[{"date_updated":"2021-01-12T08:08:43Z","extern":"1","citation":{"apa":"Kudekar, S., Kumar, S., Mondelli, M., Pfister, H. D., Sasoglu, E., &#38; Urbanke, R. L. (2017). Reed–Muller codes achieve capacity on erasure channels. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/tit.2017.2673829\">https://doi.org/10.1109/tit.2017.2673829</a>","ama":"Kudekar S, Kumar S, Mondelli M, Pfister HD, Sasoglu E, Urbanke RL. Reed–Muller codes achieve capacity on erasure channels. <i>IEEE Transactions on Information Theory</i>. 2017;63(7):4298-4316. doi:<a href=\"https://doi.org/10.1109/tit.2017.2673829\">10.1109/tit.2017.2673829</a>","ista":"Kudekar S, Kumar S, Mondelli M, Pfister HD, Sasoglu E, Urbanke RL. 2017. Reed–Muller codes achieve capacity on erasure channels. IEEE Transactions on Information Theory. 63(7), 4298–4316.","chicago":"Kudekar, Shrinivas, Santhosh Kumar, Marco Mondelli, Henry D. Pfister, Eren Sasoglu, and Ridiger L. Urbanke. “Reed–Muller Codes Achieve Capacity on Erasure Channels.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2017. <a href=\"https://doi.org/10.1109/tit.2017.2673829\">https://doi.org/10.1109/tit.2017.2673829</a>.","ieee":"S. Kudekar, S. Kumar, M. Mondelli, H. D. Pfister, E. Sasoglu, and R. L. Urbanke, “Reed–Muller codes achieve capacity on erasure channels,” <i>IEEE Transactions on Information Theory</i>, vol. 63, no. 7. IEEE, pp. 4298–4316, 2017.","short":"S. Kudekar, S. Kumar, M. Mondelli, H.D. Pfister, E. Sasoglu, R.L. Urbanke, IEEE Transactions on Information Theory 63 (2017) 4298–4316.","mla":"Kudekar, Shrinivas, et al. “Reed–Muller Codes Achieve Capacity on Erasure Channels.” <i>IEEE Transactions on Information Theory</i>, vol. 63, no. 7, IEEE, 2017, pp. 4298–316, doi:<a href=\"https://doi.org/10.1109/tit.2017.2673829\">10.1109/tit.2017.2673829</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1601.04689"]},"abstract":[{"text":"We introduce a new approach to proving that a sequence of deterministic linear codes achieves capacity on an erasure channel under maximum a posteriori decoding. Rather than relying on the precise structure of the codes, our method exploits code symmetry. In particular, the technique applies to any sequence of linear codes where the blocklengths are strictly increasing, the code rates converge, and the permutation group of each code is doubly transitive. In other words, we show that symmetry alone implies near-optimal performance. An important consequence of this result is that a sequence of Reed-Muller codes with increasing block length and converging rate achieves capacity. This possibility has been suggested previously in the literature but it has only been proven for cases where the limiting code rate is 0 or 1. Moreover, these results extend naturally to all affine-invariant codes and, thus, to extended primitive narrow-sense BCH codes. This also resolves, in the affirmative, the existence question for capacity-achieving sequences of binary cyclic codes. The primary tools used in the proof are the sharp threshold property for symmetric monotone Boolean functions and the area theorem for extrinsic information transfer functions.","lang":"eng"}],"publication_status":"published","date_published":"2017-07-01T00:00:00Z","publisher":"IEEE","title":"Reed–Muller codes achieve capacity on erasure channels","oa":1,"page":"4298-4316","day":"01","doi":"10.1109/tit.2017.2673829","year":"2017","intvolume":"        63","arxiv":1,"publication":"IEEE Transactions on Information Theory","quality_controlled":"1","oa_version":"Preprint","author":[{"full_name":"Kudekar, Shrinivas","last_name":"Kudekar","first_name":"Shrinivas"},{"last_name":"Kumar","first_name":"Santhosh","full_name":"Kumar, Santhosh"},{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco"},{"last_name":"Pfister","first_name":"Henry D.","full_name":"Pfister, Henry D."},{"first_name":"Eren","last_name":"Sasoglu","full_name":"Sasoglu, Eren"},{"full_name":"Urbanke, Ridiger L.","last_name":"Urbanke","first_name":"Ridiger L."}],"month":"07","issue":"7","language":[{"iso":"eng"}],"volume":63,"date_created":"2019-07-30T07:18:11Z","type":"journal_article","_id":"6730","status":"public","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"main_file_link":[{"url":"https://arxiv.org/abs/1601.04689","open_access":"1"}]},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.01199"}],"publication_identifier":{"isbn":["9781509059089"]},"doi":"10.1109/wcncw.2017.7919107","day":"04","status":"public","year":"2017","type":"conference","_id":"6731","oa":1,"date_created":"2019-07-31T05:56:58Z","publication":"2017 IEEE Wireless Communications and Networking Conference Workshops ","arxiv":1,"conference":{"start_date":"2017-03-19","end_date":"2017-03-22","name":"WCNCW: Wireless communications and networking conference workshops","location":"San Francisco, CA, USA"},"external_id":{"arxiv":["1611.01199"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli"},{"full_name":"Hassani, Hamed","first_name":"Hamed","last_name":"Hassani"},{"full_name":"Maric, Ivana","last_name":"Maric","first_name":"Ivana"},{"full_name":"Hui, Dennis","last_name":"Hui","first_name":"Dennis"},{"full_name":"Hong, Song-Nam","first_name":"Song-Nam","last_name":"Hong"}],"oa_version":"Preprint","citation":{"apa":"Mondelli, M., Hassani, H., Maric, I., Hui, D., &#38; Hong, S.-N. (2017). Capacity-achieving rate-compatible polar codes for general channels. In <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>. San Francisco, CA, USA: IEEE. <a href=\"https://doi.org/10.1109/wcncw.2017.7919107\">https://doi.org/10.1109/wcncw.2017.7919107</a>","ama":"Mondelli M, Hassani H, Maric I, Hui D, Hong S-N. Capacity-achieving rate-compatible polar codes for general channels. In: <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>. IEEE; 2017. doi:<a href=\"https://doi.org/10.1109/wcncw.2017.7919107\">10.1109/wcncw.2017.7919107</a>","chicago":"Mondelli, Marco, Hamed Hassani, Ivana Maric, Dennis Hui, and Song-Nam Hong. “Capacity-Achieving Rate-Compatible Polar Codes for General Channels.” In <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>. IEEE, 2017. <a href=\"https://doi.org/10.1109/wcncw.2017.7919107\">https://doi.org/10.1109/wcncw.2017.7919107</a>.","ista":"Mondelli M, Hassani H, Maric I, Hui D, Hong S-N. 2017. Capacity-achieving rate-compatible polar codes for general channels. 2017 IEEE Wireless Communications and Networking Conference Workshops . WCNCW: Wireless communications and networking conference workshops, 7919107.","ieee":"M. Mondelli, H. Hassani, I. Maric, D. Hui, and S.-N. Hong, “Capacity-achieving rate-compatible polar codes for general channels,” in <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>, San Francisco, CA, USA, 2017.","mla":"Mondelli, Marco, et al. “Capacity-Achieving Rate-Compatible Polar Codes for General Channels.” <i>2017 IEEE Wireless Communications and Networking Conference Workshops </i>, 7919107, IEEE, 2017, doi:<a href=\"https://doi.org/10.1109/wcncw.2017.7919107\">10.1109/wcncw.2017.7919107</a>.","short":"M. Mondelli, H. Hassani, I. Maric, D. Hui, S.-N. Hong, in:, 2017 IEEE Wireless Communications and Networking Conference Workshops , IEEE, 2017."},"extern":"1","quality_controlled":"1","date_updated":"2021-01-12T08:08:43Z","title":"Capacity-achieving rate-compatible polar codes for general channels","language":[{"iso":"eng"}],"publisher":"IEEE","date_published":"2017-05-04T00:00:00Z","article_number":"7919107","publication_status":"published","month":"05","abstract":[{"lang":"eng","text":"We present a rate-compatible polar coding scheme that achieves the capacity of any family of channels. Our solution generalizes the previous results [1], [2] that provide capacity-achieving rate-compatible polar codes for a degraded family of channels. The motivation for our extension comes from the fact that in many practical scenarios, e.g., MIMO systems and non-Gaussian interference, the channels cannot be ordered by degradation. The main technical contribution of this paper consists in removing the degradation condition. To do so, we exploit the ideas coming from the construction of universal polar codes. Our scheme possesses the usual attractive features of polar codes: low complexity code construction, encoding, and decoding; super-polynomial scaling of the error probability with the block length; and absence of error floors. On the negative side, the scaling of the gap to capacity with the block length is slower than in standard polar codes, and we prove an upper bound on the scaling exponent."}]},{"date_created":"2018-12-11T11:47:52Z","type":"journal_article","_id":"676","article_type":"original","publication_identifier":{"issn":["09501991"]},"status":"public","month":"05","has_accepted_license":"1","issue":"10","file":[{"date_updated":"2020-07-14T12:47:39Z","date_created":"2019-09-24T06:56:22Z","content_type":"application/pdf","file_name":"2017_Development_Krens.pdf","relation":"main_file","file_size":8194516,"access_level":"open_access","creator":"dernst","file_id":"6905","checksum":"bc25125fb664706cdf180e061429f91d"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":144,"quality_controlled":"1","oa_version":"Published Version","author":[{"orcid":"0000-0003-4761-5996","last_name":"Krens","first_name":"Gabriel","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Veldhuis","first_name":"Jim","full_name":"Veldhuis, Jim"},{"full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","first_name":"Vanessa","last_name":"Barone"},{"orcid":"0000-0001-5199-9940","last_name":"Capek","first_name":"Daniel","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jean-Léon","last_name":"Maître","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","full_name":"Maître, Jean-Léon"},{"last_name":"Brodland","first_name":"Wayne","full_name":"Brodland, Wayne"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"record":[{"id":"961","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"50","status":"public"}]},"scopus_import":1,"intvolume":"       144","publist_id":"7047","publication":"Development","oa":1,"doi":"10.1242/dev.144964","page":"1798 - 1806","year":"2017","day":"15","abstract":[{"text":"The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation.","lang":"eng"}],"publication_status":"published","ddc":["570"],"publisher":"Company of Biologists","date_published":"2017-05-15T00:00:00Z","file_date_updated":"2020-07-14T12:47:39Z","pmid":1,"title":"Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation","date_updated":"2024-03-25T23:30:13Z","department":[{"_id":"Bio"},{"_id":"CaHe"}],"citation":{"mla":"Krens, Gabriel, et al. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>, vol. 144, no. 10, Company of Biologists, 2017, pp. 1798–806, doi:<a href=\"https://doi.org/10.1242/dev.144964\">10.1242/dev.144964</a>.","short":"G. Krens, J. Veldhuis, V. Barone, D. Capek, J.-L. Maître, W. Brodland, C.-P.J. Heisenberg, Development 144 (2017) 1798–1806.","apa":"Krens, G., Veldhuis, J., Barone, V., Capek, D., Maître, J.-L., Brodland, W., &#38; Heisenberg, C.-P. J. (2017). Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>","ista":"Krens G, Veldhuis J, Barone V, Capek D, Maître J-L, Brodland W, Heisenberg C-PJ. 2017. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. Development. 144(10), 1798–1806.","ama":"Krens G, Veldhuis J, Barone V, et al. Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation. <i>Development</i>. 2017;144(10):1798-1806. doi:<a href=\"https://doi.org/10.1242/dev.144964\">10.1242/dev.144964</a>","chicago":"Krens, Gabriel, Jim Veldhuis, Vanessa Barone, Daniel Capek, Jean-Léon Maître, Wayne Brodland, and Carl-Philipp J Heisenberg. “Interstitial Fluid Osmolarity Modulates the Action of Differential Tissue Surface Tension in Progenitor Cell Segregation during Gastrulation.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.144964\">https://doi.org/10.1242/dev.144964</a>.","ieee":"G. Krens <i>et al.</i>, “Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation,” <i>Development</i>, vol. 144, no. 10. Company of Biologists, pp. 1798–1806, 2017."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28512197"]}},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","status":"public","publication_identifier":{"issn":["22111247"]},"date_created":"2018-12-11T11:47:52Z","type":"journal_article","_id":"677","pubrep_id":"899","author":[{"first_name":"Claudio","last_name":"Lademann","full_name":"Lademann, Claudio"},{"full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz"},{"first_name":"Boris","last_name":"Pfander","full_name":"Pfander, Boris"},{"first_name":"Stefan","last_name":"Jentsch","full_name":"Jentsch, Stefan"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":19,"has_accepted_license":"1","month":"05","file":[{"relation":"main_file","file_id":"5171","checksum":"efc7287d9c6354983cb151880e9ad72a","creator":"system","access_level":"open_access","file_size":3005610,"content_type":"application/pdf","date_created":"2018-12-12T10:15:48Z","date_updated":"2020-07-14T12:47:40Z","file_name":"IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf"}],"issue":"7","day":"16","doi":"10.1016/j.celrep.2017.04.051","page":"1294 - 1303","year":"2017","oa":1,"publist_id":"7046","intvolume":"        19","publication":"Cell Reports","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"department":[{"_id":"MiSi"}],"date_updated":"2021-01-12T08:08:57Z","citation":{"mla":"Lademann, Claudio, et al. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” <i>Cell Reports</i>, vol. 19, no. 7, Cell Press, 2017, pp. 1294–303, doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">10.1016/j.celrep.2017.04.051</a>.","short":"C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303.","apa":"Lademann, C., Renkawitz, J., Pfander, B., &#38; Jentsch, S. (2017). The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">https://doi.org/10.1016/j.celrep.2017.04.051</a>","ista":"Lademann C, Renkawitz J, Pfander B, Jentsch S. 2017. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 19(7), 1294–1303.","chicago":"Lademann, Claudio, Jörg Renkawitz, Boris Pfander, and Stefan Jentsch. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” <i>Cell Reports</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">https://doi.org/10.1016/j.celrep.2017.04.051</a>.","ama":"Lademann C, Renkawitz J, Pfander B, Jentsch S. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. <i>Cell Reports</i>. 2017;19(7):1294-1303. doi:<a href=\"https://doi.org/10.1016/j.celrep.2017.04.051\">10.1016/j.celrep.2017.04.051</a>","ieee":"C. Lademann, J. Renkawitz, B. Pfander, and S. Jentsch, “The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination,” <i>Cell Reports</i>, vol. 19, no. 7. Cell Press, pp. 1294–1303, 2017."},"publisher":"Cell Press","date_published":"2017-05-16T00:00:00Z","file_date_updated":"2020-07-14T12:47:40Z","title":"The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination","publication_status":"published","abstract":[{"text":"The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR.","lang":"eng"}],"ddc":["570"]},{"author":[{"full_name":"Ebner, Florian","first_name":"Florian","last_name":"Ebner"},{"last_name":"Sedlyarov","first_name":"Vitaly","full_name":"Sedlyarov, Vitaly"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","full_name":"Tasciyan, Saren","last_name":"Tasciyan","first_name":"Saren","orcid":"0000-0003-1671-393X"},{"full_name":"Ivin, Masa","first_name":"Masa","last_name":"Ivin"},{"first_name":"Franz","last_name":"Kratochvill","full_name":"Kratochvill, Franz"},{"full_name":"Gratz, Nina","last_name":"Gratz","first_name":"Nina"},{"full_name":"Kenner, Lukas","first_name":"Lukas","last_name":"Kenner"},{"last_name":"Villunger","first_name":"Andreas","full_name":"Villunger, Andreas"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179"},{"last_name":"Kovarik","first_name":"Pavel","full_name":"Kovarik, Pavel"}],"oa_version":"Submitted Version","quality_controlled":"1","project":[{"call_identifier":"FWF","grant_number":"T00817-B21","_id":"25985A36-B435-11E9-9278-68D0E5697425","name":"The biochemical basis of PAR polarization"},{"call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"}],"volume":127,"language":[{"iso":"eng"}],"issue":"6","month":"06","publication_identifier":{"issn":["00219738"]},"status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5451238/","open_access":"1"}],"type":"journal_article","_id":"679","date_created":"2018-12-11T11:47:53Z","external_id":{"pmid":["28504646"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Ebner, F., Sedlyarov, V., Tasciyan, S., Ivin, M., Kratochvill, F., Gratz, N., … Kovarik, P. (2017). The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. <i>The Journal of Clinical Investigation</i>. American Society for Clinical Investigation. <a href=\"https://doi.org/10.1172/JCI80631\">https://doi.org/10.1172/JCI80631</a>","ama":"Ebner F, Sedlyarov V, Tasciyan S, et al. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. <i>The Journal of Clinical Investigation</i>. 2017;127(6):2051-2065. doi:<a href=\"https://doi.org/10.1172/JCI80631\">10.1172/JCI80631</a>","ista":"Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt MK, Kovarik P. 2017. The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection. The Journal of Clinical Investigation. 127(6), 2051–2065.","chicago":"Ebner, Florian, Vitaly Sedlyarov, Saren Tasciyan, Masa Ivin, Franz Kratochvill, Nina Gratz, Lukas Kenner, Andreas Villunger, Michael K Sixt, and Pavel Kovarik. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” <i>The Journal of Clinical Investigation</i>. American Society for Clinical Investigation, 2017. <a href=\"https://doi.org/10.1172/JCI80631\">https://doi.org/10.1172/JCI80631</a>.","ieee":"F. Ebner <i>et al.</i>, “The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection,” <i>The Journal of Clinical Investigation</i>, vol. 127, no. 6. American Society for Clinical Investigation, pp. 2051–2065, 2017.","short":"F. Ebner, V. Sedlyarov, S. Tasciyan, M. Ivin, F. Kratochvill, N. Gratz, L. Kenner, A. Villunger, M.K. Sixt, P. Kovarik, The Journal of Clinical Investigation 127 (2017) 2051–2065.","mla":"Ebner, Florian, et al. “The RNA-Binding Protein Tristetraprolin Schedules Apoptosis of Pathogen-Engaged Neutrophils during Bacterial Infection.” <i>The Journal of Clinical Investigation</i>, vol. 127, no. 6, American Society for Clinical Investigation, 2017, pp. 2051–65, doi:<a href=\"https://doi.org/10.1172/JCI80631\">10.1172/JCI80631</a>."},"department":[{"_id":"MiSi"}],"date_updated":"2024-03-25T23:30:12Z","title":"The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection","pmid":1,"publisher":"American Society for Clinical Investigation","date_published":"2017-06-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"Protective responses against pathogens require a rapid mobilization of resting neutrophils and the timely removal of activated ones. Neutrophils are exceptionally short-lived leukocytes, yet it remains unclear whether the lifespan of pathogen-engaged neutrophils is regulated differently from that in the circulating steady-state pool. Here, we have found that under homeostatic conditions, the mRNA-destabilizing protein tristetraprolin (TTP) regulates apoptosis and the numbers of activated infiltrating murine neutrophils but not neutrophil cellularity. Activated TTP-deficient neutrophils exhibited decreased apoptosis and enhanced accumulation at the infection site. In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcus pyogenes and prevented bacterial dissemination. Neutrophil transcriptome analysis revealed that decreased apoptosis of TTP-deficient neutrophils was specifically associated with elevated expression of myeloid cell leukemia 1 (Mcl1) but not other antiapoptotic B cell leukemia/ lymphoma 2 (Bcl2) family members. Higher Mcl1 expression resulted from stabilization of Mcl1 mRNA in the absence of TTP. The low apoptosis rate of infiltrating TTP-deficient neutrophils was comparable to that of transgenic Mcl1-overexpressing neutrophils. Our study demonstrates that posttranscriptional gene regulation by TTP schedules the termination of the antimicrobial engagement of neutrophils. The balancing role of TTP comes at the cost of an increased risk of bacterial infections."}],"doi":"10.1172/JCI80631","page":"2051 - 2065","year":"2017","day":"01","acknowledgement":"This work was supported by grants from the Austrian Science Fund (FWF) (P27538-B21, I1621-B22, and SFB 43, to PK); by funding from the European Union Seventh Framework Programme Marie Curie Initial Training Networks (FP7-PEOPLE-2012-ITN) for the project INBIONET (INfection BIOlogy Training NETwork under grant agreement PITN-GA-2012-316682; and by a joint research cluster initiative of the University of Vienna and the Medical University of Vienna.","oa":1,"publication":"The Journal of Clinical Investigation","publist_id":"7038","intvolume":"       127","scopus_import":1,"related_material":{"record":[{"status":"public","id":"12401","relation":"dissertation_contains"}]}},{"date_updated":"2023-02-23T14:10:54Z","department":[{"_id":"GaTk"}],"citation":{"mla":"Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” <i>PLoS Computational Biology</i>, vol. 13, no. 6, e1005582, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">10.1371/journal.pcbi.1005582</a>.","short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017).","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts divisive reshaping of receptive fields,” <i>PLoS Computational Biology</i>, vol. 13, no. 6. Public Library of Science, 2017.","apa":"Chalk, M. J., Masset, P., Gutkin, B., &#38; Denève, S. (2017). Sensory noise predicts divisive reshaping of receptive fields. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">https://doi.org/10.1371/journal.pcbi.1005582</a>","chicago":"Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">https://doi.org/10.1371/journal.pcbi.1005582</a>.","ama":"Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping of receptive fields. <i>PLoS Computational Biology</i>. 2017;13(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">10.1371/journal.pcbi.1005582</a>","ista":"Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"abstract":[{"text":"In order to respond reliably to specific features of their environment, sensory neurons need to integrate multiple incoming noisy signals. Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics.","lang":"eng"}],"publication_status":"published","ddc":["571"],"date_published":"2017-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:40Z","publisher":"Public Library of Science","title":"Sensory noise predicts divisive reshaping of receptive fields","oa":1,"day":"01","doi":"10.1371/journal.pcbi.1005582","year":"2017","related_material":{"record":[{"status":"public","relation":"research_data","id":"9855"}]},"scopus_import":1,"intvolume":"        13","publist_id":"7035","publication":"PLoS Computational Biology","quality_controlled":"1","oa_version":"Published Version","author":[{"orcid":"0000-0001-7782-4436","first_name":"Matthew J","last_name":"Chalk","full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Masset","first_name":"Paul","full_name":"Masset, Paul"},{"full_name":"Gutkin, Boris","last_name":"Gutkin","first_name":"Boris"},{"first_name":"Sophie","last_name":"Denève","full_name":"Denève, Sophie"}],"month":"06","has_accepted_license":"1","issue":"6","file":[{"file_name":"IST-2017-898-v1+1_journal.pcbi.1005582.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:07:47Z","date_updated":"2020-07-14T12:47:40Z","file_id":"4645","checksum":"796a1026076af6f4405a47d985bc7b68","creator":"system","access_level":"open_access","file_size":14555676,"relation":"main_file"}],"article_number":"e1005582","language":[{"iso":"eng"}],"volume":13,"date_created":"2018-12-11T11:47:53Z","_id":"680","type":"journal_article","status":"public","publication_identifier":{"issn":["1553734X"]},"pubrep_id":"898"},{"ec_funded":1,"publication_identifier":{"issn":["08905401"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.3238"}],"date_created":"2018-12-11T11:47:53Z","article_type":"original","type":"journal_article","_id":"681","language":[{"iso":"eng"}],"volume":254,"article_processing_charge":"No","month":"06","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"last_name":"Filiot","first_name":"Emmanuel","full_name":"Filiot, Emmanuel"},{"full_name":"Raskin, Jean","first_name":"Jean","last_name":"Raskin"}],"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","oa_version":"Submitted Version","arxiv":1,"publist_id":"7036","intvolume":"       254","publication":"Information and Computation","scopus_import":"1","related_material":{"record":[{"id":"10885","relation":"earlier_version","status":"public"}]},"day":"01","year":"2017","doi":"10.1016/j.ic.2016.10.012","page":"296 - 315","oa":1,"publisher":"Elsevier","date_published":"2017-06-01T00:00:00Z","title":"Doomsday equilibria for omega-regular games","publication_status":"published","abstract":[{"text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information. In this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile where all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players' objective, then the objective of every player is violated. We present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games. We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games.","lang":"eng"}],"external_id":{"arxiv":["1311.3238"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"date_updated":"2023-02-21T16:06:02Z","citation":{"ama":"Chatterjee K, Doyen L, Filiot E, Raskin J. Doomsday equilibria for omega-regular games. <i>Information and Computation</i>. 2017;254:296-315. doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.012\">10.1016/j.ic.2016.10.012</a>","ista":"Chatterjee K, Doyen L, Filiot E, Raskin J. 2017. Doomsday equilibria for omega-regular games. Information and Computation. 254, 296–315.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean Raskin. “Doomsday Equilibria for Omega-Regular Games.” <i>Information and Computation</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ic.2016.10.012\">https://doi.org/10.1016/j.ic.2016.10.012</a>.","apa":"Chatterjee, K., Doyen, L., Filiot, E., &#38; Raskin, J. (2017). Doomsday equilibria for omega-regular games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2016.10.012\">https://doi.org/10.1016/j.ic.2016.10.012</a>","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J. Raskin, “Doomsday equilibria for omega-regular games,” <i>Information and Computation</i>, vol. 254. Elsevier, pp. 296–315, 2017.","short":"K. Chatterjee, L. Doyen, E. Filiot, J. Raskin, Information and Computation 254 (2017) 296–315.","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” <i>Information and Computation</i>, vol. 254, Elsevier, 2017, pp. 296–315, doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.012\">10.1016/j.ic.2016.10.012</a>."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"ieee":"H. Ukai <i>et al.</i>, “PirB regulates asymmetries in hippocampal circuitry,” <i>PLoS One</i>, vol. 12, no. 6. Public Library of Science, 2017.","ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. <i>PLoS One</i>. 2017;12(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0179377\">10.1371/journal.pone.0179377</a>","ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377.","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” <i>PLoS One</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pone.0179377\">https://doi.org/10.1371/journal.pone.0179377</a>.","apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0179377\">https://doi.org/10.1371/journal.pone.0179377</a>","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” <i>PLoS One</i>, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pone.0179377\">10.1371/journal.pone.0179377</a>."},"department":[{"_id":"RySh"}],"date_updated":"2024-03-25T23:30:07Z","title":"PirB regulates asymmetries in hippocampal circuitry","date_published":"2017-06-01T00:00:00Z","publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:47:40Z","ddc":["571"],"publication_status":"published","abstract":[{"lang":"eng","text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry."}],"doi":"10.1371/journal.pone.0179377","day":"01","year":"2017","oa":1,"publication":"PLoS One","publist_id":"7034","intvolume":"        12","scopus_import":1,"related_material":{"record":[{"status":"public","id":"51","relation":"dissertation_contains"}]},"author":[{"full_name":"Ukai, Hikari","last_name":"Ukai","first_name":"Hikari"},{"first_name":"Aiko","last_name":"Kawahara","full_name":"Kawahara, Aiko"},{"full_name":"Hirayama, Keiko","last_name":"Hirayama","first_name":"Keiko"},{"full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Case","first_name":"Matthew J"},{"full_name":"Aino, Shotaro","first_name":"Shotaro","last_name":"Aino"},{"first_name":"Masahiro","last_name":"Miyabe","full_name":"Miyabe, Masahiro"},{"first_name":"Ken","last_name":"Wakita","full_name":"Wakita, Ken"},{"first_name":"Ryohei","last_name":"Oogi","full_name":"Oogi, Ryohei"},{"full_name":"Kasayuki, Michiyo","first_name":"Michiyo","last_name":"Kasayuki"},{"first_name":"Shihomi","last_name":"Kawashima","full_name":"Kawashima, Shihomi"},{"full_name":"Sugimoto, Shunichi","last_name":"Sugimoto","first_name":"Shunichi"},{"full_name":"Chikamatsu, Kanako","last_name":"Chikamatsu","first_name":"Kanako"},{"full_name":"Nitta, Noritaka","first_name":"Noritaka","last_name":"Nitta"},{"full_name":"Koga, Tsuneyuki","first_name":"Tsuneyuki","last_name":"Koga"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"full_name":"Takai, Toshiyuki","first_name":"Toshiyuki","last_name":"Takai"},{"full_name":"Ito, Isao","last_name":"Ito","first_name":"Isao"}],"oa_version":"Published Version","quality_controlled":"1","volume":12,"language":[{"iso":"eng"}],"article_number":"e0179377","file":[{"relation":"main_file","creator":"system","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8","file_id":"4934","file_size":5798454,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:40Z","date_created":"2018-12-12T10:12:16Z","file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf"}],"issue":"6","has_accepted_license":"1","month":"06","publication_identifier":{"issn":["19326203"]},"status":"public","article_type":"original","type":"journal_article","_id":"682","date_created":"2018-12-11T11:47:54Z","pubrep_id":"897"},{"department":[{"_id":"UlWa"}],"date_updated":"2023-09-05T15:01:43Z","citation":{"ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge labelled triangulations,” presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia, 2017, vol. 77.","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">10.4230/LIPIcs.SoCG.2017.49</a>","ista":"Lubiw A, Masárová Z, Wagner U. 2017. A proof of the orbit conjecture for flipping edge labelled triangulations. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 77, 49.","chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">https://doi.org/10.4230/LIPIcs.SoCG.2017.49</a>.","apa":"Lubiw, A., Masárová, Z., &#38; Wagner, U. (2017). A proof of the orbit conjecture for flipping edge labelled triangulations (Vol. 77). Presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">https://doi.org/10.4230/LIPIcs.SoCG.2017.49</a>","mla":"Lubiw, Anna, et al. <i>A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations</i>. Vol. 77, 49, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">10.4230/LIPIcs.SoCG.2017.49</a>.","short":"A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"alternative_title":["LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","abstract":[{"lang":"eng","text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture."}],"ddc":["514","516"],"date_published":"2017-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:41Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"A proof of the orbit conjecture for flipping edge labelled triangulations","oa":1,"doi":"10.4230/LIPIcs.SoCG.2017.49","day":"01","year":"2017","scopus_import":1,"related_material":{"record":[{"status":"public","relation":"later_version","id":"5986"}]},"publist_id":"7033","intvolume":"        77","quality_controlled":"1","oa_version":"Published Version","author":[{"last_name":"Lubiw","first_name":"Anna","full_name":"Lubiw, Anna"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","full_name":"Masárová, Zuzana","first_name":"Zuzana","last_name":"Masárová","orcid":"0000-0002-6660-1322"},{"orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","month":"06","file":[{"creator":"system","checksum":"24fdde981cc513352a78dcf9b0660ae9","file_id":"5265","file_size":710007,"access_level":"open_access","relation":"main_file","file_name":"IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:41Z","date_created":"2018-12-12T10:17:12Z"}],"article_number":"49","language":[{"iso":"eng"}],"volume":77,"date_created":"2018-12-11T11:47:54Z","_id":"683","type":"conference","status":"public","pubrep_id":"896","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Brisbane, Australia","end_date":"2017-07-07","start_date":"2017-07-04"}},{"quality_controlled":"1","oa_version":"Submitted Version","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Piterman, Nir","first_name":"Nir","last_name":"Piterman"}],"month":"06","issue":"2","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":82,"date_created":"2018-12-11T11:47:54Z","type":"journal_article","_id":"684","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1206.5174"}],"publication_identifier":{"issn":["0022-4812"],"eissn":["1943-5886"]},"status":"public","date_updated":"2021-04-16T12:10:53Z","department":[{"_id":"KrCh"}],"citation":{"short":"K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452.","mla":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” <i>Journal of Symbolic Logic</i>, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:<a href=\"https://doi.org/10.1017/jsl.2016.71\">10.1017/jsl.2016.71</a>.","ieee":"K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” <i>Journal of Symbolic Logic</i>, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017.","ista":"Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” <i>Journal of Symbolic Logic</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jsl.2016.71\">https://doi.org/10.1017/jsl.2016.71</a>.","ama":"Chatterjee K, Piterman N. Obligation blackwell games and p-automata. <i>Journal of Symbolic Logic</i>. 2017;82(2):420-452. doi:<a href=\"https://doi.org/10.1017/jsl.2016.71\">10.1017/jsl.2016.71</a>","apa":"Chatterjee, K., &#38; Piterman, N. (2017). Obligation blackwell games and p-automata. <i>Journal of Symbolic Logic</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jsl.2016.71\">https://doi.org/10.1017/jsl.2016.71</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic."}],"publication_status":"published","date_published":"2017-06-01T00:00:00Z","publisher":"Cambridge University Press","title":"Obligation blackwell games and p-automata","oa":1,"day":"01","year":"2017","doi":"10.1017/jsl.2016.71","page":"420 - 452","scopus_import":"1","intvolume":"        82","publist_id":"7026","publication":"Journal of Symbolic Logic"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1610.02995"]},"author":[{"first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"oa_version":"Preprint","citation":{"mla":"Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>, International Conference on Learning Representations, 2017.","short":"G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","apa":"Martius, G. S., &#38; Lampert, C. (2017). Extrapolation and learning equations. In <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>. Toulon, France: International Conference on Learning Representations.","ista":"Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations.","chicago":"Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>. International Conference on Learning Representations, 2017.","ama":"Martius GS, Lampert C. Extrapolation and learning equations. In: <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>. International Conference on Learning Representations; 2017.","ieee":"G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>, Toulon, France, 2017."},"date_updated":"2021-01-12T08:09:17Z","project":[{"call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"department":[{"_id":"ChLa"}],"quality_controlled":"1","title":"Extrapolation and learning equations","publisher":"International Conference on Learning Representations","language":[{"iso":"eng"}],"date_published":"2017-02-21T00:00:00Z","abstract":[{"text":"In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified.","lang":"eng"}],"publication_status":"published","month":"02","day":"21","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02995"}],"status":"public","year":"2017","type":"conference","_id":"6841","date_created":"2019-09-01T22:01:00Z","oa":1,"publication":"5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings","ec_funded":1,"arxiv":1,"conference":{"location":"Toulon, France","name":"ICLR: International Conference on Learning Representations","end_date":"2017-04-26","start_date":"2017-04-24"},"scopus_import":1},{"pubrep_id":"985","ec_funded":1,"_id":"685","type":"journal_article","date_created":"2018-12-11T11:47:55Z","publication_identifier":{"issn":["09254773"]},"status":"public","file":[{"date_updated":"2020-07-14T12:47:42Z","date_created":"2019-04-17T07:58:48Z","content_type":"application/pdf","file_name":"2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf","relation":"main_file","file_size":652313,"access_level":"open_access","creator":"dernst","file_id":"6335","checksum":"727043d2e4199fbef6b3704e6d1ac105"}],"has_accepted_license":"1","month":"06","volume":145,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","project":[{"call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037"}],"quality_controlled":"1","author":[{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998"}],"scopus_import":1,"publication":"Mechanisms of Development","publist_id":"7025","intvolume":"       145","oa":1,"doi":"10.1016/j.mod.2017.03.005","page":"26 - 31","year":"2017","day":"01","ddc":["571"],"publication_status":"published","abstract":[{"text":"By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube.","lang":"eng"}],"title":"The physics of development 100 years after D'Arcy Thompson's “on growth and form”","pmid":1,"publisher":"Elsevier","date_published":"2017-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:42Z","citation":{"ista":"Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31.","ama":"Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” <i>Mechanisms of Development</i>. 2017;145:26-31. doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">10.1016/j.mod.2017.03.005</a>","chicago":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” <i>Mechanisms of Development</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">https://doi.org/10.1016/j.mod.2017.03.005</a>.","apa":"Briscoe, J., &#38; Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">https://doi.org/10.1016/j.mod.2017.03.005</a>","ieee":"J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” <i>Mechanisms of Development</i>, vol. 145. Elsevier, pp. 26–31, 2017.","mla":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” <i>Mechanisms of Development</i>, vol. 145, Elsevier, 2017, pp. 26–31, doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">10.1016/j.mod.2017.03.005</a>.","short":"J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31."},"department":[{"_id":"AnKi"}],"date_updated":"2021-01-12T08:09:20Z","external_id":{"pmid":["28366718"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publist_id":"7022","intvolume":"        68","publication":"Quarterly Journal of Mathematics","scopus_import":1,"day":"01","page":"635 - 703","year":"2017","doi":"10.1093/qmath/haw053","oa":1,"publisher":"Oxford University Press","date_published":"2017-06-01T00:00:00Z","title":"The critical CoHA of a quiver with potential","publication_status":"published","abstract":[{"lang":"eng","text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TaHa"}],"date_updated":"2021-01-12T08:09:24Z","citation":{"mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” <i>Quarterly Journal of Mathematics</i>, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:<a href=\"https://doi.org/10.1093/qmath/haw053\">10.1093/qmath/haw053</a>.","short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703.","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. <i>Quarterly Journal of Mathematics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/qmath/haw053\">https://doi.org/10.1093/qmath/haw053</a>","chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” <i>Quarterly Journal of Mathematics</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/qmath/haw053\">https://doi.org/10.1093/qmath/haw053</a>.","ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703.","ama":"Davison B. The critical CoHA of a quiver with potential. <i>Quarterly Journal of Mathematics</i>. 2017;68(2):635-703. doi:<a href=\"https://doi.org/10.1093/qmath/haw053\">10.1093/qmath/haw053</a>","ieee":"B. Davison, “The critical CoHA of a quiver with potential,” <i>Quarterly Journal of Mathematics</i>, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017."},"ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1311.7172","open_access":"1"}],"publication_identifier":{"issn":["00335606"]},"status":"public","date_created":"2018-12-11T11:47:55Z","type":"journal_article","_id":"687","language":[{"iso":"eng"}],"volume":68,"month":"06","issue":"2","author":[{"full_name":"Davison, Ben","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8944-4390","last_name":"Davison","first_name":"Ben"}],"project":[{"call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593"}],"quality_controlled":"1","oa_version":"Submitted Version"},{"day":"01","page":"391-3916","doi":"10.4230/LIPIcs.SoCG.2017.39","year":"2017","oa":1,"intvolume":"        77","publist_id":"7021","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"alternative_title":["LIPIcs"],"citation":{"apa":"Edelsbrunner, H., &#38; Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">https://doi.org/10.4230/LIPIcs.SoCG.2017.39</a>","ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916.","ama":"Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">10.4230/LIPIcs.SoCG.2017.39</a>","chicago":"Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">https://doi.org/10.4230/LIPIcs.SoCG.2017.39</a>.","ieee":"H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916.","mla":"Edelsbrunner, Herbert, and Hubert Wagner. <i>Topological Data Analysis with Bregman Divergences</i>. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">10.4230/LIPIcs.SoCG.2017.39</a>.","short":"H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916."},"date_updated":"2021-01-12T08:09:26Z","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"title":"Topological data analysis with Bregman divergences","file_date_updated":"2020-07-14T12:47:42Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2017-06-01T00:00:00Z","ddc":["514","516"],"abstract":[{"text":"We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. ","lang":"eng"}],"publication_status":"published","status":"public","publication_identifier":{"issn":["18688969"]},"type":"conference","_id":"688","date_created":"2018-12-11T11:47:56Z","conference":{"name":"Symposium on Computational Geometry, SoCG","location":"Brisbane, Australia","end_date":"2017-07-07","start_date":"2017-07-04"},"pubrep_id":"895","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert"}],"oa_version":"Published Version","quality_controlled":"1","volume":77,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","file_size":990546,"checksum":"067ab0cb3f962bae6c3af6bf0094e0f3","file_id":"4856","creator":"system","date_created":"2018-12-12T10:11:03Z","date_updated":"2020-07-14T12:47:42Z","content_type":"application/pdf","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf"}],"has_accepted_license":"1","month":"06"},{"citation":{"apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. 2017;114(26):E5246-E5255. doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>","chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>.","ieee":"T. Miki <i>et al.</i>, “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” <i>PNAS</i>, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>."},"department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"date_updated":"2023-02-23T12:54:57Z","external_id":{"pmid":["28607047"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"publication_status":"published","abstract":[{"text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ","lang":"eng"}],"title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","pmid":1,"publisher":"National Academy of Sciences","date_published":"2017-06-27T00:00:00Z","file_date_updated":"2020-07-14T12:47:44Z","oa":1,"day":"27","doi":"10.1073/pnas.1704470114","page":"E5246 - E5255","year":"2017","scopus_import":1,"publication":"PNAS","publist_id":"7013","intvolume":"       114","oa_version":"Published Version","quality_controlled":"1","author":[{"full_name":"Miki, Takafumi","last_name":"Miki","first_name":"Takafumi"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315"},{"full_name":"Malagon, Gerardo","last_name":"Malagon","first_name":"Gerardo"},{"last_name":"Gomez","first_name":"Laura","full_name":"Gomez, Laura"},{"full_name":"Tabuchi, Katsuhiko","last_name":"Tabuchi","first_name":"Katsuhiko"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marty","first_name":"Alain","full_name":"Marty, Alain"}],"file":[{"relation":"main_file","file_id":"7223","checksum":"2ab75d554f3df4a34d20fa8040589b7e","creator":"kschuh","access_level":"open_access","file_size":2721544,"content_type":"application/pdf","date_created":"2020-01-03T13:27:29Z","date_updated":"2020-07-14T12:47:44Z","file_name":"2017_PNAS_Miki.pdf"}],"issue":"26","has_accepted_license":"1","month":"06","volume":114,"article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"type":"journal_article","_id":"693","date_created":"2018-12-11T11:47:57Z","status":"public","publication_identifier":{"issn":["00278424"]}},{"scopus_import":1,"publication":"Journal of Cell Science","intvolume":"       130","publist_id":"7008","oa":1,"doi":"10.1242/jcs.200899","day":"01","year":"2017","page":"2172 - 2184","ddc":["570"],"abstract":[{"lang":"eng","text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells."}],"publication_status":"published","title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","file_date_updated":"2020-07-14T12:47:45Z","date_published":"2017-07-01T00:00:00Z","publisher":"Company of Biologists","pmid":1,"citation":{"ieee":"A. Veß <i>et al.</i>, “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” <i>Journal of Cell Science</i>, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. 2017;130(13):2172-2184. doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>.","apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., &#38; Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>.","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184."},"date_updated":"2021-01-12T08:09:41Z","department":[{"_id":"MiSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28515231"]},"type":"journal_article","_id":"694","article_type":"original","date_created":"2018-12-11T11:47:58Z","status":"public","publication_identifier":{"issn":["00219533"]},"issue":"13","file":[{"creator":"dernst","checksum":"42c81a0a4fc3128883b391c3af3f74bc","file_id":"6966","file_size":10847596,"access_level":"open_access","relation":"main_file","file_name":"2017_CellScience_Vess.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:45Z","date_created":"2019-10-24T09:43:56Z"}],"has_accepted_license":"1","month":"07","volume":130,"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","author":[{"last_name":"Veß","first_name":"Astrid","full_name":"Veß, Astrid"},{"first_name":"Ulrich","last_name":"Blache","full_name":"Blache, Ulrich"},{"first_name":"Laura","last_name":"Leitner","full_name":"Leitner, Laura"},{"full_name":"Kurz, Angela","first_name":"Angela","last_name":"Kurz"},{"last_name":"Ehrenpfordt","first_name":"Anja","full_name":"Ehrenpfordt, Anja"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Posern, Guido","last_name":"Posern","first_name":"Guido"}]},{"department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"date_updated":"2024-03-25T23:30:14Z","citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017)."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"ddc":["576"],"file_date_updated":"2020-07-14T12:47:46Z","publisher":"Public Library of Science","date_published":"2017-07-18T00:00:00Z","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","oa":1,"doi":"10.1371/journal.pcbi.1005609","year":"2017","day":"18","scopus_import":1,"related_material":{"record":[{"relation":"research_data","id":"9849","status":"public"},{"status":"public","id":"9850","relation":"research_data"},{"relation":"research_data","id":"9851","status":"public"},{"relation":"research_data","id":"9852","status":"public"},{"status":"public","relation":"dissertation_contains","id":"6263"}]},"publist_id":"7004","intvolume":"        13","publication":"PLoS Computational Biology","quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953"}],"has_accepted_license":"1","month":"07","file":[{"file_size":3775716,"access_level":"open_access","creator":"system","file_id":"5117","checksum":"9143c290fa6458ed2563bff4b295554a","relation":"main_file","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:15:01Z","content_type":"application/pdf"}],"article_number":"e1005609","issue":"7","language":[{"iso":"eng"}],"volume":13,"date_created":"2018-12-11T11:47:58Z","article_type":"original","type":"journal_article","_id":"696","publication_identifier":{"issn":["1553734X"]},"status":"public","pubrep_id":"894","ec_funded":1},{"intvolume":"        80","publist_id":"7003","scopus_import":1,"day":"01","year":"2017","doi":"10.4230/LIPIcs.ICALP.2017.39","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:47:46Z","date_published":"2017-07-01T00:00:00Z","title":"Non uniform attacks against pseudoentropy","abstract":[{"lang":"eng","text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. "}],"publication_status":"published","ddc":["005"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"alternative_title":["LIPIcs"],"date_updated":"2021-01-12T08:11:15Z","department":[{"_id":"KrPi"}],"citation":{"short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. <i>Non Uniform Attacks against Pseudoentropy</i>. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>.","apa":"Pietrzak, K. Z., &#38; Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>.","ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80."},"ec_funded":1,"conference":{"start_date":"2017-07-10","end_date":"2017-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Warsaw, Poland"},"pubrep_id":"893","status":"public","publication_identifier":{"issn":["18688969"]},"date_created":"2018-12-11T11:47:59Z","type":"conference","_id":"697","language":[{"iso":"eng"}],"volume":80,"has_accepted_license":"1","month":"07","article_number":"39","file":[{"access_level":"open_access","file_size":601004,"file_id":"4701","checksum":"e95618a001692f1af2d68f5fde43bc1f","creator":"system","relation":"main_file","file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","date_created":"2018-12-12T10:08:40Z","date_updated":"2020-07-14T12:47:46Z","content_type":"application/pdf"}],"author":[{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski"}],"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"quality_controlled":"1","oa_version":"Published Version"},{"issue":"14","file":[{"file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:10:53Z","content_type":"application/pdf","file_size":1086097,"access_level":"open_access","creator":"system","checksum":"de01dac9e30970cfa6ae902480a4e04d","file_id":"4844","relation":"main_file"}],"has_accepted_license":"1","month":"07","volume":28,"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"name":"Gaussian Graphical Models: Theory and Applications","_id":"2530CA10-B435-11E9-9278-68D0E5697425","grant_number":"Y 903-N35","call_identifier":"FWF"}],"author":[{"last_name":"Wang","first_name":"Yejun","full_name":"Wang, Yejun"},{"full_name":"Nagarajan, Mallika","first_name":"Mallika","last_name":"Nagarajan"},{"full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler"},{"full_name":"Shivashankar, Gv","last_name":"Shivashankar","first_name":"Gv"}],"pubrep_id":"892","type":"journal_article","_id":"698","date_created":"2018-12-11T11:47:59Z","publication_identifier":{"issn":["10591524"]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","status":"public","ddc":["519"],"abstract":[{"lang":"eng","text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. "}],"publication_status":"published","title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","file_date_updated":"2020-07-14T12:47:46Z","publisher":"American Society for Cell Biology","date_published":"2017-07-07T00:00:00Z","citation":{"chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2017. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>.","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. 2017;28(14):1997-2009. doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","apa":"Wang, Y., Nagarajan, M., Uhler, C., &#38; Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>.","short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009."},"date_updated":"2021-01-12T08:11:17Z","department":[{"_id":"CaUh"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publication":"Molecular Biology of the Cell","intvolume":"        28","publist_id":"7001","oa":1,"doi":"10.1091/mbc.E16-12-0825","day":"07","year":"2017","page":"1997 - 2009"},{"publication_status":"published","abstract":[{"text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ","lang":"eng"}],"pmid":1,"date_published":"2017-07-03T00:00:00Z","publisher":"National Academy of Sciences","title":"The red queen and king in finite populations","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T08:11:21Z","citation":{"mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” <i>PNAS</i>, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. <i>PNAS</i>. 2017;114(27):E5396-E5405. doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>.","apa":"Veller, C., Hayward, L., Nowak, M., &#38; Hilbe, C. (2017). The red queen and king in finite populations. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” <i>PNAS</i>, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017."},"external_id":{"pmid":["28630336"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publist_id":"7002","intvolume":"       114","publication":"PNAS","oa":1,"day":"03","year":"2017","doi":"10.1073/pnas.1702020114","page":"E5396 - E5405","month":"07","issue":"27","language":[{"iso":"eng"}],"volume":114,"quality_controlled":"1","oa_version":"Submitted Version","author":[{"last_name":"Veller","first_name":"Carl","full_name":"Veller, Carl"},{"full_name":"Hayward, Laura","first_name":"Laura","last_name":"Hayward"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:48:00Z","_id":"699","type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/","open_access":"1"}],"publication_identifier":{"issn":["00278424"]},"status":"public"}]