[{"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1038/s41467-020-15895-5","acknowledgement":"We thank Daria Siekhaus, Jiri Friml and Alexander Johnson for critical reading of the manuscript, Peter Pimpl, Christian Luschnig and Liwen Jiang for sharing published material, Lesia Rodriguez Solovey for technical assistance. This work was supported by the Austrian Science Fund (FWF01_I1774S) to A.H., K.Ö., and E.B., the German Research Foundation (DFG; He3424/6-1 to I.H.), by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] (to N.C.), by the EU in the framework of the Marie-Curie FP7 COFUND People Programme through the award of an AgreenSkills+ fellowship No. 609398 (to J.S.) and by the Scientific Service Units of IST-Austria through resources provided by the Bioimaging Facility, the Life Science Facility. The IJPB benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007).","project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","grant_number":"I 1774-B16","call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"pmid":1,"day":"01","author":[{"first_name":"Andrej","full_name":"Hurny, Andrej","last_name":"Hurny","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3638-1426"},{"orcid":"0000-0003-1923-2410","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","full_name":"Cuesta, Candela","last_name":"Cuesta"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","full_name":"Cavallari, Nicola","last_name":"Cavallari"},{"last_name":"Ötvös","first_name":"Krisztina","full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5503-4983"},{"first_name":"Jerome","full_name":"Duclercq, Jerome","last_name":"Duclercq"},{"first_name":"Ladislav","full_name":"Dokládal, Ladislav","last_name":"Dokládal"},{"first_name":"Juan C","full_name":"Montesinos López, Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099"},{"last_name":"Gallemi","first_name":"Marçal","full_name":"Gallemi, Marçal","id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893"},{"id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semeradova, Hana","first_name":"Hana","last_name":"Semeradova"},{"id":"A0385D1A-9376-11EA-A47D-9862C5E3AB22","first_name":"Thomas","full_name":"Rauter, Thomas","last_name":"Rauter"},{"last_name":"Stenzel","first_name":"Irene","full_name":"Stenzel, Irene"},{"first_name":"Geert","full_name":"Persiau, Geert","last_name":"Persiau"},{"last_name":"Benade","full_name":"Benade, Freia","first_name":"Freia"},{"first_name":"Rishikesh","full_name":"Bhalearo, Rishikesh","last_name":"Bhalearo"},{"last_name":"Sýkorová","first_name":"Eva","full_name":"Sýkorová, Eva"},{"last_name":"Gorzsás","first_name":"András","full_name":"Gorzsás, András"},{"last_name":"Sechet","first_name":"Julien","full_name":"Sechet, Julien"},{"last_name":"Mouille","full_name":"Mouille, Gregory","first_name":"Gregory"},{"first_name":"Ingo","full_name":"Heilmann, Ingo","last_name":"Heilmann"},{"first_name":"Geert","full_name":"De Jaeger, Geert","last_name":"De Jaeger"},{"first_name":"Jutta","full_name":"Ludwig-Müller, Jutta","last_name":"Ludwig-Müller"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","ec_funded":1,"citation":{"short":"A. Hurny, C. Cuesta, N. Cavallari, K. Ötvös, J. Duclercq, L. Dokládal, J.C. Montesinos López, M. Gallemi, H. Semerádová, T. Rauter, I. Stenzel, G. Persiau, F. Benade, R. Bhalearo, E. Sýkorová, A. Gorzsás, J. Sechet, G. Mouille, I. Heilmann, G. De Jaeger, J. Ludwig-Müller, E. Benková, Nature Communications 11 (2020).","ama":"Hurny A, Cuesta C, Cavallari N, et al. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-15895-5\">10.1038/s41467-020-15895-5</a>","apa":"Hurny, A., Cuesta, C., Cavallari, N., Ötvös, K., Duclercq, J., Dokládal, L., … Benková, E. (2020). Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-15895-5\">https://doi.org/10.1038/s41467-020-15895-5</a>","chicago":"Hurny, Andrej, Candela Cuesta, Nicola Cavallari, Krisztina Ötvös, Jerome Duclercq, Ladislav Dokládal, Juan C Montesinos López, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-15895-5\">https://doi.org/10.1038/s41467-020-15895-5</a>.","ista":"Hurny A, Cuesta C, Cavallari N, Ötvös K, Duclercq J, Dokládal L, Montesinos López JC, Gallemi M, Semerádová H, Rauter T, Stenzel I, Persiau G, Benade F, Bhalearo R, Sýkorová E, Gorzsás A, Sechet J, Mouille G, Heilmann I, De Jaeger G, Ludwig-Müller J, Benková E. 2020. Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance. Nature Communications. 11, 2170.","ieee":"A. Hurny <i>et al.</i>, “Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","mla":"Hurny, Andrej, et al. “Synergistic on Auxin and Cytokinin 1 Positively Regulates Growth and Attenuates Soil Pathogen Resistance.” <i>Nature Communications</i>, vol. 11, 2170, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-15895-5\">10.1038/s41467-020-15895-5</a>."},"title":"Synergistic on Auxin and Cytokinin 1 positively regulates growth and attenuates soil pathogen resistance","quality_controlled":"1","department":[{"_id":"EvBe"}],"publication":"Nature Communications","status":"public","intvolume":"        11","publisher":"Springer Nature","isi":1,"month":"05","date_created":"2020-05-10T22:00:48Z","date_updated":"2023-08-21T06:21:56Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000531425900012"],"pmid":["32358503"]},"scopus_import":"1","publication_identifier":{"eissn":["20411723"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_type":"original","has_accepted_license":"1","oa_version":"Published Version","year":"2020","file_date_updated":"2020-10-06T07:47:53Z","volume":11,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"article_number":"2170","file":[{"success":1,"date_created":"2020-10-06T07:47:53Z","file_id":"8614","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-10-06T07:47:53Z","checksum":"2cba327c9e9416d75cb96be54b0fb441","file_size":4743576,"creator":"dernst","file_name":"2020_NatureComm_Hurny.pdf"}],"abstract":[{"lang":"eng","text":"Plants as non-mobile organisms constantly integrate varying environmental signals to flexibly adapt their growth and development. Local fluctuations in water and nutrient availability, sudden changes in temperature or other abiotic and biotic stresses can trigger changes in the growth of plant organs. Multiple mutually interconnected hormonal signaling cascades act as essential endogenous translators of these exogenous signals in the adaptive responses of plants. Although the molecular backbones of hormone transduction pathways have been identified, the mechanisms underlying their interactions are largely unknown. Here, using genome wide transcriptome profiling we identify an auxin and cytokinin cross-talk component; SYNERGISTIC ON AUXIN AND CYTOKININ 1 (SYAC1), whose expression in roots is strictly dependent on both of these hormonal pathways. We show that SYAC1 is a regulator of secretory pathway, whose enhanced activity interferes with deposition of cell wall components and can fine-tune organ growth and sensitivity to soil pathogens."}],"_id":"7805","date_published":"2020-05-01T00:00:00Z","article_processing_charge":"No"},{"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611975994.47"}],"volume":"2020-January","article_processing_charge":"No","_id":"7806","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"}],"date_published":"2020-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:38Z","scopus_import":1,"publication_identifier":{"isbn":["9781611975994"]},"year":"2020","oa_version":"Published Version","publisher":"SIAM","department":[{"_id":"UlWa"}],"quality_controlled":"1","publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","status":"public","page":"767-785","month":"01","date_created":"2020-05-10T22:00:48Z","project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory"}],"language":[{"iso":"eng"}],"doi":"10.1137/1.9781611975994.47","citation":{"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.","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.","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>.","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.","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>","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>"},"conference":{"start_date":"2020-01-05","end_date":"2020-01-08","name":"SODA: Symposium on Discrete Algorithms","location":"Salt Lake City, UT, United States"},"title":"Embeddability of simplicial complexes is undecidable","day":"01","author":[{"first_name":"Marek","full_name":"Filakovský, Marek","last_name":"Filakovský","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner"},{"id":"3AA52972-F248-11E8-B48F-1D18A9856A87","last_name":"Zhechev","first_name":"Stephan Y","full_name":"Zhechev, Stephan Y"}],"type":"conference"},{"oa_version":"Submitted Version","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-04T08:51:07Z","external_id":{"arxiv":["2003.13557"]},"scopus_import":1,"publication_identifier":{"isbn":["9781611975994"]},"arxiv":1,"article_processing_charge":"No","_id":"7807","date_published":"2020-01-01T00:00:00Z","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."}],"publication_status":"published","oa":1,"main_file_link":[{"url":"https://doi.org/10.1137/1.9781611975994.172","open_access":"1"}],"volume":"2020-January","citation":{"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>.","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.","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>.","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."},"conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2020-01-05","end_date":"2020-01-08","location":"Salt Lake City, UT, United States"},"title":"Connectivity of triangulation flip graphs in the plane (Part I: Edge flips)","day":"01","type":"conference","author":[{"last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Welzl, Emo","first_name":"Emo","last_name":"Welzl"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"12129"}]},"language":[{"iso":"eng"}],"doi":"10.1137/1.9781611975994.172","page":"2823-2841","month":"01","date_created":"2020-05-10T22:00:48Z","publisher":"SIAM","quality_controlled":"1","department":[{"_id":"UlWa"}],"publication":"Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms","status":"public"},{"publisher":"Springer Nature","department":[{"_id":"ToHe"}],"quality_controlled":"1","publication":"International Conference on Tools and Algorithms for the Construction and Analysis of Systems","intvolume":"     12079","status":"public","page":"79-97","month":"04","date_created":"2020-05-10T22:00:49Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11362"}]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"ddc":["000"],"doi":"10.1007/978-3-030-45237-7_5","citation":{"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>","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>","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.","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>.","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.","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>."},"conference":{"location":"Dublin, Ireland","start_date":"2020-04-25","end_date":"2020-04-30","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"title":"How many bits does it take to quantize your neural network?","day":"17","alternative_title":["LNCS"],"type":"conference","author":[{"first_name":"Mirco","full_name":"Giacobbe, Mirco","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias"}],"publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:48:03Z","volume":12079,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","file":[{"checksum":"f19905a42891fe5ce93d69143fa3f6fb","access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","creator":"dernst","file_size":2744030,"file_name":"2020_TACAS_Giacobbe.pdf","date_created":"2020-05-26T12:48:15Z","file_id":"7893","relation":"main_file","content_type":"application/pdf"}],"_id":"7808","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","date_updated":"2023-06-23T07:01:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publication_identifier":{"isbn":["9783030452360"],"issn":["03029743"],"eissn":["16113349"]},"oa_version":"Published Version","year":"2020","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-44914-8_5","ddc":["000"],"related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","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"}],"day":"18","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"type":"conference","alternative_title":["LNCS"],"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>.","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>.","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.","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.","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>","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."},"title":"Optimal and perfectly parallel algorithms for on-demand data-flow analysis","conference":{"location":"Dublin, Ireland","end_date":"2020-04-30","start_date":"2020-04-25","name":"ESOP: Programming Languages and Systems"},"publication":"European Symposium on Programming","department":[{"_id":"KrCh"}],"quality_controlled":"1","intvolume":"     12075","status":"public","publisher":"Springer Nature","isi":1,"month":"04","date_created":"2020-05-10T22:00:50Z","page":"112-140","external_id":{"isi":["000681656800005"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-06-02T08:53:42Z","publication_identifier":{"isbn":["9783030449131"],"issn":["03029743"],"eissn":["16113349"]},"year":"2020","has_accepted_license":"1","oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:03Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":12075,"publication_status":"published","oa":1,"file":[{"content_type":"application/pdf","file_id":"7895","relation":"main_file","date_created":"2020-05-26T13:34:48Z","file_name":"2020_LNCS_Chatterjee.pdf","creator":"dernst","file_size":651250,"checksum":"8618b80f4cf7b39a60e61a6445ad9807","date_updated":"2020-07-14T12:48:03Z","access_level":"open_access"}],"abstract":[{"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.","lang":"eng"}],"_id":"7810","date_published":"2020-04-18T00:00:00Z","article_processing_charge":"No"},{"month":"05","date_created":"2020-05-11T08:18:48Z","publication":"Frontiers in Education","quality_controlled":"1","department":[{"_id":"SiHi"}],"status":"public","intvolume":"         5","publisher":"Frontiers Media","day":"08","type":"journal_article","author":[{"full_name":"Beattie, Robert J","first_name":"Robert J","last_name":"Beattie","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"}],"citation":{"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>.","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>.","ista":"Beattie RJ, Hippenmeyer S, Pauler F. 2020. SCOPES: Sparking curiosity through Open-Source platforms in education and science. Frontiers in Education. 5, 48.","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.","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>","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>","short":"R.J. Beattie, S. Hippenmeyer, F. Pauler, Frontiers in Education 5 (2020)."},"ec_funded":1,"title":"SCOPES: Sparking curiosity through Open-Source platforms in education and science","language":[{"iso":"eng"}],"doi":"10.3389/feduc.2020.00048","ddc":["570"],"project":[{"name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"48","file":[{"checksum":"a24ec24e38d843341ae620ec76c53688","access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","file_size":1402146,"creator":"dernst","file_name":"2020_FrontiersEduc_Beattie.pdf","date_created":"2020-05-11T11:34:08Z","file_id":"7818","relation":"main_file","content_type":"application/pdf"}],"_id":"7814","date_published":"2020-05-08T00:00:00Z","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."}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:48:03Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":5,"publication_status":"published","oa":1,"article_type":"original","has_accepted_license":"1","year":"2020","oa_version":"Published Version","date_updated":"2021-01-12T08:15:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2504-284X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"}]},{"publication_identifier":{"issn":["1940-087X"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-25T23:30:23Z","external_id":{"isi":["000546406600043"]},"scopus_import":"1","year":"2020","oa_version":"Published Version","has_accepted_license":"1","article_type":"original","oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:48:03Z","issue":"159","article_processing_charge":"No","_id":"7815","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"}],"file":[{"date_created":"2020-05-11T08:28:38Z","content_type":"application/pdf","file_id":"7816","relation":"main_file","date_updated":"2020-07-14T12:48:03Z","access_level":"open_access","checksum":"3154ea7f90b9fb45e084cd1c2770597d","file_name":"jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf","file_size":1352186,"creator":"rbeattie"}],"article_number":"e61147","project":[{"call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"},{"grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"id":"7902","relation":"part_of_dissertation","status":"public"}]},"doi":"10.3791/61147","ddc":["570"],"language":[{"iso":"eng"}],"title":"Lineage tracing and clonal analysis in developing cerebral cortex using mosaic analysis with double markers (MADM)","ec_funded":1,"citation":{"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>.","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>.","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.","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>","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)."},"type":"journal_article","author":[{"orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","full_name":"Beattie, Robert J","last_name":"Beattie"},{"last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"full_name":"Cheung, Giselle T","first_name":"Giselle T","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572"},{"last_name":"Contreras","full_name":"Contreras, Ximena","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hansen, Andi H","first_name":"Andi H","last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer"}],"day":"08","isi":1,"publisher":"MyJove Corporation","status":"public","quality_controlled":"1","department":[{"_id":"SiHi"}],"publication":"Journal of Visual Experiments","date_created":"2020-05-11T08:31:20Z","month":"05"},{"publication_status":"published","oa":1,"file_date_updated":"2020-09-17T08:57:16Z","volume":59,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"37","article_processing_charge":"No","file":[{"relation":"main_file","file_id":"8400","content_type":"application/pdf","success":1,"date_created":"2020-09-17T08:57:16Z","creator":"dernst","file_size":1966184,"file_name":"2020_AngChemieINT_Buchal.pdf","access_level":"open_access","date_updated":"2020-09-17T08:57:16Z","checksum":"7b6c2fc20e9b0ff4353352f7a7004e2d"}],"abstract":[{"lang":"eng","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. "}],"_id":"7847","date_published":"2020-09-07T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-05T16:02:53Z","scopus_import":"1","external_id":{"pmid":["32390281"],"isi":["000541488700001"]},"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"article_type":"original","has_accepted_license":"1","year":"2020","oa_version":"Published Version","publisher":"Wiley","isi":1,"quality_controlled":"1","department":[{"_id":"StFr"}],"publication":"Angewandte Chemie International Edition","status":"public","intvolume":"        59","page":"15913-1591","month":"09","date_created":"2020-05-14T21:00:30Z","pmid":1,"language":[{"iso":"eng"}],"doi":"10.1002/anie.202005378","ddc":["540","546"],"citation":{"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.","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.","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>.","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>.","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>","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>"},"title":"Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte","day":"07","author":[{"full_name":"Bouchal, Roza","first_name":"Roza","last_name":"Bouchal"},{"first_name":"Zhujie","full_name":"Li, 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"},{"last_name":"Berthelot","full_name":"Berthelot, Romain","first_name":"Romain"},{"first_name":"Benjamin","full_name":"Rotenberg, Benjamin","last_name":"Rotenberg"},{"last_name":"Favier","first_name":"Fréderic","full_name":"Favier, Fréderic"},{"last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Salanne","first_name":"Mathieu","full_name":"Salanne, Mathieu"},{"full_name":"Fontaine, Olivier","first_name":"Olivier","last_name":"Fontaine"}],"type":"journal_article"},{"date_created":"2020-05-17T22:00:44Z","month":"06","page":"282-289","intvolume":"        20","status":"public","quality_controlled":"1","department":[{"_id":"Bio"}],"publication":"Current opinion in allergy and clinical immunology","isi":1,"publisher":"Wolters Kluwer","author":[{"full_name":"Singer, Judit","first_name":"Judit","last_name":"Singer","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Josef","full_name":"Singer, Josef","last_name":"Singer"},{"first_name":"Erika","full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim"}],"type":"journal_article","day":"01","title":"Precision medicine in clinical oncology: the journey from IgG antibody to IgE","citation":{"ama":"Singer J, Singer J, Jensen-Jarolim E. Precision medicine in clinical oncology: the journey from IgG antibody to IgE. <i>Current opinion in allergy and clinical immunology</i>. 2020;20(3):282-289. doi:<a href=\"https://doi.org/10.1097/ACI.0000000000000637\">10.1097/ACI.0000000000000637</a>","apa":"Singer, J., Singer, J., &#38; Jensen-Jarolim, E. (2020). Precision medicine in clinical oncology: the journey from IgG antibody to IgE. <i>Current Opinion in Allergy and Clinical Immunology</i>. Wolters Kluwer. <a href=\"https://doi.org/10.1097/ACI.0000000000000637\">https://doi.org/10.1097/ACI.0000000000000637</a>","short":"J. Singer, J. Singer, E. Jensen-Jarolim, Current Opinion in Allergy and Clinical Immunology 20 (2020) 282–289.","mla":"Singer, Judit, et al. “Precision Medicine in Clinical Oncology: The Journey from IgG Antibody to IgE.” <i>Current Opinion in Allergy and Clinical Immunology</i>, vol. 20, no. 3, Wolters Kluwer, 2020, pp. 282–89, doi:<a href=\"https://doi.org/10.1097/ACI.0000000000000637\">10.1097/ACI.0000000000000637</a>.","chicago":"Singer, Judit, Josef Singer, and Erika Jensen-Jarolim. “Precision Medicine in Clinical Oncology: The Journey from IgG Antibody to IgE.” <i>Current Opinion in Allergy and Clinical Immunology</i>. Wolters Kluwer, 2020. <a href=\"https://doi.org/10.1097/ACI.0000000000000637\">https://doi.org/10.1097/ACI.0000000000000637</a>.","ieee":"J. Singer, J. Singer, and E. Jensen-Jarolim, “Precision medicine in clinical oncology: the journey from IgG antibody to IgE,” <i>Current opinion in allergy and clinical immunology</i>, vol. 20, no. 3. Wolters Kluwer, pp. 282–289, 2020.","ista":"Singer J, Singer J, Jensen-Jarolim E. 2020. Precision medicine in clinical oncology: the journey from IgG antibody to IgE. Current opinion in allergy and clinical immunology. 20(3), 282–289."},"doi":"10.1097/ACI.0000000000000637","language":[{"iso":"eng"}],"_id":"7864","abstract":[{"text":"Purpose of review: Cancer is one of the leading causes of death and the incidence rates are constantly rising. The heterogeneity of tumors poses a big challenge for the treatment of the disease and natural antibodies additionally affect disease progression. The introduction of engineered mAbs for anticancer immunotherapies has substantially improved progression-free and overall survival of cancer patients, but little efforts have been made to exploit other antibody isotypes than IgG.\r\nRecent findings: In order to improve these therapies, ‘next-generation antibodies’ were engineered to enhance a specific feature of classical antibodies and form a group of highly effective and precise therapy compounds. Advanced antibody approaches include among others antibody-drug conjugates, glyco-engineered and Fc-engineered antibodies, antibody fragments, radioimmunotherapy compounds, bispecific antibodies and alternative (non-IgG) immunoglobulin classes, especially IgE.\r\nSummary: The current review describes solutions for the needs of next-generation antibody therapies through different approaches. Careful selection of the best-suited engineering methodology is a key factor in developing personalized, more specific and more efficient mAbs against cancer to improve the outcomes of cancer patients. We highlight here the large evidence of IgE exploiting a highly cytotoxic effector arm as potential next-generation anticancer immunotherapy.","lang":"eng"}],"date_published":"2020-06-01T00:00:00Z","issue":"3","article_processing_charge":"No","volume":20,"publication_status":"published","year":"2020","oa_version":"None","article_type":"original","publication_identifier":{"eissn":["14736322"]},"date_updated":"2023-08-21T06:28:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000561358300010"]}},{"date_published":"2020-12-01T00:00:00Z","_id":"7866","abstract":[{"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.","lang":"eng"}],"file":[{"checksum":"6bc6832caacddceee1471291e93dcf1d","access_level":"open_access","date_updated":"2020-11-25T08:59:59Z","file_size":8408694,"creator":"dernst","file_name":"2020_JourEllipticParabEquat_Fellner.pdf","date_created":"2020-11-25T08:59:59Z","success":1,"relation":"main_file","file_id":"8802","content_type":"application/pdf"}],"article_processing_charge":"No","volume":6,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-11-25T08:59:59Z","oa":1,"publication_status":"published","has_accepted_license":"1","year":"2020","oa_version":"Published Version","article_type":"original","publication_identifier":{"eissn":["22969039"],"issn":["22969020"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:47Z","scopus_import":"1","date_created":"2020-05-17T22:00:45Z","month":"12","page":"529-598","status":"public","intvolume":"         6","department":[{"_id":"JuFi"}],"quality_controlled":"1","publication":"Journal of Elliptic and Parabolic Equations","publisher":"Springer Nature","author":[{"full_name":"Fellner, Klemens","first_name":"Klemens","last_name":"Fellner"},{"orcid":"0000-0001-5645-4333","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","full_name":"Kniely, Michael","first_name":"Michael","last_name":"Kniely"}],"type":"journal_article","day":"01","title":"Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model","citation":{"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>.","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>.","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.","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>","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>","short":"K. Fellner, M. Kniely, Journal of Elliptic and Parabolic Equations 6 (2020) 529–598."},"ddc":["510"],"doi":"10.1007/s41808-020-00068-8","language":[{"iso":"eng"}],"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].","project":[{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}]},{"file_date_updated":"2020-11-24T13:25:13Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":219,"publication_status":"published","oa":1,"article_number":"e201907154","file":[{"success":1,"date_created":"2020-11-24T13:25:13Z","relation":"main_file","file_id":"8801","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-11-24T13:25:13Z","checksum":"cb0b9c77842ae1214caade7b77e4d82d","file_size":7536712,"creator":"dernst","file_name":"2020_JCellBiol_Kopf.pdf"}],"_id":"7875","date_published":"2020-06-01T00:00:00Z","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."}],"article_processing_charge":"No","issue":"6","scopus_import":"1","external_id":{"isi":["000538141100020"],"pmid":["32379884"]},"date_updated":"2023-08-21T06:28:17Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1540-8140"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"}],"article_type":"original","has_accepted_license":"1","oa_version":"Published Version","year":"2020","publication":"The Journal of Cell Biology","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"quality_controlled":"1","status":"public","intvolume":"       219","publisher":"Rockefeller University Press","isi":1,"month":"06","date_created":"2020-05-24T22:00:56Z","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1083/jcb.201907154","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"281556","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425","grant_number":"P29911","name":"Mechanical adaptation of lamellipodial actin"},{"_id":"252C3B08-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W 1250-B20","name":"Nano-Analytics of Cellular Systems"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1396-2014","name":"Molecular and system level view of immune cell migration"}],"pmid":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.","day":"01","type":"journal_article","author":[{"first_name":"Aglaja","full_name":"Kopf, Aglaja","last_name":"Kopf","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","first_name":"Jörg","full_name":"Renkawitz, Jörg"},{"last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"last_name":"Girkontaite","first_name":"Irute","full_name":"Girkontaite, Irute"},{"first_name":"Kerry","full_name":"Tedford, Kerry","last_name":"Tedford"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack"},{"last_name":"Thorn-Seshold","first_name":"Oliver","full_name":"Thorn-Seshold, Oliver"},{"first_name":"Dirk","full_name":"Trauner, Dirk","last_name":"Trauner","id":"E8F27F48-3EBA-11E9-92A1-B709E6697425"},{"last_name":"Häcker","full_name":"Häcker, Hans","first_name":"Hans"},{"first_name":"Klaus Dieter","full_name":"Fischer, Klaus Dieter","last_name":"Fischer"},{"orcid":"0000-0001-6165-5738","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","full_name":"Kiermaier, Eva","first_name":"Eva","last_name":"Kiermaier"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"citation":{"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).","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>","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>","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>.","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.","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.","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>."},"ec_funded":1,"title":"Microtubules control cellular shape and coherence in amoeboid migrating cells"},{"year":"2020","oa_version":"Published Version","article_type":"original","publication_identifier":{"eissn":["10974180"],"issn":["10747613"]},"scopus_import":"1","external_id":{"isi":["000535371100002"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-21T06:27:18Z","_id":"7876","abstract":[{"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. ","lang":"eng"}],"date_published":"2020-05-19T00:00:00Z","article_processing_charge":"No","issue":"5","volume":52,"main_file_link":[{"open_access":"1","url":"https://pure.mpg.de/pubman/item/item_3265599_2/component/file_3265620/Sixt%20et%20al..pdf"}],"oa":1,"publication_status":"published","type":"journal_article","author":[{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"full_name":"Lämmermann, Tim","first_name":"Tim","last_name":"Lämmermann"}],"day":"19","title":"T cells: Bridge-and-channel commute to the white pulp","citation":{"short":"M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723.","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>","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>","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.","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>.","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>."},"doi":"10.1016/j.immuni.2020.04.020","language":[{"iso":"eng"}],"date_created":"2020-05-24T22:00:57Z","month":"05","page":"721-723","intvolume":"        52","status":"public","publication":"Immunity","department":[{"_id":"MiSi"}],"quality_controlled":"1","isi":1,"publisher":"Elsevier"},{"publication_identifier":{"eissn":["22111247"]},"external_id":{"isi":["000535655200005"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-21T06:27:47Z","year":"2020","has_accepted_license":"1","oa_version":"Published Version","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"volume":31,"file_date_updated":"2020-07-14T12:48:04Z","oa":1,"publication_status":"published","date_published":"2020-05-19T00:00:00Z","_id":"7877","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"}],"file":[{"date_created":"2020-05-26T11:05:01Z","file_id":"7892","relation":"main_file","content_type":"application/pdf","checksum":"64d8f7467731ee5c166b10b939b8310b","access_level":"open_access","date_updated":"2020-07-14T12:48:04Z","file_size":4695682,"creator":"dernst","file_name":"2020_CellReports_Parenti.pdf"}],"article_number":"107647","article_processing_charge":"No","issue":"7","doi":"10.1016/j.celrep.2020.107647","ddc":["570"],"language":[{"iso":"eng"}],"author":[{"id":"D93538B0-5B71-11E9-AC62-02EBE5697425","full_name":"Parenti, Ilaria","first_name":"Ilaria","last_name":"Parenti"},{"full_name":"Diab, Farah","first_name":"Farah","last_name":"Diab"},{"first_name":"Sara Ruiz","full_name":"Gil, Sara Ruiz","last_name":"Gil"},{"full_name":"Mulugeta, Eskeatnaf","first_name":"Eskeatnaf","last_name":"Mulugeta"},{"last_name":"Casa","full_name":"Casa, Valentina","first_name":"Valentina"},{"first_name":"Riccardo","full_name":"Berutti, Riccardo","last_name":"Berutti"},{"first_name":"Rutger W.W.","full_name":"Brouwer, Rutger W.W.","last_name":"Brouwer"},{"first_name":"Valerie","full_name":"Dupé, Valerie","last_name":"Dupé"},{"first_name":"Juliane","full_name":"Eckhold, Juliane","last_name":"Eckhold"},{"last_name":"Graf","first_name":"Elisabeth","full_name":"Graf, Elisabeth"},{"last_name":"Puisac","first_name":"Beatriz","full_name":"Puisac, Beatriz"},{"last_name":"Ramos","full_name":"Ramos, Feliciano","first_name":"Feliciano"},{"last_name":"Schwarzmayr","full_name":"Schwarzmayr, Thomas","first_name":"Thomas"},{"full_name":"Gines, Macarena Moronta","first_name":"Macarena Moronta","last_name":"Gines"},{"first_name":"Thomas","full_name":"Van Staveren, Thomas","last_name":"Van Staveren"},{"last_name":"Van Ijcken","first_name":"Wilfred F.J.","full_name":"Van Ijcken, Wilfred F.J."},{"first_name":"Tim M.","full_name":"Strom, Tim M.","last_name":"Strom"},{"last_name":"Pié","first_name":"Juan","full_name":"Pié, Juan"},{"first_name":"Erwan","full_name":"Watrin, Erwan","last_name":"Watrin"},{"first_name":"Frank J.","full_name":"Kaiser, Frank J.","last_name":"Kaiser"},{"first_name":"Kerstin S.","full_name":"Wendt, Kerstin S.","last_name":"Wendt"}],"type":"journal_article","day":"19","title":"MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome","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>.","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.","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>.","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>"},"intvolume":"        31","status":"public","publication":"Cell Reports","department":[{"_id":"GaNo"}],"quality_controlled":"1","isi":1,"publisher":"Elsevier","date_created":"2020-05-24T22:00:57Z","month":"05"},{"isi":1,"publisher":"eLife Sciences Publications","status":"public","intvolume":"         9","department":[{"_id":"RySh"}],"quality_controlled":"1","publication":"eLife","date_created":"2020-05-24T22:00:58Z","month":"05","pmid":1,"ddc":["570"],"doi":"10.7554/eLife.56839","language":[{"iso":"eng"}],"title":"Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo","citation":{"short":"J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley, R. Shigemoto, I. Llano, ELife 9 (2020).","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>","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>","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>.","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.","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.","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>."},"type":"journal_article","author":[{"full_name":"Bao, Jin","first_name":"Jin","last_name":"Bao"},{"last_name":"Graupner","first_name":"Michael","full_name":"Graupner, Michael"},{"last_name":"Astorga","first_name":"Guadalupe","full_name":"Astorga, Guadalupe"},{"last_name":"Collin","first_name":"Thibault","full_name":"Collin, Thibault"},{"last_name":"Jalil","first_name":"Abdelali","full_name":"Jalil, Abdelali"},{"last_name":"Indriati","first_name":"Dwi Wahyu","full_name":"Indriati, Dwi Wahyu"},{"last_name":"Bradley","full_name":"Bradley, Jonathan","first_name":"Jonathan"},{"last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Llano, Isabel","first_name":"Isabel","last_name":"Llano"}],"day":"13","oa":1,"publication_status":"published","volume":9,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:48:04Z","article_processing_charge":"No","_id":"7878","date_published":"2020-05-13T00:00:00Z","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."}],"file":[{"date_created":"2020-05-26T09:34:54Z","content_type":"application/pdf","relation":"main_file","file_id":"7891","checksum":"8ea99bb6660cc407dbdb00c173b01683","date_updated":"2020-07-14T12:48:04Z","access_level":"open_access","file_name":"2020_eLife_Bao.pdf","creator":"dernst","file_size":4832050}],"article_number":"e56839","publication_identifier":{"eissn":["2050084X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-21T06:26:50Z","scopus_import":"1","external_id":{"isi":["000535191600001"],"pmid":["32401196"]},"has_accepted_license":"1","oa_version":"Published Version","year":"2020","article_type":"original"},{"language":[{"iso":"eng"}],"doi":"10.1074/jbc.RA120.012628","pmid":1,"day":"17","type":"journal_article","author":[{"first_name":"Rita R.","full_name":"Fagan, Rita R.","last_name":"Fagan"},{"last_name":"Kearney","first_name":"Patrick J.","full_name":"Kearney, Patrick J."},{"last_name":"Sweeney","full_name":"Sweeney, Carolyn G.","first_name":"Carolyn G."},{"last_name":"Luethi","full_name":"Luethi, Dino","first_name":"Dino"},{"full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E","last_name":"Schoot Uiterkamp","id":"3526230C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schicker","full_name":"Schicker, Klaus","first_name":"Klaus"},{"first_name":"Brian S.","full_name":"Alejandro, Brian S.","last_name":"Alejandro"},{"last_name":"O'Connor","full_name":"O'Connor, Lauren C.","first_name":"Lauren C."},{"first_name":"Harald H.","full_name":"Sitte, Harald H.","last_name":"Sitte"},{"last_name":"Melikian","full_name":"Melikian, Haley E.","first_name":"Haley E."}],"citation":{"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.","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>","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>","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>.","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.","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.","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>."},"title":"Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact","quality_controlled":"1","department":[{"_id":"SaSi"}],"publication":"Journal of Biological Chemistry","status":"public","intvolume":"       295","publisher":"ASBMB Publications","isi":1,"month":"04","date_created":"2020-05-24T22:00:59Z","page":"5229-5244","date_updated":"2023-08-21T06:26:22Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["32132171"],"isi":["000530288000006"]},"scopus_import":"1","publication_identifier":{"eissn":["1083351X"],"issn":["00219258"]},"article_type":"original","year":"2020","oa_version":"Submitted Version","volume":295,"publication_status":"published","main_file_link":[{"url":"https://escholarship.umassmed.edu/oapubs/4187","open_access":"1"}],"oa":1,"_id":"7880","date_published":"2020-04-17T00:00:00Z","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","article_processing_charge":"No"},{"date_updated":"2023-08-21T06:23:36Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000531824100024"]},"publication_identifier":{"eissn":["22277390"]},"article_type":"original","has_accepted_license":"1","oa_version":"Published Version","year":"2020","file_date_updated":"2020-07-14T12:48:04Z","volume":8,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publication_status":"published","oa":1,"article_number":"484","file":[{"date_created":"2020-05-25T14:42:22Z","file_id":"7887","relation":"main_file","content_type":"application/pdf","checksum":"a05a7df724522203d079673a0d4de4bc","access_level":"open_access","date_updated":"2020-07-14T12:48:04Z","creator":"dernst","file_size":990540,"file_name":"2020_Mathematics_Armstrong.pdf"}],"_id":"7882","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."}],"issue":"4","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.3390/math8040484","ddc":["510"],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"day":"01","author":[{"last_name":"Armstrong","full_name":"Armstrong, Jeremy R.","first_name":"Jeremy R."},{"full_name":"Jensen, Aksel S.","first_name":"Aksel S.","last_name":"Jensen"},{"last_name":"Volosniev","full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525"},{"first_name":"Nikolaj T.","full_name":"Zinner, Nikolaj T.","last_name":"Zinner"}],"type":"journal_article","ec_funded":1,"citation":{"ista":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated tubes of tilted dipoles. Mathematics. 8(4), 484.","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.","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>.","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>.","short":"J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).","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>","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>"},"title":"Clusters in separated tubes of tilted dipoles","quality_controlled":"1","department":[{"_id":"MiLe"}],"publication":"Mathematics","status":"public","intvolume":"         8","publisher":"MDPI","isi":1,"month":"04","date_created":"2020-05-24T22:01:00Z"},{"date_created":"2020-05-24T22:01:01Z","month":"06","page":"582–585","intvolume":"       582","status":"public","publication":"Nature","quality_controlled":"1","department":[{"_id":"NanoFab"},{"_id":"Bio"},{"_id":"MiSi"}],"isi":1,"publisher":"Springer Nature","type":"journal_article","author":[{"last_name":"Reversat","first_name":"Anne","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87"},{"id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","last_name":"Gärtner","first_name":"Florian R","full_name":"Gärtner, Florian R"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"},{"last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","first_name":"Saren","last_name":"Tasciyan"},{"last_name":"Aguilera Servin","first_name":"Juan L","full_name":"Aguilera Servin, Juan L","orcid":"0000-0002-2862-8372","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","full_name":"De Vries, Ingrid","last_name":"De Vries"},{"last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","last_name":"Hons","first_name":"Miroslav","full_name":"Hons, Miroslav"},{"first_name":"Matthieu","full_name":"Piel, Matthieu","last_name":"Piel"},{"last_name":"Callan-Jones","full_name":"Callan-Jones, Andrew","first_name":"Andrew"},{"first_name":"Raphael","full_name":"Voituriez, Raphael","last_name":"Voituriez"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"day":"25","title":"Cellular locomotion using environmental topography","citation":{"short":"A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez, M.K. Sixt, Nature 582 (2020) 582–585.","apa":"Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>","ama":"Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental topography. <i>Nature</i>. 2020;582:582–585. doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>","ieee":"A. Reversat <i>et al.</i>, “Cellular locomotion using environmental topography,” <i>Nature</i>, vol. 582. Springer Nature, pp. 582–585, 2020.","ista":"Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL, de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK. 2020. Cellular locomotion using environmental topography. Nature. 582, 582–585.","chicago":"Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan, Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41586-020-2283-z\">https://doi.org/10.1038/s41586-020-2283-z</a>.","mla":"Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.” <i>Nature</i>, vol. 582, Springer Nature, 2020, pp. 582–585, doi:<a href=\"https://doi.org/10.1038/s41586-020-2283-z\">10.1038/s41586-020-2283-z</a>."},"ec_funded":1,"doi":"10.1038/s41586-020-2283-z","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"14697","status":"public"},{"id":"12401","relation":"dissertation_contains","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/off-road-mode-enables-mobile-cells-to-move-freely/","description":"News on IST Homepage","relation":"press_release"}]},"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425","name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911"},{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We thank A. Leithner and J. Renkawitz for discussion and critical reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic setups; the Bioimaging Facility of IST Austria for excellent support, as well as the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan, L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476). F.G. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747687.","_id":"7885","date_published":"2020-06-25T00:00:00Z","abstract":[{"text":"Eukaryotic cells migrate by coupling the intracellular force of the actin cytoskeleton to the environment. While force coupling is usually mediated by transmembrane adhesion receptors, especially those of the integrin family, amoeboid cells such as leukocytes can migrate extremely fast despite very low adhesive forces1. Here we show that leukocytes cannot only migrate under low adhesion but can also transmit forces in the complete absence of transmembrane force coupling. When confined within three-dimensional environments, they use the topographical features of the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton follows the texture of the substrate, creating retrograde shear forces that are sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent migration are not mutually exclusive, but rather are variants of the same principle of coupling retrograde actin flow to the environment and thus can potentially operate interchangeably and simultaneously. As adhesion-free migration is independent of the chemical composition of the environment, it renders cells completely autonomous in their locomotive behaviour.","lang":"eng"}],"article_processing_charge":"No","volume":582,"publication_status":"published","oa_version":"None","year":"2020","article_type":"original","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"publication_identifier":{"issn":["00280836"],"eissn":["14764687"]},"external_id":{"isi":["000532688300008"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2024-03-25T23:30:12Z"},{"article_processing_charge":"No","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:48:04Z","checksum":"f6aad884cf706846ae9357fcd728f8b5","creator":"dernst","file_size":7744848,"file_name":"2020_eLife_Schauer.pdf","date_created":"2020-05-25T15:15:43Z","file_id":"7890","relation":"main_file","content_type":"application/pdf"}],"article_number":"e55190","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."}],"_id":"7888","date_published":"2020-04-06T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:48:04Z","volume":9,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_type":"original","oa_version":"Published Version","has_accepted_license":"1","year":"2020","date_updated":"2023-08-21T06:25:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"pmid":["32250246"],"isi":["000531544400001"]},"publication_identifier":{"issn":["2050-084X"]},"month":"04","date_created":"2020-05-25T15:01:40Z","publisher":"eLife Sciences Publications","isi":1,"quality_controlled":"1","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publication":"eLife","intvolume":"         9","status":"public","ec_funded":1,"citation":{"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>.","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.","ista":"Schauer A, Nunes Pinheiro DC, Hauschild R, Heisenberg C-PJ. 2020. Zebrafish embryonic explants undergo genetically encoded self-assembly. eLife. 9, e55190.","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>.","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>","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)."},"title":"Zebrafish embryonic explants undergo genetically encoded self-assembly","day":"06","type":"journal_article","author":[{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","last_name":"Schauer","full_name":"Schauer, Alexandra","first_name":"Alexandra"},{"orcid":"0000-0003-4333-7503","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","full_name":"Nunes Pinheiro, Diana C","first_name":"Diana C","last_name":"Nunes Pinheiro"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"12891","status":"public"}]},"pmid":1,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"},{"name":"Coordination of mesendoderm cell fate specification and internalization during zebrafish gastrulation","grant_number":"ALTF 850-2017","_id":"26520D1E-B435-11E9-9278-68D0E5697425"},{"_id":"266BC5CE-B435-11E9-9278-68D0E5697425","name":"Coordination of mesendoderm fate specification and internalization during zebrafish gastrulation","grant_number":"LT000429"}],"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.7554/elife.55190"},{"_id":"7889","abstract":[{"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.","lang":"eng"}],"date_published":"2020-04-27T00:00:00Z","file":[{"date_created":"2020-08-28T08:57:07Z","content_type":"application/pdf","relation":"main_file","file_id":"8316","date_updated":"2021-03-02T23:30:03Z","access_level":"open_access","checksum":"1b30467500ec6277229a875b06e196d0","embargo":"2021-03-01","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","creator":"dernst","file_size":1180086}],"article_processing_charge":"No","volume":38,"file_date_updated":"2021-03-02T23:30:03Z","oa":1,"publication_status":"published","year":"2020","oa_version":"Submitted Version","has_accepted_license":"1","article_type":"original","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"scopus_import":"1","external_id":{"isi":["000529298800003"],"pmid":["32341562"]},"date_updated":"2023-09-05T15:30:34Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2020-05-25T15:02:00Z","month":"04","page":"944-946","status":"public","intvolume":"        38","publication":"Nature Biotechnology","quality_controlled":"1","department":[{"_id":"FyKo"}],"isi":1,"publisher":"Springer Nature","type":"journal_article","author":[{"last_name":"Mitiouchkina","first_name":"Tatiana","full_name":"Mitiouchkina, Tatiana"},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","last_name":"Gonzalez Somermeyer"},{"last_name":"Markina","full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M."},{"first_name":"Tatiana V.","full_name":"Chepurnyh, Tatiana V.","last_name":"Chepurnyh"},{"last_name":"Guglya","full_name":"Guglya, Elena B.","first_name":"Elena B."},{"last_name":"Karataeva","first_name":"Tatiana A.","full_name":"Karataeva, Tatiana A."},{"first_name":"Kseniia A.","full_name":"Palkina, Kseniia A.","last_name":"Palkina"},{"first_name":"Ekaterina S.","full_name":"Shakhova, Ekaterina S.","last_name":"Shakhova"},{"full_name":"Fakhranurova, Liliia I.","first_name":"Liliia I.","last_name":"Fakhranurova"},{"last_name":"Chekova","full_name":"Chekova, Sofia V.","first_name":"Sofia V."},{"last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S.","first_name":"Aleksandra S."},{"first_name":"Yaroslav V.","full_name":"Golubev, Yaroslav V.","last_name":"Golubev"},{"first_name":"Vadim V.","full_name":"Negrebetsky, Vadim V.","last_name":"Negrebetsky"},{"full_name":"Dolgushin, Sergey A.","first_name":"Sergey A.","last_name":"Dolgushin"},{"full_name":"Shalaev, Pavel V.","first_name":"Pavel V.","last_name":"Shalaev"},{"last_name":"Shlykov","first_name":"Dmitry","full_name":"Shlykov, Dmitry"},{"first_name":"Olesya A.","full_name":"Melnik, Olesya A.","last_name":"Melnik"},{"last_name":"Shipunova","full_name":"Shipunova, Victoria O.","first_name":"Victoria O."},{"full_name":"Deyev, Sergey M.","first_name":"Sergey M.","last_name":"Deyev"},{"first_name":"Andrey I.","full_name":"Bubyrev, Andrey I.","last_name":"Bubyrev"},{"last_name":"Pushin","first_name":"Alexander S.","full_name":"Pushin, Alexander S."},{"first_name":"Vladimir V.","full_name":"Choob, Vladimir V.","last_name":"Choob"},{"last_name":"Dolgov","first_name":"Sergey V.","full_name":"Dolgov, Sergey V."},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ilia V.","full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky"},{"last_name":"Sarkisyan","first_name":"Karen S.","full_name":"Sarkisyan, Karen S."}],"day":"27","title":"Plants with genetically encoded autoluminescence","citation":{"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.","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>","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>","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>.","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.","ieee":"T. Mitiouchkina <i>et al.</i>, “Plants with genetically encoded autoluminescence,” <i>Nature Biotechnology</i>, vol. 38. Springer Nature, pp. 944–946, 2020.","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>."},"ec_funded":1,"ddc":["570"],"doi":"10.1038/s41587-020-0500-9","language":[{"iso":"eng"}],"project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"pmid":1,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41587-020-0578-0"}]},"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."},{"project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","id":"6677","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"ddc":["000"],"doi":"10.15479/AT:ISTA:7896","citation":{"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>","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>","short":"C. Kamath Hosdurg, On the Average-Case Hardness of Total Search Problems, Institute of Science and Technology Austria, 2020.","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>.","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>.","ista":"Kamath Hosdurg C. 2020. On the average-case hardness of total search problems. Institute of Science and Technology Austria.","ieee":"C. Kamath Hosdurg, “On the average-case hardness of total search problems,” Institute of Science and Technology Austria, 2020."},"ec_funded":1,"title":"On the average-case hardness of total search problems","day":"25","type":"dissertation","author":[{"full_name":"Kamath Hosdurg, Chethan","first_name":"Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"KrPi"}],"status":"public","page":"126","month":"05","supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"date_created":"2020-05-26T14:08:55Z","date_updated":"2023-09-07T13:15:55Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","oa_version":"Published Version","year":"2020","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:48:04Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:48:04Z","checksum":"b39e2e1c376f5819b823fb7077491c64","creator":"dernst","file_size":1622742,"file_name":"2020_Thesis_Kamath.pdf","date_created":"2020-05-26T14:08:13Z","file_id":"7897","relation":"main_file","content_type":"application/pdf"},{"date_created":"2020-05-26T14:08:23Z","file_id":"7898","relation":"source_file","content_type":"application/x-zip-compressed","checksum":"8b26ba729c1a85ac6bea775f5d73cdc7","access_level":"closed","date_updated":"2020-07-14T12:48:04Z","file_size":15301529,"creator":"dernst","file_name":"Thesis_Kamath.zip"}],"abstract":[{"lang":"eng","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. "}],"_id":"7896","date_published":"2020-05-25T00:00:00Z"}]