R., et al. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” <i>Journal of Biological Chemistry</i>, vol. 295, no. 16, ASBMB Publications, 2020, pp. 5229–44, doi:<a href=\"https://doi.org/10.1074/jbc.RA120.012628\">10.1074/jbc.RA120.012628</a>.","short":"R.R. Fagan, P.J. Kearney, C.G. Sweeney, D. Luethi, F.E. Schoot Uiterkamp, K. Schicker, B.S. Alejandro, L.C. O’Connor, H.H. Sitte, H.E. Melikian, Journal of Biological Chemistry 295 (2020) 5229–5244.","chicago":"Fagan, Rita R., Patrick J. Kearney, Carolyn G. Sweeney, Dino Luethi, Florianne E Schoot Uiterkamp, Klaus Schicker, Brian S. Alejandro, Lauren C. O’Connor, Harald H. Sitte, and Haley E. Melikian. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” <i>Journal of Biological Chemistry</i>. ASBMB Publications, 2020. <a href=\"https://doi.org/10.1074/jbc.RA120.012628\">https://doi.org/10.1074/jbc.RA120.012628</a>.","ama":"Fagan RR, Kearney PJ, Sweeney CG, et al. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. <i>Journal of Biological Chemistry</i>. 2020;295(16):5229-5244. doi:<a href=\"https://doi.org/10.1074/jbc.RA120.012628\">10.1074/jbc.RA120.012628</a>"},"article_processing_charge":"No","isi":1,"quality_controlled":"1","department":[{"_id":"SaSi"}],"external_id":{"pmid":["32132171"],"isi":["000530288000006"]},"doi":"10.1074/jbc.RA120.012628","intvolume":"       295","page":"5229-5244","_id":"7880","author":[{"first_name":"Rita R.","last_name":"Fagan","full_name":"Fagan, Rita R."},{"first_name":"Patrick J.","last_name":"Kearney","full_name":"Kearney, Patrick J."},{"full_name":"Sweeney, Carolyn G.","last_name":"Sweeney","first_name":"Carolyn G."},{"first_name":"Dino","last_name":"Luethi","full_name":"Luethi, Dino"},{"last_name":"Schoot Uiterkamp","first_name":"Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E"},{"first_name":"Klaus","last_name":"Schicker","full_name":"Schicker, Klaus"},{"full_name":"Alejandro, Brian S.","first_name":"Brian S.","last_name":"Alejandro"},{"last_name":"O'Connor","first_name":"Lauren C.","full_name":"O'Connor, Lauren C."},{"full_name":"Sitte, Harald H.","last_name":"Sitte","first_name":"Harald H."},{"full_name":"Melikian, Haley E.","last_name":"Melikian","first_name":"Haley E."}],"date_published":"2020-04-17T00:00:00Z","volume":295,"abstract":[{"text":"Following its evoked release, dopamine (DA) signaling is rapidly terminated by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT). DAT surface availability is dynamically regulated by endocytic trafficking, and direct protein kinase C (PKC) activation acutely diminishes DAT surface expression by accelerating DAT internalization. Previous cell line studies demonstrated that PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT. However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis in DAergic terminals or whether there are region- and/or sex-dependent differences in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important questions. Ex vivo studies revealed that PKC activation acutely decreased DAT surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated, conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular distribution in DAergic terminals from female ventral, but not dorsal, striatum. Further, Rit2 was required for PKC-stimulated DAT internalization in both male and female ventral striatum. FRET and surface pulldown studies in cell lines revealed that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization. Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate PKC-stimulated DAT endocytosis. Together, our data provide greater insight into mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic terminals. ","lang":"eng"}],"issue":"16","publication":"Journal of Biological Chemistry","language":[{"iso":"eng"}],"year":"2020","day":"17","scopus_import":"1","pmid":1,"main_file_link":[{"open_access":"1","url":"https://escholarship.umassmed.edu/oapubs/4187"}],"publisher":"ASBMB Publications","date_created":"2020-05-24T22:00:59Z","article_type":"original"},{"isi":1,"article_processing_charge":"No","citation":{"ieee":"J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in separated tubes of tilted dipoles,” <i>Mathematics</i>, vol. 8, no. 4. MDPI, 2020.","ista":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated tubes of tilted dipoles. Mathematics. 8(4), 484.","chicago":"Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T. Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” <i>Mathematics</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/math8040484\">https://doi.org/10.3390/math8040484</a>.","short":"J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).","ama":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes of tilted dipoles. <i>Mathematics</i>. 2020;8(4). doi:<a href=\"https://doi.org/10.3390/math8040484\">10.3390/math8040484</a>","mla":"Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.” <i>Mathematics</i>, vol. 8, no. 4, 484, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/math8040484\">10.3390/math8040484</a>.","apa":"Armstrong, J. R., Jensen, A. S., Volosniev, A., &#38; Zinner, N. T. (2020). Clusters in separated tubes of tilted dipoles. <i>Mathematics</i>. MDPI. <a href=\"https://doi.org/10.3390/math8040484\">https://doi.org/10.3390/math8040484</a>"},"status":"public","type":"journal_article","title":"Clusters in separated tubes of tilted dipoles","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":"         8","_id":"7882","external_id":{"isi":["000531824100024"]},"doi":"10.3390/math8040484","department":[{"_id":"MiLe"}],"quality_controlled":"1","has_accepted_license":"1","article_number":"484","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","oa_version":"Published Version","publication_identifier":{"eissn":["22277390"]},"date_updated":"2023-08-21T06:23:36Z","ddc":["510"],"publication_status":"published","oa":1,"file":[{"date_updated":"2020-07-14T12:48:04Z","content_type":"application/pdf","file_name":"2020_Mathematics_Armstrong.pdf","file_size":990540,"access_level":"open_access","file_id":"7887","creator":"dernst","date_created":"2020-05-25T14:42:22Z","relation":"main_file","checksum":"a05a7df724522203d079673a0d4de4bc"}],"publisher":"MDPI","scopus_import":"1","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-05-24T22:01:00Z","article_type":"original","issue":"4","file_date_updated":"2020-07-14T12:48:04Z","date_published":"2020-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"A few-body cluster is a building block of a many-body system in a gas phase provided the temperature at most is of the order of the binding energy of this cluster. Here we illustrate this statement by considering a system of tubes filled with dipolar distinguishable particles. We calculate the partition function, which determines the probability to find a few-body cluster at a given temperature. The input for our calculations—the energies of few-body clusters—is estimated using the harmonic approximation. We first describe and demonstrate the validity of our numerical procedure. Then we discuss the results featuring melting of the zero-temperature many-body state into a gas of free particles and few-body clusters. For temperature higher than its binding energy threshold, the dimers overwhelmingly dominate the ensemble, where the remaining probability is in free particles. At very high temperatures free (harmonic oscillator trap-bound) particle dominance is eventually reached. This structure evolution appears both for one and two particles in each layer providing crucial information about the behavior of ultracold dipolar gases. The investigation addresses the transition region between few- and many-body physics as a function of temperature using a system of ten dipoles in five tubes."}],"volume":8,"author":[{"last_name":"Armstrong","first_name":"Jeremy R.","full_name":"Armstrong, Jeremy R."},{"full_name":"Jensen, Aksel S.","last_name":"Jensen","first_name":"Aksel S."},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev"},{"full_name":"Zinner, Nikolaj T.","last_name":"Zinner","first_name":"Nikolaj T."}],"year":"2020","language":[{"iso":"eng"}],"day":"01","publication":"Mathematics","ec_funded":1},{"title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","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)"},"type":"journal_article","status":"public","citation":{"ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","ieee":"A. Schauer, D. C. Nunes Pinheiro, R. Hauschild, and C.-P. J. Heisenberg, “Zebrafish embryonic explants undergo genetically encoded self-assembly,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","chicago":"Schauer, Alexandra, Diana C Nunes Pinheiro, Robert Hauschild, and Carl-Philipp J Heisenberg. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>.","ama":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>","short":"A. Schauer, D.C. Nunes Pinheiro, R. Hauschild, C.-P.J. Heisenberg, ELife 9 (2020).","mla":"Schauer, Alexandra, et al. “Zebrafish Embryonic Explants Undergo Genetically Encoded Self-Assembly.” <i>ELife</i>, vol. 9, e55190, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.55190\">10.7554/elife.55190</a>.","apa":"Schauer, A., Nunes Pinheiro, D. C., Hauschild, R., &#38; Heisenberg, C.-P. J. (2020). Zebrafish embryonic explants undergo genetically encoded self-assembly. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.55190\">https://doi.org/10.7554/elife.55190</a>"},"article_processing_charge":"No","isi":1,"quality_controlled":"1","department":[{"_id":"CaHe"},{"_id":"Bio"}],"doi":"10.7554/elife.55190","external_id":{"isi":["000531544400001"],"pmid":["32250246"]},"_id":"7888","intvolume":"         9","article_number":"e55190","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["570"],"date_updated":"2023-08-21T06:25:49Z","publication_identifier":{"issn":["2050-084X"]},"oa_version":"Published Version","month":"04","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"relation":"dissertation_contains","id":"12891","status":"public"}]},"scopus_import":"1","publisher":"eLife Sciences Publications","file":[{"file_id":"7890","creator":"dernst","date_created":"2020-05-25T15:15:43Z","checksum":"f6aad884cf706846ae9357fcd728f8b5","relation":"main_file","date_updated":"2020-07-14T12:48:04Z","content_type":"application/pdf","file_name":"2020_eLife_Schauer.pdf","access_level":"open_access","file_size":7744848}],"pmid":1,"date_created":"2020-05-25T15:01:40Z","article_type":"original","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020"},{"grant_number":"25239","name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"},{"_id":"26520D1E-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017"},{"grant_number":"LT000429","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","_id":"266BC5CE-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","first_name":"Alexandra","last_name":"Schauer"},{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","first_name":"Diana C","last_name":"Nunes Pinheiro"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Embryonic stem cell cultures are thought to self-organize into embryoid bodies, able to undergo symmetry-breaking, germ layer specification and even morphogenesis. Yet, it is unclear how to reconcile this remarkable self-organization capacity with classical experiments demonstrating key roles for extrinsic biases by maternal factors and/or extraembryonic tissues in embryogenesis. Here, we show that zebrafish embryonic tissue explants, prepared prior to germ layer induction and lacking extraembryonic tissues, can specify all germ layers and form a seemingly complete mesendoderm anlage. Importantly, explant organization requires polarized inheritance of maternal factors from dorsal-marginal regions of the blastoderm. Moreover, induction of endoderm and head-mesoderm, which require peak Nodal-signaling levels, is highly variable in explants, reminiscent of embryos with reduced Nodal signals from the extraembryonic tissues. Together, these data suggest that zebrafish explants do not undergo bona fide self-organization, but rather display features of genetically encoded self-assembly, where intrinsic genetic programs control the emergence of order."}],"volume":9,"date_published":"2020-04-06T00:00:00Z","file_date_updated":"2020-07-14T12:48:04Z","ec_funded":1,"publication":"eLife","day":"06","year":"2020","language":[{"iso":"eng"}]},{"publisher":"Springer Nature","file":[{"embargo":"2021-03-01","file_id":"8316","date_created":"2020-08-28T08:57:07Z","creator":"dernst","relation":"main_file","checksum":"1b30467500ec6277229a875b06e196d0","date_updated":"2021-03-02T23:30:03Z","content_type":"application/pdf","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","access_level":"open_access","file_size":1180086}],"pmid":1,"scopus_import":"1","project":[{"call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-05-25T15:02:00Z","article_type":"original","file_date_updated":"2021-03-02T23:30:03Z","abstract":[{"lang":"eng","text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants."}],"volume":38,"date_published":"2020-04-27T00:00:00Z","author":[{"full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana","last_name":"Mitiouchkina"},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"last_name":"Gonzalez Somermeyer","first_name":"Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa"},{"full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M.","last_name":"Markina"},{"full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V.","last_name":"Chepurnyh"},{"last_name":"Guglya","first_name":"Elena B.","full_name":"Guglya, Elena B."},{"first_name":"Tatiana A.","last_name":"Karataeva","full_name":"Karataeva, Tatiana A."},{"last_name":"Palkina","first_name":"Kseniia A.","full_name":"Palkina, Kseniia A."},{"first_name":"Ekaterina S.","last_name":"Shakhova","full_name":"Shakhova, Ekaterina S."},{"last_name":"Fakhranurova","first_name":"Liliia I.","full_name":"Fakhranurova, Liliia I."},{"full_name":"Chekova, Sofia V.","last_name":"Chekova","first_name":"Sofia V."},{"first_name":"Aleksandra S.","last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S."},{"full_name":"Golubev, Yaroslav V.","last_name":"Golubev","first_name":"Yaroslav V."},{"full_name":"Negrebetsky, Vadim V.","first_name":"Vadim V.","last_name":"Negrebetsky"},{"full_name":"Dolgushin, Sergey A.","first_name":"Sergey A.","last_name":"Dolgushin"},{"first_name":"Pavel V.","last_name":"Shalaev","full_name":"Shalaev, Pavel V."},{"last_name":"Shlykov","first_name":"Dmitry","full_name":"Shlykov, Dmitry"},{"full_name":"Melnik, Olesya A.","first_name":"Olesya A.","last_name":"Melnik"},{"full_name":"Shipunova, Victoria O.","last_name":"Shipunova","first_name":"Victoria O."},{"full_name":"Deyev, Sergey M.","last_name":"Deyev","first_name":"Sergey M."},{"last_name":"Bubyrev","first_name":"Andrey I.","full_name":"Bubyrev, Andrey I."},{"full_name":"Pushin, Alexander S.","first_name":"Alexander S.","last_name":"Pushin"},{"full_name":"Choob, Vladimir V.","last_name":"Choob","first_name":"Vladimir V."},{"last_name":"Dolgov","first_name":"Sergey V.","full_name":"Dolgov, Sergey V."},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694"},{"full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky","first_name":"Ilia V."},{"full_name":"Sarkisyan, Karen S.","last_name":"Sarkisyan","first_name":"Karen S."}],"day":"27","year":"2020","language":[{"iso":"eng"}],"publication":"Nature Biotechnology","ec_funded":1,"isi":1,"citation":{"ieee":"T. Mitiouchkina <i>et al.</i>, “Plants with genetically encoded autoluminescence,” <i>Nature Biotechnology</i>, vol. 38. Springer Nature, pp. 944–946, 2020.","ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” <i>Nature Biotechnology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41587-020-0500-9\">https://doi.org/10.1038/s41587-020-0500-9</a>.","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. <i>Nature Biotechnology</i>. 2020;38:944-946. doi:<a href=\"https://doi.org/10.1038/s41587-020-0500-9\">10.1038/s41587-020-0500-9</a>","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946.","mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” <i>Nature Biotechnology</i>, vol. 38, Springer Nature, 2020, pp. 944–46, doi:<a href=\"https://doi.org/10.1038/s41587-020-0500-9\">10.1038/s41587-020-0500-9</a>.","apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-020-0500-9\">https://doi.org/10.1038/s41587-020-0500-9</a>"},"article_processing_charge":"No","type":"journal_article","status":"public","title":"Plants with genetically encoded autoluminescence","_id":"7889","page":"944-946","intvolume":"        38","doi":"10.1038/s41587-020-0500-9","external_id":{"pmid":["32341562"],"isi":["000529298800003"]},"department":[{"_id":"FyKo"}],"acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","quality_controlled":"1","has_accepted_license":"1","related_material":{"link":[{"url":"https://doi.org/10.1038/s41587-020-0578-0","relation":"erratum"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"04","oa_version":"Submitted Version","ddc":["570"],"date_updated":"2023-09-05T15:30:34Z","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"oa":1,"publication_status":"published"},{"date_created":"2020-05-26T14:08:55Z","project":[{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7"},{"name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020"}],"supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"}],"file":[{"file_name":"2020_Thesis_Kamath.pdf","file_size":1622742,"access_level":"open_access","date_updated":"2020-07-14T12:48:04Z","content_type":"application/pdf","date_created":"2020-05-26T14:08:13Z","creator":"dernst","relation":"main_file","checksum":"b39e2e1c376f5819b823fb7077491c64","file_id":"7897"},{"relation":"source_file","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","date_created":"2020-05-26T14:08:23Z","creator":"dernst","file_id":"7898","file_size":15301529,"access_level":"closed","file_name":"Thesis_Kamath.zip","content_type":"application/x-zip-compressed","date_updated":"2020-07-14T12:48:04Z"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"language":[{"iso":"eng"}],"year":"2020","day":"25","date_published":"2020-05-25T00:00:00Z","abstract":[{"text":"A search problem lies in the complexity class FNP if a solution to the given instance of the problem can be verified efficiently. The complexity class TFNP consists of all search problems in FNP that are total in the sense that a solution is guaranteed to exist. TFNP contains a host of interesting problems from fields such as algorithmic game theory, computational topology, number theory and combinatorics. Since TFNP is a semantic class, it is unlikely to have a complete problem. Instead, one studies its syntactic subclasses which are defined based on the combinatorial principle used to argue totality. Of particular interest is the subclass PPAD, which contains important problems\r\nlike computing Nash equilibrium for bimatrix games and computational counterparts of several fixed-point theorems as complete. In the thesis, we undertake the study of averagecase hardness of TFNP, and in particular its subclass PPAD.\r\nAlmost nothing was known about average-case hardness of PPAD before a series of recent results showed how to achieve it using a cryptographic primitive called program obfuscation.\r\nHowever, it is currently not known how to construct program obfuscation from standard cryptographic assumptions. Therefore, it is desirable to relax the assumption under which average-case hardness of PPAD can be shown. In the thesis we take a step in this direction. First, we show that assuming the (average-case) hardness of a numbertheoretic\r\nproblem related to factoring of integers, which we call Iterated-Squaring, PPAD is hard-on-average in the random-oracle model. Then we strengthen this result to show that the average-case hardness of PPAD reduces to the (adaptive) soundness of the Fiat-Shamir Transform, a well-known technique used to compile a public-coin interactive protocol into a non-interactive one. As a corollary, we obtain average-case hardness for PPAD in the random-oracle model assuming the worst-case hardness of #SAT. Moreover, the above results can all be strengthened to obtain average-case hardness for the class CLS ⊆ PPAD.\r\nOur main technical contribution is constructing incrementally-verifiable procedures for computing Iterated-Squaring and #SAT. By incrementally-verifiable, we mean that every intermediate state of the computation includes a proof of its correctness, and the proof can be updated and verified in polynomial time. Previous constructions of such procedures relied on strong, non-standard assumptions. Instead, we introduce a technique called recursive proof-merging to obtain the same from weaker assumptions. ","lang":"eng"}],"author":[{"last_name":"Kamath Hosdurg","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:48:04Z","department":[{"_id":"KrPi"}],"degree_awarded":"PhD","page":"126","_id":"7896","doi":"10.15479/AT:ISTA:7896","type":"dissertation","status":"public","title":"On the average-case hardness of total search problems","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","citation":{"mla":"Kamath Hosdurg, Chethan. <i>On the Average-Case Hardness of Total Search Problems</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7896\">10.15479/AT:ISTA:7896</a>.","apa":"Kamath Hosdurg, C. (2020). <i>On the average-case hardness of total search problems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7896\">https://doi.org/10.15479/AT:ISTA:7896</a>","ama":"Kamath Hosdurg C. On the average-case hardness of total search problems. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7896\">10.15479/AT:ISTA:7896</a>","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","chicago":"Kamath Hosdurg, Chethan. “On the Average-Case Hardness of Total Search Problems.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7896\">https://doi.org/10.15479/AT:ISTA:7896</a>.","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020.","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria."},"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T13:15:55Z","ddc":["000"],"oa":1,"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"part_of_dissertation","id":"6677","status":"public"}]},"month":"05","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"has_accepted_license":"1"},{"related_material":{"record":[{"status":"public","id":"6830","relation":"dissertation_contains"},{"status":"public","id":"28","relation":"dissertation_contains"},{"status":"public","id":"7815","relation":"dissertation_contains"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-10-18T08:45:16Z","ddc":["570"],"oa":1,"publication_status":"published","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","page":"214","_id":"7902","doi":"10.15479/AT:ISTA:7902","department":[{"_id":"SiHi"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"article_processing_charge":"No","citation":{"ieee":"X. Contreras, “Genetic dissection of neural development in health and disease at single cell resolution,” Institute of Science and Technology Austria, 2020.","ista":"Contreras X. 2020. Genetic dissection of neural development in health and disease at single cell resolution. Institute of Science and Technology Austria.","apa":"Contreras, X. (2020). <i>Genetic dissection of neural development in health and disease at single cell resolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>","mla":"Contreras, Ximena. <i>Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>.","ama":"Contreras X. Genetic dissection of neural development in health and disease at single cell resolution. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7902\">10.15479/AT:ISTA:7902</a>","chicago":"Contreras, Ximena. “Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7902\">https://doi.org/10.15479/AT:ISTA:7902</a>.","short":"X. Contreras, Genetic Dissection of Neural Development in Health and Disease at Single Cell Resolution, Institute of Science and Technology Austria, 2020."},"type":"dissertation","status":"public","title":"Genetic dissection of neural development in health and disease at single cell resolution","year":"2020","language":[{"iso":"eng"}],"day":"05","ec_funded":1,"file_date_updated":"2021-06-07T22:30:03Z","date_published":"2020-06-05T00:00:00Z","abstract":[{"lang":"eng","text":"Mosaic genetic analysis has been widely used in different model organisms such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific fashion. More recently, and less easily conducted, mosaic genetic analysis in mice has also been enabled with the ambition to shed light on human gene function and disease. These genetic tools are of particular interest, but not restricted to, the study of the brain. Notably, the MADM technology offers a genetic approach in mice to visualize and concomitantly manipulate small subsets of genetically defined cells at a clonal level and single cell resolution. MADM-based analysis has already advanced the study of genetic mechanisms regulating brain development and is expected that further MADM-based analysis of genetic alterations will continue to reveal important insights on the fundamental principles of development and disease to potentially assist in the development of new therapies or treatments.\r\nIn summary, this work completed and characterized the necessary genome-wide genetic tools to perform MADM-based analysis at single cell level of the vast majority of mouse genes in virtually any cell type and provided a protocol to perform lineage tracing using the novel MADM resource. Importantly, this work also explored and revealed novel aspects of biologically relevant events in an in vivo context, such as the chromosome-specific bias of chromatid sister segregation pattern, the generation of cell-type diversity in the cerebral cortex and in the cerebellum and finally, the relevance of the interplay between the cell-autonomous gene function and cell-non-autonomous (community) effects in radial glial progenitor lineage progression.\r\nThis work provides a foundation and opens the door to further elucidating the molecular mechanisms underlying neuronal diversity and astrocyte generation."}],"author":[{"full_name":"Contreras, Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras"}],"date_created":"2020-05-29T08:27:32Z","project":[{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"file":[{"file_name":"PhDThesis_Contreras.docx","file_size":53134142,"access_level":"closed","date_updated":"2021-06-07T22:30:03Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2020-06-05T08:18:08Z","creator":"xcontreras","relation":"source_file","checksum":"43c172bf006c95b65992d473c7240d13","file_id":"7927"},{"file_name":"PhDThesis_Contreras.pdf","file_size":35117191,"access_level":"open_access","date_updated":"2021-06-07T22:30:03Z","content_type":"application/pdf","creator":"xcontreras","date_created":"2020-06-05T08:18:07Z","relation":"main_file","checksum":"addfed9128271be05cae3608e03a6ec0","file_id":"7928","embargo":"2021-06-06"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061"}]},{"doi":"10.1523/JNEUROSCI.2946-19.2020","external_id":{"isi":["000535694700004"]},"_id":"7908","page":"4103-4115","intvolume":"        40","quality_controlled":"1","department":[{"_id":"RySh"}],"citation":{"short":"H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience 40 (2020) 4103–4115.","chicago":"Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2020. <a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">https://doi.org/10.1523/JNEUROSCI.2946-19.2020</a>.","ama":"Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. <i>Journal of Neuroscience</i>. 2020;40(21):4103-4115. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">10.1523/JNEUROSCI.2946-19.2020</a>","apa":"Wang, H. Y., Eguchi, K., Yamashita, T., &#38; Takahashi, T. (2020). Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">https://doi.org/10.1523/JNEUROSCI.2946-19.2020</a>","mla":"Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” <i>Journal of Neuroscience</i>, vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">10.1523/JNEUROSCI.2946-19.2020</a>.","ista":"Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 40(21), 4103–4115.","ieee":"H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,” <i>Journal of Neuroscience</i>, vol. 40, no. 21. Society for Neuroscience, pp. 4103–4115, 2020."},"article_processing_charge":"No","isi":1,"title":"Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms","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)"},"type":"journal_article","status":"public","month":"05","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","oa":1,"ddc":["570"],"date_updated":"2023-08-21T06:31:25Z","publication_identifier":{"eissn":["15292401"]},"has_accepted_license":"1","article_type":"original","date_created":"2020-05-31T22:00:48Z","publisher":"Society for Neuroscience","file":[{"file_size":3817360,"access_level":"open_access","file_name":"2020_JourNeuroscience_Wang.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:05Z","relation":"main_file","checksum":"6571607ea9036154b67cc78e848a7f7d","date_created":"2020-06-02T09:12:16Z","creator":"dernst","file_id":"7912"}],"scopus_import":"1","publication":"Journal of Neuroscience","day":"20","language":[{"iso":"eng"}],"year":"2020","file_date_updated":"2020-07-14T12:48:05Z","issue":"21","author":[{"last_name":"Wang","first_name":"Han Ying","full_name":"Wang, Han Ying"},{"id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku","first_name":"Kohgaku","last_name":"Eguchi","orcid":"0000-0002-6170-2546"},{"full_name":"Yamashita, Takayuki","last_name":"Yamashita","first_name":"Takayuki"},{"last_name":"Takahashi","first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki"}],"volume":40,"abstract":[{"text":"Volatile anesthetics are widely used for surgery, but neuronal mechanisms of anesthesia remain unidentified. At the calyx of Held in brainstem slices from rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing the release probability and the number of readily releasable vesicles. In presynaptic recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization, whereas it inhibited exocytosis evoked by a prolonged depolarization via directly blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia is likely mediated by distinct dual mechanisms, depending on input frequencies. In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane impaired the fidelity of repetitive spike transmission, more strongly at higher frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited monosynaptic corticocortical spike transmission, preferentially at a higher frequency. We conclude that dual presynaptic mechanisms operate for the anesthetic action of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass filtering role in spike transmission at central excitatory synapses.","lang":"eng"}],"date_published":"2020-05-20T00:00:00Z"},{"publication":"eLife","day":"11","language":[{"iso":"eng"}],"year":"2020","ec_funded":1,"file_date_updated":"2020-07-14T12:48:05Z","author":[{"last_name":"Damiano-Guercio","first_name":"Julia","full_name":"Damiano-Guercio, Julia"},{"full_name":"Kurzawa, Laëtitia","last_name":"Kurzawa","first_name":"Laëtitia"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan","first_name":"Jan","last_name":"Müller"},{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","last_name":"Dimchev","first_name":"Georgi A","orcid":"0000-0001-8370-6161"},{"first_name":"Matthias","last_name":"Schaks","full_name":"Schaks, Matthias"},{"last_name":"Nemethova","first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria"},{"first_name":"Thomas","last_name":"Pokrant","full_name":"Pokrant, Thomas"},{"last_name":"Brühmann","first_name":"Stefan","full_name":"Brühmann, Stefan"},{"first_name":"Joern","last_name":"Linkner","full_name":"Linkner, Joern"},{"first_name":"Laurent","last_name":"Blanchoin","full_name":"Blanchoin, Laurent"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"}],"abstract":[{"text":"Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration.","lang":"eng"}],"volume":9,"date_published":"2020-05-11T00:00:00Z","date_created":"2020-05-31T22:00:49Z","article_type":"original","project":[{"call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"file":[{"file_id":"7914","checksum":"d33bd4441b9a0195718ce1ba5d2c48a6","relation":"main_file","creator":"dernst","date_created":"2020-06-02T10:35:37Z","content_type":"application/pdf","date_updated":"2020-07-14T12:48:05Z","access_level":"open_access","file_size":10535713,"file_name":"2020_eLife_Damiano_Guercio.pdf"}],"publisher":"eLife Sciences Publications","scopus_import":"1","oa_version":"Published Version","month":"05","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publication_status":"published","date_updated":"2023-08-21T06:32:25Z","ddc":["570"],"publication_identifier":{"eissn":["2050084X"]},"has_accepted_license":"1","article_number":"e55351","doi":"10.7554/eLife.55351","external_id":{"isi":["000537208000001"]},"_id":"7909","intvolume":"         9","quality_controlled":"1","department":[{"_id":"MiSi"}],"article_processing_charge":"No","citation":{"mla":"Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” <i>ELife</i>, vol. 9, e55351, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.55351\">10.7554/eLife.55351</a>.","apa":"Damiano-Guercio, J., Kurzawa, L., Müller, J., Dimchev, G. A., Schaks, M., Nemethova, M., … Faix, J. (2020). Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.55351\">https://doi.org/10.7554/eLife.55351</a>","chicago":"Damiano-Guercio, Julia, Laëtitia Kurzawa, Jan Müller, Georgi A Dimchev, Matthias Schaks, Maria Nemethova, Thomas Pokrant, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.55351\">https://doi.org/10.7554/eLife.55351</a>.","short":"J. Damiano-Guercio, L. Kurzawa, J. Müller, G.A. Dimchev, M. Schaks, M. Nemethova, T. Pokrant, S. Brühmann, J. Linkner, L. Blanchoin, M.K. Sixt, K. Rottner, J. Faix, ELife 9 (2020).","ama":"Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.55351\">10.7554/eLife.55351</a>","ista":"Damiano-Guercio J, Kurzawa L, Müller J, Dimchev GA, Schaks M, Nemethova M, Pokrant T, Brühmann S, Linkner J, Blanchoin L, Sixt MK, Rottner K, Faix J. 2020. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 9, e55351.","ieee":"J. Damiano-Guercio <i>et al.</i>, “Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020."},"isi":1,"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)"},"title":"Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion","type":"journal_article","status":"public"}]