[{"publisher":"Springer Nature","publication":"Combinatorial image analysis","quality_controlled":"1","department":[{"_id":"HeEd"}],"status":"public","intvolume":"     10256","page":"93-104","month":"05","place":"Cham","extern":"1","date_created":"2019-01-08T20:42:56Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-59108-7_8","citation":{"short":"R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2017, pp. 93–104.","apa":"Biswas, R., &#38; Bhowmick, P. (2017). Construction of persistent Voronoi diagram on 3D digital plane. In <i>Combinatorial image analysis</i> (Vol. 10256, pp. 93–104). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">https://doi.org/10.1007/978-3-319-59108-7_8</a>","ama":"Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital plane. In: <i>Combinatorial Image Analysis</i>. Vol 10256. Cham: Springer Nature; 2017:93-104. doi:<a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">10.1007/978-3-319-59108-7_8</a>","ista":"Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.","ieee":"R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on 3D digital plane,” in <i>Combinatorial image analysis</i>, vol. 10256, Cham: Springer Nature, 2017, pp. 93–104.","chicago":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” In <i>Combinatorial Image Analysis</i>, 10256:93–104. Cham: Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">https://doi.org/10.1007/978-3-319-59108-7_8</a>.","mla":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” <i>Combinatorial Image Analysis</i>, vol. 10256, Springer Nature, 2017, pp. 93–104, doi:<a href=\"https://doi.org/10.1007/978-3-319-59108-7_8\">10.1007/978-3-319-59108-7_8</a>."},"title":"Construction of persistent Voronoi diagram on 3D digital plane","conference":{"location":"Plovdiv, Bulgaria","name":"IWCIA: International Workshop on Combinatorial Image Analysis","end_date":"2017-06-21","start_date":"2017-06-19"},"day":"17","type":"book_chapter","author":[{"orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","full_name":"Biswas, Ranita","last_name":"Biswas"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"alternative_title":["LNCS"],"publication_status":"published","volume":10256,"article_processing_charge":"No","date_published":"2017-05-17T00:00:00Z","_id":"5803","abstract":[{"lang":"eng","text":"Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-01-28T07:48:24Z","publication_identifier":{"isbn":["978-3-319-59107-0","978-3-319-59108-7"],"issn":["0302-9743","1611-3349"]},"year":"2017","oa_version":"None"},{"month":"04","extern":"1","date_published":"2017-04-03T00:00:00Z","_id":"593","date_created":"2018-12-11T11:47:23Z","abstract":[{"lang":"eng","text":"Bell correlations, indicating nonlocality in composite quantum systems, were until recently only seen in small systems. Here, we demonstrate Bell correlations in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective measurements as witnesses and are statistically significant to 124 standard deviations. The states are both generated and characterized using optical-cavity aided measurements."}],"issue":"14","publication":"Physical Review Letters","intvolume":"       118","status":"public","volume":118,"publication_status":"published","publisher":"American Physical Society","day":"03","publist_id":"7212","author":[{"last_name":"Engelsen","full_name":"Engelsen, Nils","first_name":"Nils"},{"full_name":"Krishnakumar, Rajiv","first_name":"Rajiv","last_name":"Krishnakumar"},{"last_name":"Hosten","first_name":"Onur","full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X"},{"last_name":"Kasevich","first_name":"Mark","full_name":"Kasevich, Mark"}],"type":"journal_article","year":"2017","oa_version":"None","citation":{"short":"N. Engelsen, R. Krishnakumar, O. Hosten, M. Kasevich, Physical Review Letters 118 (2017).","apa":"Engelsen, N., Krishnakumar, R., Hosten, O., &#38; Kasevich, M. (2017). Bell correlations in spin-squeezed states of 500 000 atoms. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">https://doi.org/10.1103/PhysRevLett.118.140401</a>","ama":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. Bell correlations in spin-squeezed states of 500 000 atoms. <i>Physical Review Letters</i>. 2017;118(14). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">10.1103/PhysRevLett.118.140401</a>","ista":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. 2017. Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. 118(14).","ieee":"N. Engelsen, R. Krishnakumar, O. Hosten, and M. Kasevich, “Bell correlations in spin-squeezed states of 500 000 atoms,” <i>Physical Review Letters</i>, vol. 118, no. 14. American Physical Society, 2017.","chicago":"Engelsen, Nils, Rajiv Krishnakumar, Onur Hosten, and Mark Kasevich. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” <i>Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">https://doi.org/10.1103/PhysRevLett.118.140401</a>.","mla":"Engelsen, Nils, et al. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” <i>Physical Review Letters</i>, vol. 118, no. 14, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.118.140401\">10.1103/PhysRevLett.118.140401</a>."},"title":"Bell correlations in spin-squeezed states of 500 000 atoms","date_updated":"2021-01-12T08:05:16Z","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevLett.118.140401"},{"date_updated":"2021-01-12T08:05:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2017.03.003","publication_identifier":{"issn":["00928674"]},"citation":{"chicago":"Engel, Christoph, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, and Patrick Cramer. “Structural Basis of RNA Polymerase I Transcription Initiation.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">https://doi.org/10.1016/j.cell.2017.03.003</a>.","ieee":"C. Engel <i>et al.</i>, “Structural basis of RNA polymerase I transcription initiation,” <i>Cell</i>, vol. 169, no. 1. Cell Press, p. 120–131.e22, 2017.","ista":"Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation. Cell. 169(1), 120–131.e22.","mla":"Engel, Christoph, et al. “Structural Basis of RNA Polymerase I Transcription Initiation.” <i>Cell</i>, vol. 169, no. 1, Cell Press, 2017, p. 120–131.e22, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">10.1016/j.cell.2017.03.003</a>.","short":"C. Engel, T. Gubbey, S. Neyer, S. Sainsbury, C. Oberthuer, C. Baejen, C. Bernecky, P. Cramer, Cell 169 (2017) 120–131.e22.","ama":"Engel C, Gubbey T, Neyer S, et al. Structural basis of RNA polymerase I transcription initiation. <i>Cell</i>. 2017;169(1):120-131.e22. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">10.1016/j.cell.2017.03.003</a>","apa":"Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C., … Cramer, P. (2017). Structural basis of RNA polymerase I transcription initiation. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.03.003\">https://doi.org/10.1016/j.cell.2017.03.003</a>"},"title":"Structural basis of RNA polymerase I transcription initiation","publist_id":"7204","day":"23","year":"2017","oa_version":"None","type":"journal_article","author":[{"full_name":"Engel, Christoph","first_name":"Christoph","last_name":"Engel"},{"full_name":"Gubbey, Tobias","first_name":"Tobias","last_name":"Gubbey"},{"last_name":"Neyer","first_name":"Simon","full_name":"Neyer, Simon"},{"last_name":"Sainsbury","full_name":"Sainsbury, Sarah","first_name":"Sarah"},{"last_name":"Oberthuer","first_name":"Christiane","full_name":"Oberthuer, Christiane"},{"first_name":"Carlo","full_name":"Baejen, Carlo","last_name":"Baejen"},{"first_name":"Carrie A","full_name":"Bernecky, Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Patrick","full_name":"Cramer, Patrick","last_name":"Cramer"}],"publisher":"Cell Press","publication_status":"published","quality_controlled":"1","publication":"Cell","volume":169,"status":"public","intvolume":"       169","page":"120 - 131.e22","issue":"1","article_processing_charge":"No","extern":"1","month":"03","date_published":"2017-03-23T00:00:00Z","_id":"600","date_created":"2018-12-11T11:47:25Z","abstract":[{"text":"Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct “bendability” and “meltability” of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase.","lang":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:05:40Z","publication_identifier":{"issn":["20411723"]},"publist_id":"7203","has_accepted_license":"1","year":"2017","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:16Z","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,"file":[{"date_updated":"2020-07-14T12:47:16Z","access_level":"open_access","checksum":"940742282a9a285dc4aeae0c2b5ebe96","file_name":"2017_NatureComm_Xu.pdf","creator":"dernst","file_size":3018075,"date_created":"2019-01-21T14:48:10Z","content_type":"application/pdf","relation":"main_file","file_id":"5865"}],"article_number":"15741","date_published":"2017-06-06T00:00:00Z","_id":"601","abstract":[{"lang":"eng","text":"The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. "}],"article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1038/ncomms15741","ddc":["570"],"day":"06","author":[{"full_name":"Xu, Youwei","first_name":"Youwei","last_name":"Xu"},{"orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A","full_name":"Bernecky, Carrie A"},{"full_name":"Lee, Chung","first_name":"Chung","last_name":"Lee"},{"last_name":"Maier","full_name":"Maier, Kerstin","first_name":"Kerstin"},{"full_name":"Schwalb, Björn","first_name":"Björn","last_name":"Schwalb"},{"last_name":"Tegunov","first_name":"Dimitri","full_name":"Tegunov, Dimitri"},{"last_name":"Plitzko","first_name":"Jürgen","full_name":"Plitzko, Jürgen"},{"last_name":"Urlaub","full_name":"Urlaub, Henning","first_name":"Henning"},{"last_name":"Cramer","first_name":"Patrick","full_name":"Cramer, Patrick"}],"type":"journal_article","citation":{"mla":"Xu, Youwei, et al. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” <i>Nature Communications</i>, vol. 8, 15741, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms15741\">10.1038/ncomms15741</a>.","ieee":"Y. Xu <i>et al.</i>, “Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","ista":"Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 8, 15741.","chicago":"Xu, Youwei, Carrie Bernecky, Chung Lee, Kerstin Maier, Björn Schwalb, Dimitri Tegunov, Jürgen Plitzko, Henning Urlaub, and Patrick Cramer. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms15741\">https://doi.org/10.1038/ncomms15741</a>.","apa":"Xu, Y., Bernecky, C., Lee, C., Maier, K., Schwalb, B., Tegunov, D., … Cramer, P. (2017). Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms15741\">https://doi.org/10.1038/ncomms15741</a>","ama":"Xu Y, Bernecky C, Lee C, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms15741\">10.1038/ncomms15741</a>","short":"Y. Xu, C. Bernecky, C. Lee, K. Maier, B. Schwalb, D. Tegunov, J. Plitzko, H. Urlaub, P. Cramer, Nature Communications 8 (2017)."},"title":"Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex","quality_controlled":"1","publication":"Nature Communications","intvolume":"         8","status":"public","publisher":"Nature Publishing Group","extern":"1","month":"06","date_created":"2018-12-11T11:47:25Z"},{"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.03701"}],"oa":1,"volume":119,"arxiv":1,"issue":"2","article_number":"023201","abstract":[{"text":"The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”","lang":"eng"}],"_id":"6013","date_published":"2017-07-14T00:00:00Z","date_updated":"2023-02-23T11:13:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1611.03701"]},"scopus_import":1,"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"oa_version":"Preprint","year":"2017","publisher":"American Physical Society","quality_controlled":"1","department":[{"_id":"MiLe"}],"publication":"Physical Review Letters","status":"public","intvolume":"       119","month":"07","date_created":"2019-02-14T15:24:13Z","related_material":{"record":[{"id":"313","relation":"earlier_version","status":"public"}]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.119.023201","citation":{"mla":"Camus, Nicolas, et al. “Experimental Evidence for Quantum Tunneling Time.” <i>Physical Review Letters</i>, vol. 119, no. 2, 023201, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.119.023201\">10.1103/PhysRevLett.119.023201</a>.","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Z. Hatsagortsyan, Thomas Pfeifer, Christoph H. Keitel, and Robert Moshammer. “Experimental Evidence for Quantum Tunneling Time.” <i>Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevLett.119.023201\">https://doi.org/10.1103/PhysRevLett.119.023201</a>.","ieee":"N. Camus <i>et al.</i>, “Experimental evidence for quantum tunneling time,” <i>Physical Review Letters</i>, vol. 119, no. 2. American Physical Society, 2017.","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan KZ, Pfeifer T, Keitel CH, Moshammer R. 2017. Experimental evidence for quantum tunneling time. Physical Review Letters. 119(2), 023201.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for quantum tunneling time. <i>Physical Review Letters</i>. 2017;119(2). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.119.023201\">10.1103/PhysRevLett.119.023201</a>","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for quantum tunneling time. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.119.023201\">https://doi.org/10.1103/PhysRevLett.119.023201</a>","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K.Z. Hatsagortsyan, T. Pfeifer, C.H. Keitel, R. Moshammer, Physical Review Letters 119 (2017)."},"title":"Experimental evidence for quantum tunneling time","day":"14","author":[{"last_name":"Camus","first_name":"Nicolas","full_name":"Camus, Nicolas"},{"full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fechner, Lutz","first_name":"Lutz","last_name":"Fechner"},{"last_name":"Klaiber","full_name":"Klaiber, Michael","first_name":"Michael"},{"full_name":"Laux, Martin","first_name":"Martin","last_name":"Laux"},{"first_name":"Yonghao","full_name":"Mi, Yonghao","last_name":"Mi"},{"last_name":"Hatsagortsyan","first_name":"Karen Z.","full_name":"Hatsagortsyan, Karen Z."},{"full_name":"Pfeifer, Thomas","first_name":"Thomas","last_name":"Pfeifer"},{"full_name":"Keitel, Christoph H.","first_name":"Christoph H.","last_name":"Keitel"},{"last_name":"Moshammer","full_name":"Moshammer, Robert","first_name":"Robert"}],"type":"journal_article"},{"type":"journal_article","author":[{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky"},{"last_name":"Plitzko","full_name":"Plitzko, Jürgen","first_name":"Jürgen"},{"last_name":"Cramer","first_name":"Patrick","full_name":"Cramer, Patrick"}],"year":"2017","oa_version":"None","day":"05","publist_id":"7202","title":"Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp","citation":{"chicago":"Bernecky, Carrie, Jürgen Plitzko, and Patrick Cramer. “Structure of a Transcribing RNA Polymerase II-DSIF Complex Reveals a Multidentate DNA-RNA Clamp.” <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/nsmb.3465\">https://doi.org/10.1038/nsmb.3465</a>.","ieee":"C. Bernecky, J. Plitzko, and P. Cramer, “Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp,” <i>Nature Structural and Molecular Biology</i>, vol. 24, no. 10. Nature Publishing Group, pp. 809–815, 2017.","ista":"Bernecky C, Plitzko J, Cramer P. 2017. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature Structural and Molecular Biology. 24(10), 809–815.","mla":"Bernecky, Carrie, et al. “Structure of a Transcribing RNA Polymerase II-DSIF Complex Reveals a Multidentate DNA-RNA Clamp.” <i>Nature Structural and Molecular Biology</i>, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 809–15, doi:<a href=\"https://doi.org/10.1038/nsmb.3465\">10.1038/nsmb.3465</a>.","short":"C. Bernecky, J. Plitzko, P. Cramer, Nature Structural and Molecular Biology 24 (2017) 809–815.","ama":"Bernecky C, Plitzko J, Cramer P. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. <i>Nature Structural and Molecular Biology</i>. 2017;24(10):809-815. doi:<a href=\"https://doi.org/10.1038/nsmb.3465\">10.1038/nsmb.3465</a>","apa":"Bernecky, C., Plitzko, J., &#38; Cramer, P. (2017). Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. <i>Nature Structural and Molecular Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nsmb.3465\">https://doi.org/10.1038/nsmb.3465</a>"},"publication_identifier":{"issn":["15459993"]},"doi":"10.1038/nsmb.3465","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:05:47Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:47:26Z","_id":"603","date_published":"2017-10-05T00:00:00Z","abstract":[{"text":"During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.","lang":"eng"}],"month":"10","extern":"1","article_processing_charge":"No","issue":"10","page":"809 - 815","status":"public","intvolume":"        24","volume":24,"publication":"Nature Structural and Molecular Biology","quality_controlled":"1","publisher":"Nature Publishing Group","publication_status":"published"},{"date_published":"2017-12-14T00:00:00Z","_id":"604","abstract":[{"lang":"eng","text":"In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies."}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.06753","open_access":"1"}],"publication_status":"published","volume":11,"editor":[{"first_name":"Oliver","full_name":"Dulieu, Oliver","last_name":"Dulieu"},{"full_name":"Osterwalder, Andreas","first_name":"Andreas","last_name":"Osterwalder"}],"oa_version":"Submitted Version","year":"2017","publist_id":"7201","publication_identifier":{"issn":["20413181"]},"scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:05:50Z","page":"444 - 495","date_created":"2018-12-11T11:47:27Z","series_title":"Theoretical and Computational Chemistry Series","month":"12","publisher":"The Royal Society of Chemistry","intvolume":"        11","status":"public","publication":"Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ","department":[{"_id":"MiLe"}],"quality_controlled":"1","title":"Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets","citation":{"apa":"Lemeshko, M., &#38; Schmidt, R. (2017). Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In O. Dulieu &#38; A. Osterwalder (Eds.), <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i> (Vol. 11, pp. 444–495). The Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/9781782626800-00444\">https://doi.org/10.1039/9781782626800-00444</a>","ama":"Lemeshko M, Schmidt R. Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Dulieu O, Osterwalder A, eds. <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i>. Vol 11. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry; 2017:444-495. doi:<a href=\"https://doi.org/10.1039/9781782626800-00444\">10.1039/9781782626800-00444</a>","short":"M. Lemeshko, R. Schmidt, in:, O. Dulieu, A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , The Royal Society of Chemistry, 2017, pp. 444–495.","mla":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i>, edited by Oliver Dulieu and Andreas Osterwalder, vol. 11, The Royal Society of Chemistry, 2017, pp. 444–95, doi:<a href=\"https://doi.org/10.1039/9781782626800-00444\">10.1039/9781782626800-00444</a>.","ista":"Lemeshko M, Schmidt R. 2017.Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Theoretical and Computational Chemistry Series, vol. 11, 444–495.","ieee":"M. Lemeshko and R. Schmidt, “Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets,” in <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i>, vol. 11, O. Dulieu and A. Osterwalder, Eds. The Royal Society of Chemistry, 2017, pp. 444–495.","chicago":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” In <i>Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero </i>, edited by Oliver Dulieu and Andreas Osterwalder, 11:444–95. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry, 2017. <a href=\"https://doi.org/10.1039/9781782626800-00444\">https://doi.org/10.1039/9781782626800-00444</a>."},"author":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"},{"last_name":"Schmidt","full_name":"Schmidt, Richard","first_name":"Richard"}],"type":"book_chapter","alternative_title":["Theoretical and Computational Chemistry Series"],"day":"14","doi":"10.1039/9781782626800-00444","language":[{"iso":"eng"}]},{"editor":[{"last_name":"Kalai","full_name":"Kalai, Yael","first_name":"Yael"},{"last_name":"Reyzin","full_name":"Reyzin, Leonid","first_name":"Leonid"}],"publist_id":"7200","oa_version":"Submitted Version","year":"2017","scopus_import":1,"date_updated":"2021-01-12T08:05:53Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-331970499-9"]},"_id":"605","abstract":[{"lang":"eng","text":"Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes."}],"date_published":"2017-11-05T00:00:00Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/536"}],"oa":1,"volume":10677,"citation":{"apa":"Brody, J., Dziembowski, S., Faust, S., &#38; Pietrzak, K. Z. (2017). Position based cryptography and multiparty communication complexity. In Y. Kalai &#38; L. Reyzin (Eds.) (Vol. 10677, pp. 56–81). Presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-70500-2_3\">https://doi.org/10.1007/978-3-319-70500-2_3</a>","ama":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. Position based cryptography and multiparty communication complexity. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:56-81. doi:<a href=\"https://doi.org/10.1007/978-3-319-70500-2_3\">10.1007/978-3-319-70500-2_3</a>","short":"J. Brody, S. Dziembowski, S. Faust, K.Z. Pietrzak, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 56–81.","mla":"Brody, Joshua, et al. <i>Position Based Cryptography and Multiparty Communication Complexity</i>. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 56–81, doi:<a href=\"https://doi.org/10.1007/978-3-319-70500-2_3\">10.1007/978-3-319-70500-2_3</a>.","ieee":"J. Brody, S. Dziembowski, S. Faust, and K. Z. Pietrzak, “Position based cryptography and multiparty communication complexity,” presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States, 2017, vol. 10677, pp. 56–81.","ista":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. 2017. Position based cryptography and multiparty communication complexity. TCC: Theory of Cryptography Conference, LNCS, vol. 10677, 56–81.","chicago":"Brody, Joshua, Stefan Dziembowski, Sebastian Faust, and Krzysztof Z Pietrzak. “Position Based Cryptography and Multiparty Communication Complexity.” edited by Yael Kalai and Leonid Reyzin, 10677:56–81. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-70500-2_3\">https://doi.org/10.1007/978-3-319-70500-2_3</a>."},"ec_funded":1,"title":"Position based cryptography and multiparty communication complexity","conference":{"location":"Baltimore, MD, United States","name":"TCC: Theory of Cryptography Conference","start_date":"2017-11-12","end_date":"2017-11-15"},"day":"05","type":"conference","author":[{"last_name":"Brody","first_name":"Joshua","full_name":"Brody, Joshua"},{"full_name":"Dziembowski, Stefan","first_name":"Stefan","last_name":"Dziembowski"},{"full_name":"Faust, Sebastian","first_name":"Sebastian","last_name":"Faust"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"alternative_title":["LNCS"],"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-70500-2_3","page":"56 - 81","month":"11","date_created":"2018-12-11T11:47:27Z","publisher":"Springer","department":[{"_id":"KrPi"}],"quality_controlled":"1","status":"public","intvolume":"     10677"},{"date_created":"2019-02-26T13:45:17Z","_id":"6059","abstract":[{"text":"Neutrophils or polymorphonuclear cells (PMN) eliminate bacteria via phagocytosis and/or NETosis. Apartfrom these conventional roles, PMN also have immune-regulatory functions. They can transdifferentiateand upregulate MHCII as well as ligands for costimulatory receptors which enables them to behave asantigen presenting cells (APC). The initial step for activating T-cells is the formation of an immunesynapse between T-cells and antigen-presenting cells. However, the immune synapse that develops atthe PMN/T-cell contact zone is as yet hardly investigated due to the non-availability of methods foranalysis of large number of PMN interactions. In order to overcome these obstacles, we introduce herea workflow to analyse the immune synapse of primary human PMN and T-cells using multispectral imag-ing flow cytometry (InFlow microscopy) and super-resolution microscopy. For that purpose, we used CD3and CD66b as the lineage markers for T-cells and PMN, respectively. Thereafter, we applied and criticallydiscussed various ‘‘masks” for identification of T-cell PMN interactions. Using this approach, we foundthat a small fraction of transdifferentiated PMN (CD66b+CD86high) formed stable PMN/T-cell conjugates.Interestingly, while both CD3 and CD66b accumulation in the immune synapse was dependent on thematuration state of the PMN, only CD3 accumulation was greatly enhanced by the presence of superanti-gen. The actin cytoskeleton was weakly rearranged at the PMN side on the immune synapse upon contactwith a T-cell in the presence of superantigen. A more detailed analysis using super-resolution microscopy(structured-illumination microscopy, SIM) confirmed this finding. Together, we present an InFlow micro-scopy based approach for the large scale analysis of PMN/T-cell interactions and – combined with SIM – apossibility for an in-depth analysis of protein translocation at the site of interactions.","lang":"eng"}],"date_published":"2017-01-01T00:00:00Z","extern":"1","month":"01","issue":"1","page":"25-38","volume":112,"status":"public","intvolume":"       112","quality_controlled":"1","publication":"Methods","publisher":"Elsevier","publication_status":"published","oa_version":"None","year":"2017","type":"journal_article","author":[{"first_name":"Emre","full_name":"Balta, Emre","last_name":"Balta"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A"},{"last_name":"Castelletti","first_name":"Laura","full_name":"Castelletti, Laura"},{"last_name":"Kirchgessner","full_name":"Kirchgessner, Henning","first_name":"Henning"},{"first_name":"Yvonne","full_name":"Samstag, Yvonne","last_name":"Samstag"},{"first_name":"Guido H.","full_name":"Wabnitz, Guido H.","last_name":"Wabnitz"}],"day":"01","title":"Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy","citation":{"apa":"Balta, E., Stopp, J. A., Castelletti, L., Kirchgessner, H., Samstag, Y., &#38; Wabnitz, G. H. (2017). Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy. <i>Methods</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ymeth.2016.09.013\">https://doi.org/10.1016/j.ymeth.2016.09.013</a>","ama":"Balta E, Stopp JA, Castelletti L, Kirchgessner H, Samstag Y, Wabnitz GH. Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy. <i>Methods</i>. 2017;112(1):25-38. doi:<a href=\"https://doi.org/10.1016/j.ymeth.2016.09.013\">10.1016/j.ymeth.2016.09.013</a>","short":"E. Balta, J.A. Stopp, L. Castelletti, H. Kirchgessner, Y. Samstag, G.H. Wabnitz, Methods 112 (2017) 25–38.","mla":"Balta, Emre, et al. “Qualitative and Quantitative Analysis of PMN/T-Cell Interactions by InFlow and Super-Resolution Microscopy.” <i>Methods</i>, vol. 112, no. 1, Elsevier, 2017, pp. 25–38, doi:<a href=\"https://doi.org/10.1016/j.ymeth.2016.09.013\">10.1016/j.ymeth.2016.09.013</a>.","ista":"Balta E, Stopp JA, Castelletti L, Kirchgessner H, Samstag Y, Wabnitz GH. 2017. Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy. Methods. 112(1), 25–38.","ieee":"E. Balta, J. A. Stopp, L. Castelletti, H. Kirchgessner, Y. Samstag, and G. H. Wabnitz, “Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy,” <i>Methods</i>, vol. 112, no. 1. Elsevier, pp. 25–38, 2017.","chicago":"Balta, Emre, Julian A Stopp, Laura Castelletti, Henning Kirchgessner, Yvonne Samstag, and Guido H. Wabnitz. “Qualitative and Quantitative Analysis of PMN/T-Cell Interactions by InFlow and Super-Resolution Microscopy.” <i>Methods</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ymeth.2016.09.013\">https://doi.org/10.1016/j.ymeth.2016.09.013</a>."},"doi":"10.1016/j.ymeth.2016.09.013","publication_identifier":{"issn":["1046-2023"]},"date_updated":"2021-01-12T08:05:57Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["27693880"]},"pmid":1,"related_material":{"link":[{"url":"http://dx.doi.org/10.1016/j.ymeth.2016.09.013","relation":"supplementary_material"}]}},{"publisher":"Springer","quality_controlled":"1","department":[{"_id":"KrPi"}],"intvolume":"     10677","status":"public","page":"493 - 526","month":"11","date_created":"2018-12-11T11:47:28Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-70500-2_17","citation":{"mla":"Alwen, Joel F., and Björn Tackmann. <i>Moderately Hard Functions: Definition, Instantiations, and Applications</i>. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 493–526, doi:<a href=\"https://doi.org/10.1007/978-3-319-70500-2_17\">10.1007/978-3-319-70500-2_17</a>.","ieee":"J. F. Alwen and B. Tackmann, “Moderately hard functions: Definition, instantiations, and applications,” presented at the TCC: Theory of Cryptography, Baltimore, MD, United States, 2017, vol. 10677, pp. 493–526.","ista":"Alwen JF, Tackmann B. 2017. Moderately hard functions: Definition, instantiations, and applications. TCC: Theory of Cryptography, LNCS, vol. 10677, 493–526.","chicago":"Alwen, Joel F, and Björn Tackmann. “Moderately Hard Functions: Definition, Instantiations, and Applications.” edited by Yael Kalai and Leonid Reyzin, 10677:493–526. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-70500-2_17\">https://doi.org/10.1007/978-3-319-70500-2_17</a>.","apa":"Alwen, J. F., &#38; Tackmann, B. (2017). Moderately hard functions: Definition, instantiations, and applications. In Y. Kalai &#38; L. Reyzin (Eds.) (Vol. 10677, pp. 493–526). Presented at the TCC: Theory of Cryptography, Baltimore, MD, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-70500-2_17\">https://doi.org/10.1007/978-3-319-70500-2_17</a>","ama":"Alwen JF, Tackmann B. Moderately hard functions: Definition, instantiations, and applications. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:493-526. doi:<a href=\"https://doi.org/10.1007/978-3-319-70500-2_17\">10.1007/978-3-319-70500-2_17</a>","short":"J.F. Alwen, B. Tackmann, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 493–526."},"conference":{"location":"Baltimore, MD, United States","name":"TCC: Theory of Cryptography","end_date":"2017-11-15","start_date":"2017-11-12"},"title":"Moderately hard functions: Definition, instantiations, and applications","day":"05","alternative_title":["LNCS"],"type":"conference","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tackmann, Björn","first_name":"Björn","last_name":"Tackmann"}],"publication_status":"published","main_file_link":[{"url":"https://eprint.iacr.org/2017/945","open_access":"1"}],"oa":1,"volume":10677,"abstract":[{"lang":"eng","text":"Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover."}],"_id":"609","date_published":"2017-11-05T00:00:00Z","date_updated":"2021-01-12T08:06:04Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publication_identifier":{"isbn":["978-331970499-9"]},"editor":[{"last_name":"Kalai","first_name":"Yael","full_name":"Kalai, Yael"},{"last_name":"Reyzin","first_name":"Leonid","full_name":"Reyzin, Leonid"}],"publist_id":"7196","oa_version":"Submitted Version","year":"2017"},{"department":[{"_id":"UlWa"}],"quality_controlled":"1","publication":"Israel Journal of Mathematics","intvolume":"       222","status":"public","publisher":"Springer","month":"10","date_created":"2018-12-11T11:47:29Z","page":"841 - 866","language":[{"iso":"eng"}],"doi":"10.1007/s11856-017-1607-7","acknowledgement":"The work by Z. P. was partially supported by the Israel Science Foundation grant ISF-768/12. The work by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of the Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research work of M.T. was conducted at IST Austria, supported by an IST Fellowship. The research of P. P. was supported by the ERC Advanced grant no. 320924. The work by I. M. and U. W. was supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948). The collaboration between U. W. and X. G. was partially supported by the LabEx Bézout (ANR-10-LABX-58).","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","id":"1511","relation":"earlier_version"}]},"day":"01","type":"journal_article","author":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"last_name":"Mabillard","full_name":"Mabillard, Isaac","first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pavel","full_name":"Paták, Pavel","last_name":"Paták"},{"last_name":"Patakova","full_name":"Patakova, Zuzana","first_name":"Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","full_name":"Tancer, Martin","first_name":"Martin","last_name":"Tancer"},{"last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"ec_funded":1,"citation":{"ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result,” <i>Israel Journal of Mathematics</i>, vol. 222, no. 2. Springer, pp. 841–866, 2017.","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2017. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 222(2), 841–866.","chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” <i>Israel Journal of Mathematics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11856-017-1607-7\">https://doi.org/10.1007/s11856-017-1607-7</a>.","mla":"Goaoc, Xavier, et al. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” <i>Israel Journal of Mathematics</i>, vol. 222, no. 2, Springer, 2017, pp. 841–66, doi:<a href=\"https://doi.org/10.1007/s11856-017-1607-7\">10.1007/s11856-017-1607-7</a>.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel Journal of Mathematics 222 (2017) 841–866.","apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2017). On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. <i>Israel Journal of Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s11856-017-1607-7\">https://doi.org/10.1007/s11856-017-1607-7</a>","ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. <i>Israel Journal of Mathematics</i>. 2017;222(2):841-866. doi:<a href=\"https://doi.org/10.1007/s11856-017-1607-7\">10.1007/s11856-017-1607-7</a>"},"title":"On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result","volume":222,"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1610.09063","open_access":"1"}],"oa":1,"abstract":[{"lang":"eng","text":"The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition."}],"_id":"610","date_published":"2017-10-01T00:00:00Z","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T10:02:13Z","scopus_import":1,"publist_id":"7194","oa_version":"Preprint","year":"2017"},{"title":"Evolution of flower color pattern through selection on regulatory small RNAs","citation":{"short":"D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman, L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358 (2017) 925–928.","ama":"Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through selection on regulatory small RNAs. <i>Science</i>. 2017;358(6365):925-928. doi:<a href=\"https://doi.org/10.1126/science.aao3526\">10.1126/science.aao3526</a>","apa":"Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aao3526\">https://doi.org/10.1126/science.aao3526</a>","chicago":"Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aao3526\">https://doi.org/10.1126/science.aao3526</a>.","ista":"Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928.","ieee":"D. Bradley <i>et al.</i>, “Evolution of flower color pattern through selection on regulatory small RNAs,” <i>Science</i>, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017.","mla":"Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” <i>Science</i>, vol. 358, no. 6365, American Association for the Advancement of Science, 2017, pp. 925–28, doi:<a href=\"https://doi.org/10.1126/science.aao3526\">10.1126/science.aao3526</a>."},"year":"2017","oa_version":"None","type":"journal_article","author":[{"last_name":"Bradley","full_name":"Bradley, Desmond","first_name":"Desmond"},{"last_name":"Xu","full_name":"Xu, Ping","first_name":"Ping"},{"first_name":"Irina","full_name":"Mohorianu, Irina","last_name":"Mohorianu"},{"full_name":"Whibley, Annabel","first_name":"Annabel","last_name":"Whibley"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"first_name":"Hugo","full_name":"Tavares, Hugo","last_name":"Tavares"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"last_name":"Copsey","first_name":"Lucy","full_name":"Copsey, Lucy"},{"full_name":"Carpenter, Rosemary","first_name":"Rosemary","last_name":"Carpenter"},{"full_name":"Li, Miaomiao","first_name":"Miaomiao","last_name":"Li"},{"full_name":"Li, Qun","first_name":"Qun","last_name":"Li"},{"full_name":"Xue, Yongbiao","first_name":"Yongbiao","last_name":"Xue"},{"full_name":"Dalmay, Tamas","first_name":"Tamas","last_name":"Dalmay"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"publist_id":"7193","day":"17","doi":"10.1126/science.aao3526","publication_identifier":{"issn":["00368075"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:06:10Z","language":[{"iso":"eng"}],"scopus_import":1,"issue":"6365","page":"925 - 928","_id":"611","abstract":[{"lang":"eng","text":"Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity."}],"date_created":"2018-12-11T11:47:29Z","date_published":"2017-11-17T00:00:00Z","month":"11","publication_status":"published","publisher":"American Association for the Advancement of Science","volume":358,"status":"public","intvolume":"       358","quality_controlled":"1","department":[{"_id":"NiBa"}],"publication":"Science"},{"publication_identifier":{"issn":["0027-8424","1091-6490"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:06:11Z","external_id":{"pmid":["28536200"]},"oa_version":"Published Version","has_accepted_license":"1","year":"2017","volume":114,"file_date_updated":"2020-07-14T12:47:19Z","oa":1,"publication_status":"published","_id":"6113","date_published":"2017-06-06T00:00:00Z","file":[{"date_created":"2019-03-19T13:42:58Z","content_type":"application/pdf","relation":"main_file","file_id":"6114","checksum":"9e42ce47090ecdad7d76f2dbdebb924e","date_updated":"2020-07-14T12:47:19Z","access_level":"open_access","file_name":"2017_PNAS_Oda.pdf","file_size":1469622,"creator":"kschuh"}],"issue":"23","ddc":["570"],"doi":"10.1073/pnas.1614596114","language":[{"iso":"eng"}],"pmid":1,"type":"journal_article","author":[{"last_name":"Oda","first_name":"Shigekazu","full_name":"Oda, Shigekazu"},{"full_name":"Toyoshima, Yu","first_name":"Yu","last_name":"Toyoshima"},{"first_name":"Mario","full_name":"de Bono, Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"day":"06","title":"Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans","citation":{"mla":"Oda, Shigekazu, et al. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 23, National Academy of Sciences, 2017, pp. E4658–65, doi:<a href=\"https://doi.org/10.1073/pnas.1614596114\">10.1073/pnas.1614596114</a>.","chicago":"Oda, Shigekazu, Yu Toyoshima, and Mario de Bono. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1614596114\">https://doi.org/10.1073/pnas.1614596114</a>.","ieee":"S. Oda, Y. Toyoshima, and M. de Bono, “Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 23. National Academy of Sciences, pp. E4658–E4665, 2017.","ista":"Oda S, Toyoshima Y, de Bono M. 2017. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(23), E4658–E4665.","ama":"Oda S, Toyoshima Y, de Bono M. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(23):E4658-E4665. doi:<a href=\"https://doi.org/10.1073/pnas.1614596114\">10.1073/pnas.1614596114</a>","apa":"Oda, S., Toyoshima, Y., &#38; de Bono, M. (2017). Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1614596114\">https://doi.org/10.1073/pnas.1614596114</a>","short":"S. Oda, Y. Toyoshima, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) E4658–E4665."},"status":"public","intvolume":"       114","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences","publisher":"National Academy of Sciences","date_created":"2019-03-19T13:29:51Z","extern":"1","month":"06","page":"E4658-E4665"},{"publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:20Z","volume":114,"issue":"16","file":[{"relation":"main_file","file_id":"6116","content_type":"application/pdf","date_created":"2019-03-19T14:00:42Z","creator":"kschuh","file_size":1217696,"file_name":"2017_PNAS_Fenk.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:20Z","checksum":"1801bc8319b752fa17598004ec375279"}],"_id":"6115","date_published":"2017-04-18T00:00:00Z","abstract":[{"text":"Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that Caenorhabditis elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2-sensing neurons reprograms the properties of their postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.","lang":"eng"}],"date_updated":"2021-01-12T08:06:11Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28373553"]},"publication_identifier":{"issn":["0027-8424","1091-6490"]},"has_accepted_license":"1","year":"2017","oa_version":"Published Version","publisher":"National Academy of Sciences","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences","intvolume":"       114","status":"public","page":"4195-4200","extern":"1","month":"04","date_created":"2019-03-19T13:46:36Z","pmid":1,"language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1073/pnas.1618934114","citation":{"mla":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 16, National Academy of Sciences, 2017, pp. 4195–200, doi:<a href=\"https://doi.org/10.1073/pnas.1618934114\">10.1073/pnas.1618934114</a>.","chicago":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1618934114\">https://doi.org/10.1073/pnas.1618934114</a>.","ieee":"L. A. Fenk and M. de Bono, “Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans,” <i>Proceedings of the National Academy of Sciences</i>, vol. 114, no. 16. National Academy of Sciences, pp. 4195–4200, 2017.","ista":"Fenk LA, de Bono M. 2017. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(16), 4195–4200.","ama":"Fenk LA, de Bono M. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. 2017;114(16):4195-4200. doi:<a href=\"https://doi.org/10.1073/pnas.1618934114\">10.1073/pnas.1618934114</a>","apa":"Fenk, L. A., &#38; de Bono, M. (2017). Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1618934114\">https://doi.org/10.1073/pnas.1618934114</a>","short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) 4195–4200."},"title":"Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans","day":"18","type":"journal_article","author":[{"full_name":"Fenk, Lorenz A.","first_name":"Lorenz A.","last_name":"Fenk"},{"last_name":"de Bono","full_name":"de Bono, Mario","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443"}]},{"publication_identifier":{"issn":["0028-0836","1476-4687"]},"date_updated":"2021-01-12T08:06:12Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["    28099418"]},"year":"2017","oa_version":"Submitted Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/28099418"}],"publication_status":"published","volume":542,"issue":"7639","_id":"6117","date_published":"2017-02-02T00:00:00Z","abstract":[{"lang":"eng","text":"Interleukin-17 (IL-17) is a major pro-inflammatory cytokine: it mediates responses to pathogens or tissue damage, and drives autoimmune diseases. Little is known about its role in the nervous system. Here we show that IL-17 has neuromodulator-like properties in Caenorhabditis elegans. IL-17 can act directly on neurons to alter their response properties and contribution to behaviour. Using unbiased genetic screens, we delineate an IL-17 signalling pathway and show that it acts in the RMG hub interneurons. Disrupting IL-17 signalling reduces RMG responsiveness to input from oxygen sensors, and renders sustained escape from 21% oxygen transient and contingent on additional stimuli. Over-activating IL-17 receptors abnormally heightens responses to 21% oxygen in RMG neurons and whole animals. IL-17 deficiency can be bypassed by optogenetic stimulation of RMG. Inducing IL-17 expression in adults can rescue mutant defects within 6 h. These findings reveal a non-immunological role of IL-17 modulating circuit function and behaviour."}],"pmid":1,"doi":"10.1038/nature20818","language":[{"iso":"eng"}],"title":"IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses","citation":{"short":"C. Chen, E. Itakura, G.M. Nelson, M. Sheng, P. Laurent, L.A. Fenk, R.A. Butcher, R.S. Hegde, M. de Bono, Nature 542 (2017) 43–48.","ama":"Chen C, Itakura E, Nelson GM, et al. IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses. <i>Nature</i>. 2017;542(7639):43-48. doi:<a href=\"https://doi.org/10.1038/nature20818\">10.1038/nature20818</a>","apa":"Chen, C., Itakura, E., Nelson, G. M., Sheng, M., Laurent, P., Fenk, L. A., … de Bono, M. (2017). IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature20818\">https://doi.org/10.1038/nature20818</a>","chicago":"Chen, Changchun, Eisuke Itakura, Geoffrey M. Nelson, Ming Sheng, Patrick Laurent, Lorenz A. Fenk, Rebecca A. Butcher, Ramanujan S. Hegde, and Mario de Bono. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans Sensory Responses.” <i>Nature</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/nature20818\">https://doi.org/10.1038/nature20818</a>.","ista":"Chen C, Itakura E, Nelson GM, Sheng M, Laurent P, Fenk LA, Butcher RA, Hegde RS, de Bono M. 2017. IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses. Nature. 542(7639), 43–48.","ieee":"C. Chen <i>et al.</i>, “IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses,” <i>Nature</i>, vol. 542, no. 7639. Springer Nature, pp. 43–48, 2017.","mla":"Chen, Changchun, et al. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans Sensory Responses.” <i>Nature</i>, vol. 542, no. 7639, Springer Nature, 2017, pp. 43–48, doi:<a href=\"https://doi.org/10.1038/nature20818\">10.1038/nature20818</a>."},"type":"journal_article","author":[{"first_name":"Changchun","full_name":"Chen, Changchun","last_name":"Chen"},{"last_name":"Itakura","first_name":"Eisuke","full_name":"Itakura, Eisuke"},{"last_name":"Nelson","first_name":"Geoffrey M.","full_name":"Nelson, Geoffrey M."},{"first_name":"Ming","full_name":"Sheng, Ming","last_name":"Sheng"},{"full_name":"Laurent, Patrick","first_name":"Patrick","last_name":"Laurent"},{"full_name":"Fenk, Lorenz A.","first_name":"Lorenz A.","last_name":"Fenk"},{"first_name":"Rebecca A.","full_name":"Butcher, Rebecca A.","last_name":"Butcher"},{"last_name":"Hegde","full_name":"Hegde, Ramanujan S.","first_name":"Ramanujan S."},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","first_name":"Mario","last_name":"de Bono"}],"day":"02","publisher":"Springer Nature","status":"public","intvolume":"       542","quality_controlled":"1","publication":"Nature","page":"43-48","date_created":"2019-03-19T14:06:41Z","extern":"1","month":"02"},{"publist_id":"7191","has_accepted_license":"1","oa_version":"Published Version","year":"2017","date_updated":"2021-01-12T08:06:15Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publication_identifier":{"issn":["20411723"]},"issue":"1","article_processing_charge":"Yes (in subscription journal)","file":[{"date_created":"2018-12-12T10:16:05Z","file_id":"5190","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:20Z","checksum":"44bb5d0229926c23a9955d9fe0f9723f","file_size":1951699,"creator":"system","file_name":"IST-2017-911-v1+1_s41467-017-01683-1.pdf"}],"article_number":"1535","abstract":[{"text":"Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.","lang":"eng"}],"_id":"613","date_published":"2017-12-01T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:20Z","volume":8,"pubrep_id":"911","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)"},"ec_funded":1,"citation":{"mla":"Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” <i>Nature Communications</i>, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01683-1\">10.1038/s41467-017-01683-1</a>.","ieee":"R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.","chicago":"Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01683-1\">https://doi.org/10.1038/s41467-017-01683-1</a>.","apa":"Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., &#38; Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01683-1\">https://doi.org/10.1038/s41467-017-01683-1</a>","ama":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01683-1\">10.1038/s41467-017-01683-1</a>","short":"R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017)."},"title":"Shaping bacterial population behavior through computer interfaced control of individual cells","day":"01","type":"journal_article","author":[{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","last_name":"Chait","full_name":"Chait, Remy P","first_name":"Remy P"},{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","first_name":"Jakob","full_name":"Ruess, Jakob","last_name":"Ruess"},{"last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG).","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"language":[{"iso":"eng"}],"ddc":["576","579"],"doi":"10.1038/s41467-017-01683-1","month":"12","date_created":"2018-12-11T11:47:30Z","publisher":"Nature Publishing Group","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"quality_controlled":"1","publication":"Nature Communications","intvolume":"         8","status":"public"},{"publication_identifier":{"issn":["20411723"]},"date_updated":"2024-02-21T13:47:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["29133797"]},"scopus_import":1,"has_accepted_license":"1","year":"2017","oa_version":"Published Version","publist_id":"7190","article_type":"original","oa":1,"publication_status":"published","volume":8,"pubrep_id":"910","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":"2020-07-14T12:47:20Z","issue":"1","article_processing_charge":"No","_id":"614","abstract":[{"text":"Moths and butterflies (Lepidoptera) usually have a pair of differentiated WZ sex chromosomes. However, in most lineages outside of the division Ditrysia, as well as in the sister order Trichoptera, females lack a W chromosome. The W is therefore thought to have been acquired secondarily. Here we compare the genomes of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment of a B chromosome). We show that the gene content of the Z is highly conserved across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome fusion). Our comparative genomics analysis therefore supports the secondary acquisition of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme stability of well-differentiated sex chromosomes.","lang":"eng"}],"date_published":"2017-12-01T00:00:00Z","file":[{"file_id":"7562","relation":"main_file","content_type":"application/pdf","date_created":"2020-03-03T15:55:50Z","file_size":1201520,"creator":"dernst","file_name":"2017_NatureComm_Fraisse.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:20Z","checksum":"4da2651303c8afc2f7fc419be42a2433"}],"article_number":"1486","pmid":1,"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"relation":"popular_science","id":"7163","status":"public"}]},"ddc":["570","576"],"doi":"10.1038/s41467-017-01663-5","language":[{"iso":"eng"}],"title":"The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W","citation":{"ama":"Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>","apa":"Fraisse, C., Picard, M. A. L., &#38; Vicoso, B. (2017). The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>","short":"C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).","mla":"Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>, vol. 8, no. 1, 1486, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01663-5\">10.1038/s41467-017-01663-5</a>.","chicago":"Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01663-5\">https://doi.org/10.1038/s41467-017-01663-5</a>.","ieee":"C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature Communications. 8(1), 1486."},"author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","last_name":"Picard","first_name":"Marion A","full_name":"Picard, Marion A"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"type":"journal_article","day":"01","publisher":"Nature Publishing Group","status":"public","intvolume":"         8","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"quality_controlled":"1","publication":"Nature Communications","date_created":"2018-12-11T11:47:30Z","month":"12"},{"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"doi":"10.1214/16-AIHP765","language":[{"iso":"eng"}],"title":"Universality for random matrix flows with time dependent density","ec_funded":1,"citation":{"short":"L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability and Statistics 53 (2017) 1606–1656.","apa":"Erdös, L., &#38; Schnelli, K. (2017). Universality for random matrix flows with time dependent density. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/16-AIHP765\">https://doi.org/10.1214/16-AIHP765</a>","ama":"Erdös L, Schnelli K. Universality for random matrix flows with time dependent density. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. 2017;53(4):1606-1656. doi:<a href=\"https://doi.org/10.1214/16-AIHP765\">10.1214/16-AIHP765</a>","ieee":"L. Erdös and K. Schnelli, “Universality for random matrix flows with time dependent density,” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 53, no. 4. Institute of Mathematical Statistics, pp. 1606–1656, 2017.","ista":"Erdös L, Schnelli K. 2017. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 53(4), 1606–1656.","chicago":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics, 2017. <a href=\"https://doi.org/10.1214/16-AIHP765\">https://doi.org/10.1214/16-AIHP765</a>.","mla":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 53, no. 4, Institute of Mathematical Statistics, 2017, pp. 1606–56, doi:<a href=\"https://doi.org/10.1214/16-AIHP765\">10.1214/16-AIHP765</a>."},"type":"journal_article","author":[{"first_name":"László","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"first_name":"Kevin","full_name":"Schnelli, Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231"}],"day":"01","publisher":"Institute of Mathematical Statistics","intvolume":"        53","status":"public","quality_controlled":"1","department":[{"_id":"LaEr"}],"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","page":"1606 - 1656","date_created":"2018-12-11T11:47:30Z","month":"11","publication_identifier":{"issn":["02460203"]},"date_updated":"2021-01-12T08:06:22Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"year":"2017","oa_version":"Submitted Version","publist_id":"7189","main_file_link":[{"url":"https://arxiv.org/abs/1504.00650","open_access":"1"}],"oa":1,"publication_status":"published","volume":53,"issue":"4","_id":"615","date_published":"2017-11-01T00:00:00Z","abstract":[{"lang":"eng","text":"We show that the Dyson Brownian Motion exhibits local universality after a very short time assuming that local rigidity and level repulsion of the eigenvalues hold. These conditions are verified, hence bulk spectral universality is proven, for a large class of Wigner-like matrices, including deformed Wigner ensembles and ensembles with non-stochastic variance matrices whose limiting densities differ from Wigner's semicircle law."}]},{"publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:22Z","volume":10,"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":"252","article_number":"52","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:22Z","checksum":"742943377a38ee208108705b8e2f4dbf","file_size":671807,"creator":"dernst","file_name":"2017_Parasites_Franke.pdf","date_created":"2019-01-21T13:45:36Z","relation":"main_file","file_id":"5864","content_type":"application/pdf"}],"_id":"618","date_published":"2017-06-02T00:00:00Z","abstract":[{"lang":"eng","text":"Background: Increasing temperatures are predicted to strongly impact host-parasite interactions, but empirical tests are rare. Host species that are naturally exposed to a broad temperature spectrum offer the possibility to investigate the effects of elevated temperatures on hosts and parasites. Using three-spined sticklebacks, Gasterosteus aculeatus L., and tapeworms, Schistocephalus solidus (Müller, 1776), originating from a cold and a warm water site of a volcanic lake, we subjected sympatric and allopatric host-parasite combinations to cold and warm conditions in a fully crossed design. We predicted that warm temperatures would promote the development of the parasites, while the hosts might benefit from cooler temperatures. We further expected adaptations to the local temperature and mutual adaptations of local host-parasite pairs. Results: Overall, S. solidus parasites grew faster at warm temperatures and stickleback hosts at cold temperatures. On a finer scale, we observed that parasites were able to exploit their hosts more efficiently at the parasite’s temperature of origin. In contrast, host tolerance towards parasite infection was higher when sticklebacks were infected with parasites at the parasite’s ‘foreign’ temperature. Cold-origin sticklebacks tended to grow faster and parasite infection induced a stronger immune response. Conclusions: Our results suggest that increasing environmental temperatures promote the parasite rather than the host and that host tolerance is dependent on the interaction between parasite infection and temperature. Sticklebacks might use tolerance mechanisms towards parasite infection in combination with their high plasticity towards temperature changes to cope with increasing parasite infection pressures and rising temperatures."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:06:35Z","publication_identifier":{"issn":["17563305"]},"publist_id":"7186","oa_version":"Published Version","year":"2017","has_accepted_license":"1","publisher":"BioMed Central","quality_controlled":"1","publication":"Parasites & Vectors","intvolume":"        10","status":"public","extern":"1","month":"06","date_created":"2018-12-11T11:47:31Z","language":[{"iso":"eng"}],"ddc":["570"],"doi":"10.1186/s13071-017-2192-7","citation":{"ista":"Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. 2017. Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association . Parasites &#38; Vectors. 10(252), 52.","ieee":"F. Franke, S. Armitage, M. Kutzer, J. Kurtz, and J. Scharsack, “Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association ,” <i>Parasites &#38; Vectors</i>, vol. 10, no. 252. BioMed Central, 2017.","chicago":"Franke, Frederik, Sophie Armitage, Megan Kutzer, Joachim Kurtz, and Jörn Scharsack. “Environmental Temperature Variation Influences Fitness Trade-Offs in a Fish-Tapeworm Association .” <i>Parasites &#38; Vectors</i>. BioMed Central, 2017. <a href=\"https://doi.org/10.1186/s13071-017-2192-7\">https://doi.org/10.1186/s13071-017-2192-7</a>.","mla":"Franke, Frederik, et al. “Environmental Temperature Variation Influences Fitness Trade-Offs in a Fish-Tapeworm Association .” <i>Parasites &#38; Vectors</i>, vol. 10, no. 252, 52, BioMed Central, 2017, doi:<a href=\"https://doi.org/10.1186/s13071-017-2192-7\">10.1186/s13071-017-2192-7</a>.","short":"F. Franke, S. Armitage, M. Kutzer, J. Kurtz, J. Scharsack, Parasites &#38; Vectors 10 (2017).","apa":"Franke, F., Armitage, S., Kutzer, M., Kurtz, J., &#38; Scharsack, J. (2017). Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association . <i>Parasites &#38; Vectors</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13071-017-2192-7\">https://doi.org/10.1186/s13071-017-2192-7</a>","ama":"Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association . <i>Parasites &#38; Vectors</i>. 2017;10(252). doi:<a href=\"https://doi.org/10.1186/s13071-017-2192-7\">10.1186/s13071-017-2192-7</a>"},"title":"Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association ","day":"02","type":"journal_article","author":[{"last_name":"Franke","full_name":"Franke, Frederik","first_name":"Frederik"},{"last_name":"Armitage","full_name":"Armitage, Sophie","first_name":"Sophie"},{"id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978","last_name":"Kutzer","first_name":"Megan","full_name":"Kutzer, Megan"},{"last_name":"Kurtz","full_name":"Kurtz, Joachim","first_name":"Joachim"},{"first_name":"Jörn","full_name":"Scharsack, Jörn","last_name":"Scharsack"}]},{"related_material":{"record":[{"id":"838","relation":"dissertation_contains","status":"public"}]},"project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"ddc":["000"],"doi":"10.13154/TOSC.V2016.I2.145-161","ec_funded":1,"citation":{"mla":"Gazi, Peter, et al. “The Exact Security of PMAC.” <i>IACR Transactions on Symmetric Cryptology</i>, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:<a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">10.13154/TOSC.V2016.I2.145-161</a>.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security of PMAC.” <i>IACR Transactions on Symmetric Cryptology</i>. Ruhr University Bochum, 2017. <a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">https://doi.org/10.13154/TOSC.V2016.I2.145-161</a>.","ista":"Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2016(2), 145–161.","ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” <i>IACR Transactions on Symmetric Cryptology</i>, vol. 2016, no. 2. Ruhr University Bochum, pp. 145–161, 2017.","ama":"Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. <i>IACR Transactions on Symmetric Cryptology</i>. 2017;2016(2):145-161. doi:<a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">10.13154/TOSC.V2016.I2.145-161</a>","apa":"Gazi, P., Pietrzak, K. Z., &#38; Rybar, M. (2017). The exact security of PMAC. <i>IACR Transactions on Symmetric Cryptology</i>. Ruhr University Bochum. <a href=\"https://doi.org/10.13154/TOSC.V2016.I2.145-161\">https://doi.org/10.13154/TOSC.V2016.I2.145-161</a>","short":"P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology 2016 (2017) 145–161."},"title":"The exact security of PMAC","day":"03","author":[{"id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Gazi, Peter","last_name":"Gazi"},{"first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rybar, Michal","last_name":"Rybar"}],"type":"journal_article","publisher":"Ruhr University Bochum","quality_controlled":"1","department":[{"_id":"KrPi"}],"publication":"IACR Transactions on Symmetric Cryptology","status":"public","intvolume":"      2016","page":"145-161","month":"02","date_created":"2019-04-04T13:48:23Z","date_updated":"2023-09-07T12:02:27Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2519-173X"]},"year":"2017","has_accepted_license":"1","oa_version":"Published Version","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:24Z","volume":2016,"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":"2","file":[{"checksum":"f23161d685dd957ae8d7274132999684","date_updated":"2020-07-14T12:47:24Z","access_level":"open_access","file_name":"2017_IACR_Gazi.pdf","file_size":597335,"creator":"dernst","date_created":"2019-04-04T13:53:58Z","content_type":"application/pdf","relation":"main_file","file_id":"6197"}],"_id":"6196","date_published":"2017-02-03T00:00:00Z","abstract":[{"lang":"eng","text":"PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of  Ο(σ2/2n), while the currently best bound is  Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem."}]}]