[{"oa_version":"Published Version","type":"journal_article","issue":"2","license":"https://creativecommons.org/licenses/by/4.0/","_id":"7093","volume":10,"abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how \"simple\" or \"thin\" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth.\r\nIn view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs).\r\nWe derive these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann, Schultens and Saito by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 18(k+1) (resp. 4(3k+1))."}],"has_accepted_license":"1","intvolume":"        10","related_material":{"record":[{"id":"285","status":"public","relation":"earlier_version"},{"status":"public","relation":"part_of_dissertation","id":"8032"}]},"date_published":"2019-11-01T00:00:00Z","publication":"Journal of Computational Geometry","arxiv":1,"publication_identifier":{"issn":["1920-180X"]},"day":"01","language":[{"iso":"eng"}],"ddc":["514"],"status":"public","publication_status":"published","article_processing_charge":"No","title":"On the treewidth of triangulated 3-manifolds","article_type":"original","citation":{"ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. <i>Journal of Computational Geometry</i>. 2019;10(2):70–98. doi:<a href=\"https://doi.org/10.20382/JOGC.V10I2A5\">10.20382/JOGC.V10I2A5</a>","apa":"Huszár, K., Spreer, J., &#38; Wagner, U. (2019). On the treewidth of triangulated 3-manifolds. <i>Journal of Computational Geometry</i>. Computational Geometry Laborartoy. <a href=\"https://doi.org/10.20382/JOGC.V10I2A5\">https://doi.org/10.20382/JOGC.V10I2A5</a>","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” <i>Journal of Computational Geometry</i>, vol. 10, no. 2. Computational Geometry Laborartoy, pp. 70–98, 2019.","ista":"Huszár K, Spreer J, Wagner U. 2019. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 10(2), 70–98.","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds.” <i>Journal of Computational Geometry</i>. Computational Geometry Laborartoy, 2019. <a href=\"https://doi.org/10.20382/JOGC.V10I2A5\">https://doi.org/10.20382/JOGC.V10I2A5</a>.","mla":"Huszár, Kristóf, et al. “On the Treewidth of Triangulated 3-Manifolds.” <i>Journal of Computational Geometry</i>, vol. 10, no. 2, Computational Geometry Laborartoy, 2019, pp. 70–98, doi:<a href=\"https://doi.org/10.20382/JOGC.V10I2A5\">10.20382/JOGC.V10I2A5</a>.","short":"K. Huszár, J. Spreer, U. Wagner, Journal of Computational Geometry 10 (2019) 70–98."},"oa":1,"file":[{"creator":"khuszar","date_created":"2019-11-23T12:35:16Z","file_id":"7094","file_name":"479-1917-1-PB.pdf","file_size":857590,"access_level":"open_access","date_updated":"2020-07-14T12:47:49Z","checksum":"c872d590d38d538404782bca20c4c3f5","content_type":"application/pdf","relation":"main_file"}],"publisher":"Computational Geometry Laborartoy","file_date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-23T12:14:09Z","quality_controlled":"1","year":"2019","date_updated":"2023-09-07T13:18:26Z","doi":"10.20382/JOGC.V10I2A5","page":"70–98","external_id":{"arxiv":["1712.00434"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"author":[{"orcid":"0000-0002-5445-5057","full_name":"Huszár, Kristóf","last_name":"Huszár","id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf"},{"last_name":"Spreer","full_name":"Spreer, Jonathan","first_name":"Jonathan"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"department":[{"_id":"UlWa"}],"month":"11"},{"status":"public","publication_status":"published","article_type":"original","title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","article_processing_charge":"No","publisher":"Springer Nature","file":[{"access_level":"open_access","file_size":6467393,"file_name":"2019_ScientificReports_Maes.pdf","file_id":"7096","creator":"dernst","date_created":"2019-11-25T07:49:52Z","relation":"main_file","content_type":"application/pdf","checksum":"9ab397ed9c1c454b34bffb8cc863d734","date_updated":"2020-07-14T12:47:49Z"}],"oa":1,"citation":{"mla":"Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” <i>Scientific Reports</i>, vol. 9, 16565, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-019-53049-w\">10.1038/s41598-019-53049-w</a>.","chicago":"Maes, Margaret E, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” <i>Scientific Reports</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41598-019-53049-w\">https://doi.org/10.1038/s41598-019-53049-w</a>.","short":"M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific Reports 9 (2019).","ama":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. <i>Scientific Reports</i>. 2019;9. doi:<a href=\"https://doi.org/10.1038/s41598-019-53049-w\">10.1038/s41598-019-53049-w</a>","apa":"Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., &#38; Nickells, R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-019-53049-w\">https://doi.org/10.1038/s41598-019-53049-w</a>","ieee":"M. E. Maes, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells, “Completion of BAX recruitment correlates with mitochondrial fission during apoptosis,” <i>Scientific Reports</i>, vol. 9. Springer Nature, 2019.","ista":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. 2019. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 9, 16565."},"quality_controlled":"1","date_created":"2019-11-25T07:45:17Z","file_date_updated":"2020-07-14T12:47:49Z","year":"2019","doi":"10.1038/s41598-019-53049-w","date_updated":"2023-08-30T07:26:54Z","pmid":1,"department":[{"_id":"SaSi"}],"author":[{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","last_name":"Maes","full_name":"Maes, Margaret E","orcid":"0000-0001-9642-1085"},{"first_name":"J. A.","full_name":"Grosser, J. A.","last_name":"Grosser"},{"first_name":"R. L.","full_name":"Fehrman, R. L.","last_name":"Fehrman"},{"last_name":"Schlamp","full_name":"Schlamp, C. L.","first_name":"C. L."},{"full_name":"Nickells, R. W.","last_name":"Nickells","first_name":"R. W."}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"16565","external_id":{"pmid":["31719602"],"isi":["000495857600019"]},"month":"11","type":"journal_article","oa_version":"Published Version","isi":1,"_id":"7095","abstract":[{"text":"BAX, a member of the BCL2 gene family, controls the committed step of the intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed feature of apoptosis, which occurs through the process of mitochondrial fission. BAX has consistently been associated with mitochondrial fission, yet how BAX participates in the process of mitochondrial fragmentation during apoptosis remains to be tested. Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates that rapid mitochondrial fragmentation during apoptosis occurs after the complete recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement of a fully functioning BAX protein for the fission process was demonstrated further in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant performed fusion to restore the mitochondrial network. but was not demonstrably recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial fragmentation was blocked. Additionally, we show that loss of the fission protein, dynamin-like protein 1 (DRP1), does not temporally affect the initiation time or rate of BAX recruitment, but does reduce the final level of BAX recruited to the MOM during the late phase of BAX recruitment. These correlative observations suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial fragmentation machinery in apoptotic cells.","lang":"eng"}],"volume":9,"has_accepted_license":"1","date_published":"2019-11-12T00:00:00Z","scopus_import":"1","intvolume":"         9","publication_identifier":{"eissn":["2045-2322"]},"publication":"Scientific Reports","ddc":["570"],"day":"12","language":[{"iso":"eng"}]},{"intvolume":"         2","scopus_import":"1","date_published":"2019-11-15T00:00:00Z","has_accepted_license":"1","language":[{"iso":"eng"}],"day":"15","ddc":["570"],"publication":"Communications Biology","publication_identifier":{"issn":["2399-3642"]},"isi":1,"issue":"1","oa_version":"Published Version","type":"journal_article","volume":2,"abstract":[{"lang":"eng","text":"Early endosomes, also called sorting endosomes, are known to mature into late endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early endosome existence isthought to be maintained by the continual fusion of transport vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial for the formation of endosomes andthe subsequent endolysosomal traffic regulated by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide exchange on Vps21p arefirst recruited to theTGN  before  transport  to  the  endosome,  namely  the  GEF  Vps9p and  the  epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation and identify the TGN as a critical location forregulating progress through the endolysosomal trafficking pathway."}],"_id":"7097","date_updated":"2023-08-30T07:27:55Z","doi":"10.1038/s42003-019-0670-5","year":"2019","month":"11","article_number":"419","external_id":{"isi":["000496767800005"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"author":[{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"first_name":"Junko Y.","full_name":"Toshima, Junko Y.","last_name":"Toshima"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"first_name":"Jiro","full_name":"Toshima, Jiro","last_name":"Toshima"}],"department":[{"_id":"DaSi"}],"article_processing_charge":"No","title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","article_type":"original","publication_status":"published","status":"public","file_date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T07:55:01Z","quality_controlled":"1","citation":{"short":"M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019).","mla":"Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” <i>Communications Biology</i>, vol. 2, no. 1, 419, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s42003-019-0670-5\">10.1038/s42003-019-0670-5</a>.","chicago":"Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” <i>Communications Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s42003-019-0670-5\">https://doi.org/10.1038/s42003-019-0670-5</a>.","ista":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. 2019. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2(1), 419.","ieee":"M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome formation is regulated at the trans-Golgi network,” <i>Communications Biology</i>, vol. 2, no. 1. Springer Nature, 2019.","apa":"Nagano, M., Toshima, J. Y., Siekhaus, D. E., &#38; Toshima, J. (2019). Rab5-mediated endosome formation is regulated at the trans-Golgi network. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-019-0670-5\">https://doi.org/10.1038/s42003-019-0670-5</a>","ama":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation is regulated at the trans-Golgi network. <i>Communications Biology</i>. 2019;2(1). doi:<a href=\"https://doi.org/10.1038/s42003-019-0670-5\">10.1038/s42003-019-0670-5</a>"},"oa":1,"publisher":"Springer Nature","file":[{"file_size":2626069,"access_level":"open_access","date_created":"2019-11-25T07:58:05Z","creator":"dernst","file_id":"7098","file_name":"2019_CommunicBiology_Nagano.pdf","relation":"main_file","content_type":"application/pdf","checksum":"c63c69a264fc8a0e52f2b0d482f3bdae","date_updated":"2020-07-14T12:47:49Z"}]},{"pmid":1,"department":[{"_id":"RySh"}],"author":[{"first_name":"Yu","last_name":"Kasugai","full_name":"Kasugai, Yu"},{"full_name":"Vogel, Elisabeth","last_name":"Vogel","first_name":"Elisabeth"},{"full_name":"Hörtnagl, Heide","last_name":"Hörtnagl","first_name":"Heide"},{"last_name":"Schönherr","full_name":"Schönherr, Sabine","first_name":"Sabine"},{"full_name":"Paradiso, Enrica","last_name":"Paradiso","first_name":"Enrica"},{"full_name":"Hauschild, Markus","last_name":"Hauschild","first_name":"Markus"},{"last_name":"Göbel","full_name":"Göbel, Georg","first_name":"Georg"},{"last_name":"Milenkovic","full_name":"Milenkovic, Ivan","first_name":"Ivan"},{"first_name":"Yvan","full_name":"Peterschmitt, Yvan","last_name":"Peterschmitt"},{"first_name":"Ramon","full_name":"Tasan, Ramon","last_name":"Tasan"},{"first_name":"Günther","full_name":"Sperk, Günther","last_name":"Sperk"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"full_name":"Sieghart, Werner","last_name":"Sieghart","first_name":"Werner"},{"last_name":"Singewald","full_name":"Singewald, Nicolas","first_name":"Nicolas"},{"last_name":"Lüthi","full_name":"Lüthi, Andreas","first_name":"Andreas"},{"first_name":"Francesco","full_name":"Ferraguti, Francesco","last_name":"Ferraguti"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000497963500017"],"pmid":["31543297"]},"page":"781-794.e4","month":"11","year":"2019","doi":"10.1016/j.neuron.2019.08.013","date_updated":"2023-08-30T07:28:22Z","publisher":"Elsevier","oa":1,"citation":{"chicago":"Kasugai, Yu, Elisabeth Vogel, Heide Hörtnagl, Sabine Schönherr, Enrica Paradiso, Markus Hauschild, Georg Göbel, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">https://doi.org/10.1016/j.neuron.2019.08.013</a>.","mla":"Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” <i>Neuron</i>, vol. 104, no. 4, Elsevier, 2019, p. 781–794.e4, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">10.1016/j.neuron.2019.08.013</a>.","short":"Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild, G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W. Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4.","ama":"Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. <i>Neuron</i>. 2019;104(4):781-794.e4. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">10.1016/j.neuron.2019.08.013</a>","apa":"Kasugai, Y., Vogel, E., Hörtnagl, H., Schönherr, S., Paradiso, E., Hauschild, M., … Ferraguti, F. (2019). Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">https://doi.org/10.1016/j.neuron.2019.08.013</a>","ieee":"Y. Kasugai <i>et al.</i>, “Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning,” <i>Neuron</i>, vol. 104, no. 4. Elsevier, p. 781–794.e4, 2019.","ista":"Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4."},"acknowledgement":"The authors thank Gabi Schmid for excellent technical support. We also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the specificity\r\nof some of the antibodies used in this study on replicas. Funding was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung) Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.), and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous version of the manuscript.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.013"}],"quality_controlled":"1","date_created":"2019-11-25T08:02:39Z","status":"public","publication_status":"published","article_type":"original","title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","article_processing_charge":"No","publication_identifier":{"issn":["0896-6273"]},"publication":"Neuron","ddc":["571","599"],"language":[{"iso":"eng"}],"day":"20","has_accepted_license":"1","date_published":"2019-11-20T00:00:00Z","intvolume":"       104","scopus_import":"1","_id":"7099","volume":104,"oa_version":"Published Version","type":"journal_article","issue":"4","isi":1},{"title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","article_processing_charge":"Yes (via OA deal)","article_type":"original","ec_funded":1,"status":"public","publication_status":"published","quality_controlled":"1","date_created":"2019-11-25T08:08:02Z","file_date_updated":"2020-07-14T12:47:49Z","acknowledgement":"OA fund by IST Austria","publisher":"Springer Nature","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"cd283b475dd739e04655315abd46f528","date_updated":"2020-07-14T12:47:49Z","access_level":"open_access","file_size":884469,"file_name":"2019_CommMathPhys_Jeblick.pdf","file_id":"7101","date_created":"2019-11-25T08:11:11Z","creator":"dernst"}],"oa":1,"citation":{"short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69.","mla":"Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” <i>Communications in Mathematical Physics</i>, vol. 372, no. 1, Springer Nature, 2019, pp. 1–69, doi:<a href=\"https://doi.org/10.1007/s00220-019-03599-x\">10.1007/s00220-019-03599-x</a>.","chicago":"Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00220-019-03599-x\">https://doi.org/10.1007/s00220-019-03599-x</a>.","ieee":"M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent Gross–Pitaevskii equation in two dimensions,” <i>Communications in Mathematical Physics</i>, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019.","ista":"Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69.","ama":"Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. <i>Communications in Mathematical Physics</i>. 2019;372(1):1-69. doi:<a href=\"https://doi.org/10.1007/s00220-019-03599-x\">10.1007/s00220-019-03599-x</a>","apa":"Jeblick, M., Leopold, N. K., &#38; Pickl, P. (2019). Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03599-x\">https://doi.org/10.1007/s00220-019-03599-x</a>"},"date_updated":"2023-09-06T10:47:43Z","doi":"10.1007/s00220-019-03599-x","year":"2019","month":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"1-69","external_id":{"isi":["000495193700002"]},"department":[{"_id":"RoSe"}],"author":[{"last_name":"Jeblick","full_name":"Jeblick, Maximilian","first_name":"Maximilian"},{"full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","last_name":"Leopold","first_name":"Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"isi":1,"issue":"1","type":"journal_article","oa_version":"Published Version","volume":372,"abstract":[{"text":"We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics.","lang":"eng"}],"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"_id":"7100","intvolume":"       372","scopus_import":"1","date_published":"2019-11-08T00:00:00Z","has_accepted_license":"1","ddc":["510"],"language":[{"iso":"eng"}],"day":"08","publication":"Communications in Mathematical Physics","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]}},{"month":"11","department":[{"_id":"GaTk"}],"pmid":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"author":[{"last_name":"Wang","full_name":"Wang, Jilin W. J. L.","first_name":"Jilin W. J. L."},{"first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"first_name":"Christelle","last_name":"Anaclet","full_name":"Anaclet, Christelle"},{"last_name":"Ivanov","full_name":"Ivanov, Plamen Ch.","first_name":"Plamen Ch."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000500976100014"],"pmid":["31725712"]},"article_number":"e1007268","doi":"10.1371/journal.pcbi.1007268","date_updated":"2023-10-17T12:30:07Z","year":"2019","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T08:20:47Z","file":[{"content_type":"application/pdf","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","relation":"main_file","date_updated":"2020-07-14T12:47:49Z","access_level":"open_access","file_size":3982516,"file_name":"2019_PLOSComBio_Wang.pdf","file_id":"7104","date_created":"2019-11-25T08:24:01Z","creator":"dernst"}],"publisher":"Public Library of Science","citation":{"ama":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. <i>PLoS Computational Biology</i>. 2019;15(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">10.1371/journal.pcbi.1007268</a>","apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., &#38; Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">https://doi.org/10.1371/journal.pcbi.1007268</a>","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” <i>PLoS Computational Biology</i>, vol. 15, no. 11. Public Library of Science, 2019.","ista":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268.","chicago":"Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">https://doi.org/10.1371/journal.pcbi.1007268</a>.","mla":"Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” <i>PLoS Computational Biology</i>, vol. 15, no. 11, e1007268, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">10.1371/journal.pcbi.1007268</a>.","short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019)."},"oa":1,"article_type":"original","title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","article_processing_charge":"No","status":"public","publication_status":"published","ec_funded":1,"ddc":["570","000"],"day":"01","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7358"]},"publication":"PLoS Computational Biology","date_published":"2019-11-01T00:00:00Z","intvolume":"        15","scopus_import":"1","has_accepted_license":"1","abstract":[{"text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics.","lang":"eng"}],"volume":15,"_id":"7103","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"issue":"11","type":"journal_article","oa_version":"Published Version"},{"year":"2019","doi":"10.1038/s41556-019-0411-5","date_updated":"2023-09-06T11:08:52Z","pmid":1,"department":[{"_id":"MiSi"}],"author":[{"last_name":"Yolland","full_name":"Yolland, Lawrence","first_name":"Lawrence"},{"first_name":"Mubarik","full_name":"Burki, Mubarik","last_name":"Burki"},{"last_name":"Marcotti","full_name":"Marcotti, Stefania","first_name":"Stefania"},{"last_name":"Luchici","full_name":"Luchici, Andrei","first_name":"Andrei"},{"last_name":"Kenny","full_name":"Kenny, Fiona N.","first_name":"Fiona N."},{"first_name":"John Robert","last_name":"Davis","full_name":"Davis, John Robert"},{"full_name":"Serna-Morales, Eduardo","last_name":"Serna-Morales","first_name":"Eduardo"},{"last_name":"Müller","full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Davidson, Andrew","last_name":"Davidson","first_name":"Andrew"},{"first_name":"Will","last_name":"Wood","full_name":"Wood, Will"},{"first_name":"Linus J.","last_name":"Schumacher","full_name":"Schumacher, Linus J."},{"last_name":"Endres","full_name":"Endres, Robert G.","first_name":"Robert G."},{"first_name":"Mark","full_name":"Miodownik, Mark","last_name":"Miodownik"},{"first_name":"Brian M.","last_name":"Stramer","full_name":"Stramer, Brian M."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"1370-1381","external_id":{"pmid":["31685997"],"isi":["000495888300009"]},"month":"11","status":"public","publication_status":"published","article_type":"original","title":"Persistent and polarized global actin flow is essential for directionality during cell migration","article_processing_charge":"No","publisher":"Springer Nature","citation":{"ieee":"L. Yolland <i>et al.</i>, “Persistent and polarized global actin flow is essential for directionality during cell migration,” <i>Nature Cell Biology</i>, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. <i>Nature Cell Biology</i>. 2019;21(11):1370-1381. doi:<a href=\"https://doi.org/10.1038/s41556-019-0411-5\">10.1038/s41556-019-0411-5</a>","apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-019-0411-5\">https://doi.org/10.1038/s41556-019-0411-5</a>","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” <i>Nature Cell Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41556-019-0411-5\">https://doi.org/10.1038/s41556-019-0411-5</a>.","mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” <i>Nature Cell Biology</i>, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:<a href=\"https://doi.org/10.1038/s41556-019-0411-5\">10.1038/s41556-019-0411-5</a>."},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891","open_access":"1"}],"quality_controlled":"1","date_created":"2019-11-25T08:55:00Z","date_published":"2019-11-01T00:00:00Z","intvolume":"        21","scopus_import":"1","publication_identifier":{"eissn":["1476-4679"],"issn":["1465-7392"]},"publication":"Nature Cell Biology","language":[{"iso":"eng"}],"day":"01","oa_version":"Submitted Version","type":"journal_article","isi":1,"issue":"11","_id":"7105","abstract":[{"lang":"eng","text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence."}],"volume":21},{"issue":"11","isi":1,"oa_version":"Submitted Version","type":"journal_article","volume":5,"abstract":[{"text":"PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes.","lang":"eng"}],"project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"_id":"7106","intvolume":"         5","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","has_accepted_license":"1","day":"01","language":[{"iso":"eng"}],"ddc":["580"],"publication":"Nature Plants","publication_identifier":{"issn":["2055-0278"]},"article_processing_charge":"No","title":"PIN-driven auxin transport emerged early in streptophyte evolution","article_type":"original","ec_funded":1,"publication_status":"published","status":"public","date_created":"2019-11-25T09:08:04Z","file_date_updated":"2020-10-14T08:54:49Z","quality_controlled":"1","citation":{"ista":"Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119.","ieee":"R. Skokan <i>et al.</i>, “PIN-driven auxin transport emerged early in streptophyte evolution,” <i>Nature Plants</i>, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019.","apa":"Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-019-0542-5\">https://doi.org/10.1038/s41477-019-0542-5</a>","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. <i>Nature Plants</i>. 2019;5(11):1114-1119. doi:<a href=\"https://doi.org/10.1038/s41477-019-0542-5\">10.1038/s41477-019-0542-5</a>","short":"R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.","chicago":"Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” <i>Nature Plants</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41477-019-0542-5\">https://doi.org/10.1038/s41477-019-0542-5</a>.","mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” <i>Nature Plants</i>, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:<a href=\"https://doi.org/10.1038/s41477-019-0542-5\">10.1038/s41477-019-0542-5</a>."},"oa":1,"publisher":"Springer Nature","file":[{"relation":"main_file","checksum":"94e0426856aad9a9bd0135d5436efbf1","content_type":"application/pdf","date_updated":"2020-10-14T08:54:49Z","file_size":1980851,"access_level":"open_access","success":1,"creator":"dernst","date_created":"2020-10-14T08:54:49Z","file_name":"2019_NaturePlants_Skokan_accepted.pdf","file_id":"8660"}],"date_updated":"2023-09-06T11:09:49Z","doi":"10.1038/s41477-019-0542-5","year":"2019","month":"11","external_id":{"isi":["000496526100010"],"pmid":["31712756"]},"page":"1114-1119","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Skokan, Roman","last_name":"Skokan","first_name":"Roman"},{"full_name":"Medvecká, Eva","last_name":"Medvecká","first_name":"Eva"},{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"last_name":"Müller","full_name":"Müller, Karel","first_name":"Karel"},{"first_name":"Petr","last_name":"Skůpa","full_name":"Skůpa, Petr"},{"last_name":"Karady","full_name":"Karady, Michal","first_name":"Michal"},{"first_name":"Yuzhou","full_name":"Zhang, Yuzhou","last_name":"Zhang"},{"first_name":"Dorina P.","last_name":"Janacek","full_name":"Janacek, Dorina P."},{"last_name":"Hammes","full_name":"Hammes, Ulrich Z.","first_name":"Ulrich Z."},{"last_name":"Ljung","full_name":"Ljung, Karin","first_name":"Karin"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"pmid":1,"department":[{"_id":"JiFr"}]},{"intvolume":"        66","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","related_material":{"record":[{"id":"184","relation":"earlier_version","status":"public"}]},"publication":"Journal of the ACM","arxiv":1,"publication_identifier":{"issn":["0004-5411"]},"language":[{"iso":"eng"}],"day":"01","type":"journal_article","oa_version":"Preprint","isi":1,"issue":"3","_id":"7108","volume":66,"abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable."}],"year":"2019","date_updated":"2023-09-06T11:10:58Z","doi":"10.1145/3314024","external_id":{"isi":["000495406300007"],"arxiv":["1711.08436"]},"article_number":"21","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"last_name":"Patak","full_name":"Patak, Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83","first_name":"Pavel"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova","first_name":"Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"department":[{"_id":"UlWa"}],"month":"06","publication_status":"published","status":"public","article_processing_charge":"No","title":"Shellability is NP-complete","article_type":"original","oa":1,"citation":{"short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019).","mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” <i>Journal of the ACM</i>, vol. 66, no. 3, 21, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3314024\">10.1145/3314024</a>.","chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” <i>Journal of the ACM</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3314024\">https://doi.org/10.1145/3314024</a>.","ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” <i>Journal of the ACM</i>, vol. 66, no. 3. ACM, 2019.","apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2019). Shellability is NP-complete. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3314024\">https://doi.org/10.1145/3314024</a>","ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. <i>Journal of the ACM</i>. 2019;66(3). doi:<a href=\"https://doi.org/10.1145/3314024\">10.1145/3314024</a>"},"publisher":"ACM","date_created":"2019-11-26T10:13:59Z","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1711.08436.pdf"}]},{"title":"From real-time logic to timed automata","article_processing_charge":"No","article_type":"original","publication_status":"published","status":"public","quality_controlled":"1","date_created":"2019-11-26T10:22:32Z","publisher":"ACM","citation":{"short":"T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).","mla":"Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” <i>Journal of the ACM</i>, vol. 66, no. 3, 19, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3286976\">10.1145/3286976</a>.","chicago":"Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time Logic to Timed Automata.” <i>Journal of the ACM</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3286976\">https://doi.org/10.1145/3286976</a>.","ieee":"T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to timed automata,” <i>Journal of the ACM</i>, vol. 66, no. 3. ACM, 2019.","ista":"Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed automata. Journal of the ACM. 66(3), 19.","ama":"Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata. <i>Journal of the ACM</i>. 2019;66(3). doi:<a href=\"https://doi.org/10.1145/3286976\">10.1145/3286976</a>","apa":"Ferrere, T., Maler, O., Ničković, D., &#38; Pnueli, A. (2019). From real-time logic to timed automata. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3286976\">https://doi.org/10.1145/3286976</a>"},"date_updated":"2023-09-06T11:11:56Z","doi":"10.1145/3286976","year":"2019","month":"05","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000495406300005"]},"article_number":"19","department":[{"_id":"ToHe"}],"author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"},{"full_name":"Ničković, Dejan","last_name":"Ničković","first_name":"Dejan"},{"first_name":"Amir","full_name":"Pnueli, Amir","last_name":"Pnueli"}],"isi":1,"issue":"3","oa_version":"None","type":"journal_article","volume":66,"abstract":[{"text":"We show how to construct temporal testers for the logic MITL, a prominent linear-time logic for real-time systems. A temporal tester is a transducer that inputs a signal holding the Boolean value of atomic propositions and outputs the truth value of a formula along time. Here we consider testers over continuous-time Boolean signals that use clock variables to enforce duration constraints, as in timed automata. We first rewrite the MITL formula into a “simple” formula using a limited set of temporal modalities. We then build testers for these specific modalities and show how to compose testers for simple formulae into complex ones. Temporal testers can be turned into acceptors, yielding a compositional translation from MITL to timed automata. This construction is much simpler than previously known and remains asymptotically optimal. It supports both past and future operators and can easily be extended.","lang":"eng"}],"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"_id":"7109","scopus_import":"1","intvolume":"        66","date_published":"2019-05-01T00:00:00Z","day":"01","language":[{"iso":"eng"}],"publication":"Journal of the ACM","publication_identifier":{"issn":["0004-5411"]}},{"doi":"10.1145/3355089.3356576","date_updated":"2024-03-25T23:30:26Z","year":"2019","month":"11","department":[{"_id":"BeBi"}],"author":[{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hafner, Christian","last_name":"Hafner"},{"first_name":"Christian","full_name":"Schumacher, Christian","last_name":"Schumacher"},{"first_name":"Espen","full_name":"Knoop, Espen","last_name":"Knoop"},{"last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"},{"last_name":"Bächer","full_name":"Bächer, Moritz","first_name":"Moritz"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000498397300007"]},"article_number":"157","article_type":"original","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","article_processing_charge":"No","publication_status":"published","status":"public","ec_funded":1,"quality_controlled":"1","date_created":"2019-11-26T14:22:09Z","file_date_updated":"2020-07-14T12:47:49Z","file":[{"file_id":"7119","file_name":"xcad_sup_mat_siga19.pdf","date_created":"2019-11-26T14:24:26Z","creator":"bbickel","access_level":"open_access","file_size":1673176,"title":"X-CAD Supplemental Material","date_updated":"2020-07-14T12:47:49Z","relation":"supplementary_material","content_type":"application/pdf","checksum":"56a2fb019adcb556d2b022f5e5acb68c"},{"description":"This is the author's version of the work.","date_created":"2019-11-26T14:24:27Z","creator":"bbickel","file_name":"XCAD_authors_version.pdf","file_id":"7120","file_size":14563618,"access_level":"open_access","date_updated":"2020-07-14T12:47:49Z","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","content_type":"application/pdf","checksum":"5f29d76aceb5102e766cbab9b17d776e","relation":"main_file"},{"access_level":"open_access","file_size":259979129,"file_name":"XCAD_video.mp4","file_id":"7121","date_created":"2019-11-26T14:27:37Z","creator":"bbickel","relation":"main_file","checksum":"0d31e123286cbec9e28b2001c2bb0d55","content_type":"video/mp4","date_updated":"2020-07-14T12:47:49Z"}],"publisher":"ACM","oa":1,"citation":{"apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., &#38; Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3355089.3356576\">https://doi.org/10.1145/3355089.3356576</a>","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. <i>ACM Transactions on Graphics</i>. 2019;38(6). doi:<a href=\"https://doi.org/10.1145/3355089.3356576\">10.1145/3355089.3356576</a>","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6. ACM, 2019.","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3355089.3356576\">https://doi.org/10.1145/3355089.3356576</a>.","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6, 157, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3355089.3356576\">10.1145/3355089.3356576</a>.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019)."},"related_material":{"record":[{"id":"12897","relation":"dissertation_contains","status":"public"}]},"date_published":"2019-11-06T00:00:00Z","intvolume":"        38","scopus_import":"1","has_accepted_license":"1","ddc":["000"],"language":[{"iso":"eng"}],"day":"06","publication_identifier":{"issn":["0730-0301"]},"publication":"ACM Transactions on Graphics","isi":1,"issue":"6","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"volume":38,"_id":"7117","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}]},{"oa_version":"None","type":"conference","status":"public","publication_status":"published","title":"Gradient compression for communication-limited convex optimization","isi":1,"article_processing_charge":"No","conference":{"start_date":"2018-12-17","location":"Miami Beach, FL, United States","end_date":"2018-12-19","name":"CDC: Conference on Decision and Control"},"publisher":"IEEE","_id":"7122","citation":{"mla":"Khirirat, Sarit, et al. “Gradient Compression for Communication-Limited Convex Optimization.” <i>2018 IEEE Conference on Decision and Control</i>, 8619625, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/cdc.2018.8619625\">10.1109/cdc.2018.8619625</a>.","chicago":"Khirirat, Sarit, Mikael Johansson, and Dan-Adrian Alistarh. “Gradient Compression for Communication-Limited Convex Optimization.” In <i>2018 IEEE Conference on Decision and Control</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/cdc.2018.8619625\">https://doi.org/10.1109/cdc.2018.8619625</a>.","short":"S. Khirirat, M. Johansson, D.-A. Alistarh, in:, 2018 IEEE Conference on Decision and Control, IEEE, 2019.","ama":"Khirirat S, Johansson M, Alistarh D-A. Gradient compression for communication-limited convex optimization. In: <i>2018 IEEE Conference on Decision and Control</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/cdc.2018.8619625\">10.1109/cdc.2018.8619625</a>","apa":"Khirirat, S., Johansson, M., &#38; Alistarh, D.-A. (2019). Gradient compression for communication-limited convex optimization. In <i>2018 IEEE Conference on Decision and Control</i>. Miami Beach, FL, United States: IEEE. <a href=\"https://doi.org/10.1109/cdc.2018.8619625\">https://doi.org/10.1109/cdc.2018.8619625</a>","ieee":"S. Khirirat, M. Johansson, and D.-A. Alistarh, “Gradient compression for communication-limited convex optimization,” in <i>2018 IEEE Conference on Decision and Control</i>, Miami Beach, FL, United States, 2019.","ista":"Khirirat S, Johansson M, Alistarh D-A. 2019. Gradient compression for communication-limited convex optimization. 2018 IEEE Conference on Decision and Control. CDC: Conference on Decision and Control, 8619625."},"quality_controlled":"1","date_created":"2019-11-26T15:07:49Z","abstract":[{"text":"Data-rich applications in machine-learning and control have motivated an intense research on large-scale optimization. Novel algorithms have been proposed and shown to have optimal convergence rates in terms of iteration counts. However, their practical performance is severely degraded by the cost of exchanging high-dimensional gradient vectors between computing nodes. Several gradient compression heuristics have recently been proposed to reduce communications, but few theoretical results exist that quantify how they impact algorithm convergence. This paper establishes and strengthens the convergence guarantees for gradient descent under a family of gradient compression techniques. For convex optimization problems, we derive admissible step sizes and quantify both the number of iterations and the number of bits that need to be exchanged to reach a target accuracy. Finally, we validate the performance of different gradient compression techniques in simulations. The numerical results highlight the properties of different gradient compression algorithms and confirm that fast convergence with limited information exchange is possible.","lang":"eng"}],"year":"2019","date_updated":"2023-09-06T11:14:55Z","scopus_import":"1","date_published":"2019-01-21T00:00:00Z","doi":"10.1109/cdc.2018.8619625","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"2018 IEEE Conference on Decision and Control","article_number":"8619625","external_id":{"isi":["000458114800023"]},"publication_identifier":{"isbn":["9781538613955"],"issn":["0743-1546"]},"department":[{"_id":"DaAl"}],"author":[{"first_name":"Sarit","last_name":"Khirirat","full_name":"Khirirat, Sarit"},{"first_name":"Mikael","full_name":"Johansson, Mikael","last_name":"Johansson"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"month":"01","language":[{"iso":"eng"}],"day":"21"},{"ddc":["576"],"day":"28","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2211-1247"]},"publication":"Cell Reports","date_published":"2019-05-28T00:00:00Z","intvolume":"        27","has_accepted_license":"1","abstract":[{"text":"Loss of functional cardiomyocytes is a major determinant of heart failure after myocardial infarction. Previous high throughput screening studies have identified a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate cardiac regeneration in mice. Here, we show that all of the most effective of these miRNAs activate nuclear localization of the master transcriptional cofactor Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization by targeting Cofilin2, a process that by itself activates YAP nuclear translocation. Thus, activation of YAP and modulation of the actin cytoskeleton are major components of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte proliferation.","lang":"eng"}],"volume":27,"_id":"7128","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"9","type":"journal_article","oa_version":"Published Version","month":"05","pmid":1,"author":[{"full_name":"Torrini, Consuelo","last_name":"Torrini","first_name":"Consuelo"},{"last_name":"Cubero","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"full_name":"Dirkx, Ellen","last_name":"Dirkx","first_name":"Ellen"},{"last_name":"Braga","full_name":"Braga, Luca","first_name":"Luca"},{"last_name":"Ali","full_name":"Ali, Hashim","first_name":"Hashim"},{"last_name":"Prosdocimo","full_name":"Prosdocimo, Giulia","first_name":"Giulia"},{"first_name":"Maria Ines","last_name":"Gutierrez","full_name":"Gutierrez, Maria Ines"},{"last_name":"Collesi","full_name":"Collesi, Chiara","first_name":"Chiara"},{"first_name":"Danilo","full_name":"Licastro, Danilo","last_name":"Licastro"},{"last_name":"Zentilin","full_name":"Zentilin, Lorena","first_name":"Lorena"},{"first_name":"Miguel","full_name":"Mano, Miguel","last_name":"Mano"},{"first_name":"Serena","last_name":"Zacchigna","full_name":"Zacchigna, Serena"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"full_name":"Marsili, Matteo","last_name":"Marsili","first_name":"Matteo"},{"full_name":"Samal, Areejit","last_name":"Samal","first_name":"Areejit"},{"first_name":"Mauro","full_name":"Giacca, Mauro","last_name":"Giacca"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2759-2771.e5","external_id":{"pmid":["31141697"]},"doi":"10.1016/j.celrep.2019.05.005","date_updated":"2021-01-12T08:11:56Z","year":"2019","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:50Z","date_created":"2019-11-26T22:30:07Z","publisher":"Elsevier","file":[{"file_size":4650750,"access_level":"open_access","date_created":"2019-11-26T22:30:43Z","creator":"rcubero","file_id":"7129","file_name":"torrini_cellreports_2019.pdf","relation":"main_file","checksum":"c5d855d07263bfec718673385d0ea2d7","content_type":"application/pdf","date_updated":"2020-07-14T12:47:50Z"}],"oa":1,"citation":{"chicago":"Torrini, Consuelo, Ryan J Cubero, Ellen Dirkx, Luca Braga, Hashim Ali, Giulia Prosdocimo, Maria Ines Gutierrez, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">https://doi.org/10.1016/j.celrep.2019.05.005</a>.","mla":"Torrini, Consuelo, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>, vol. 27, no. 9, Elsevier, 2019, p. 2759–2771.e5, doi:<a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">10.1016/j.celrep.2019.05.005</a>.","short":"C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I. Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo, M. Marsili, A. Samal, M. Giacca, Cell Reports 27 (2019) 2759–2771.e5.","apa":"Torrini, C., Cubero, R. J., Dirkx, E., Braga, L., Ali, H., Prosdocimo, G., … Giacca, M. (2019). Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">https://doi.org/10.1016/j.celrep.2019.05.005</a>","ama":"Torrini C, Cubero RJ, Dirkx E, et al. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. <i>Cell Reports</i>. 2019;27(9):2759-2771.e5. doi:<a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">10.1016/j.celrep.2019.05.005</a>","ista":"Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI, Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili M, Samal A, Giacca M. 2019. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. Cell Reports. 27(9), 2759–2771.e5.","ieee":"C. Torrini <i>et al.</i>, “Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation,” <i>Cell Reports</i>, vol. 27, no. 9. Elsevier, p. 2759–2771.e5, 2019."},"keyword":["cardiomyocyte","cell cycle","Cofilin2","cytoskeleton","Hippo","microRNA","regeneration","YAP"],"extern":"1","article_type":"original","title":"Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation","article_processing_charge":"Yes","publication_status":"published","status":"public"},{"publication_status":"published","status":"public","extern":"1","article_type":"original","title":"Statistical criticality arises in most informative representations","article_processing_charge":"No","publisher":"IOP Publishing","oa":1,"citation":{"ista":"Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. 2019. Statistical criticality arises in most informative representations. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063402.","ieee":"R. J. Cubero, J. Jo, M. Marsili, Y. Roudi, and J. Song, “Statistical criticality arises in most informative representations,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2019, no. 6. IOP Publishing, 2019.","apa":"Cubero, R. J., Jo, J., Marsili, M., Roudi, Y., &#38; Song, J. (2019). Statistical criticality arises in most informative representations. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">https://doi.org/10.1088/1742-5468/ab16c8</a>","ama":"Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. Statistical criticality arises in most informative representations. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2019;2019(6). doi:<a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">10.1088/1742-5468/ab16c8</a>","short":"R.J. Cubero, J. Jo, M. Marsili, Y. Roudi, J. Song, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).","mla":"Cubero, Ryan J., et al. “Statistical Criticality Arises in Most Informative Representations.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2019, no. 6, 063402, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">10.1088/1742-5468/ab16c8</a>.","chicago":"Cubero, Ryan J, Junghyo Jo, Matteo Marsili, Yasser Roudi, and Juyong Song. “Statistical Criticality Arises in Most Informative Representations.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">https://doi.org/10.1088/1742-5468/ab16c8</a>."},"keyword":["optimization under uncertainty","source coding","large deviation"],"acknowledgement":"We acknowledge interesting discussions with M Abbott, E Aurell, J Barbier, R Monasson, T Mora, I Nemenman, N Tishby and R Zecchina. This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation) (RJC and YR), by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (2016R1D1A1B03932264) (JJ), and, in part, by the ICTP through the OEA-AC-98 (JS).","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.00249"}],"quality_controlled":"1","date_created":"2019-11-26T22:36:09Z","year":"2019","doi":"10.1088/1742-5468/ab16c8","date_updated":"2021-01-12T08:11:57Z","author":[{"full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J"},{"full_name":"Jo, Junghyo","last_name":"Jo","first_name":"Junghyo"},{"first_name":"Matteo","full_name":"Marsili, Matteo","last_name":"Marsili"},{"full_name":"Roudi, Yasser","last_name":"Roudi","first_name":"Yasser"},{"full_name":"Song, Juyong","last_name":"Song","first_name":"Juyong"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1808.00249"]},"article_number":"063402","month":"06","type":"journal_article","oa_version":"Preprint","issue":"6","_id":"7130","abstract":[{"text":"We show that statistical criticality, i.e. the occurrence of power law frequency distributions, arises in samples that are maximally informative about the underlying generating process. In order to reach this conclusion, we first identify the frequency with which different outcomes occur in a sample, as the variable carrying useful information on the generative process. The entropy of the frequency, that we call relevance, provides an upper bound to the number of informative bits. This differs from the entropy of the data, that we take as a measure of resolution. Samples that maximise relevance at a given resolution—that we call maximally informative samples—exhibit statistical criticality. In particular, Zipf's law arises at the optimal trade-off between resolution (i.e. compression) and relevance. As a byproduct, we derive a bound of the maximal number of parameters that can be estimated from a dataset, in the absence of prior knowledge on the generative model.\r\n\r\nFurthermore, we relate criticality to the statistical properties of the representation of the data generating process. We show that, as a consequence of the concentration property of the asymptotic equipartition property, representations that are maximally informative about the data generating process are characterised by an exponential distribution of energy levels. This arises from a principle of minimal entropy, that is conjugate of the maximum entropy principle in statistical mechanics. This explains why statistical criticality requires no parameter fine tuning in maximally informative samples.","lang":"eng"}],"volume":2019,"date_published":"2019-06-17T00:00:00Z","intvolume":"      2019","publication_identifier":{"issn":["1742-5468"]},"arxiv":1,"publication":"Journal of Statistical Mechanics: Theory and Experiment","language":[{"iso":"eng"}],"day":"17"},{"abstract":[{"lang":"eng","text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing."}],"_id":"7132","supervisor":[{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"}],"oa_version":"Published Version","type":"dissertation","degree_awarded":"PhD","language":[{"iso":"eng"}],"day":"27","ddc":["571","573"],"publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"6266","relation":"old_edition","status":"public"}]},"date_published":"2019-06-27T00:00:00Z","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:50Z","date_created":"2019-11-27T09:07:14Z","citation":{"ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019.","ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:7132\">10.15479/at:ista:7132</a>","apa":"Mckenzie, C. (2019). <i>Design and characterization of methods and biological components to realize synthetic neurotransmission</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:7132\">https://doi.org/10.15479/at:ista:7132</a>","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019.","mla":"Mckenzie, Catherine. <i>Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:7132\">10.15479/at:ista:7132</a>.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:7132\">https://doi.org/10.15479/at:ista:7132</a>."},"oa":1,"file":[{"relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"34d0fe0f6e0af97b5937205a3e350423","date_updated":"2020-07-14T12:47:50Z","access_level":"closed","file_size":5054633,"file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx","file_id":"7133","creator":"dernst","date_created":"2019-11-27T09:06:10Z"},{"access_level":"open_access","file_size":3231837,"file_id":"7134","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","creator":"dernst","date_created":"2019-11-27T09:06:10Z","relation":"main_file","checksum":"140dfb5e3df7edca34f4b6fcc55d876f","content_type":"application/pdf","date_updated":"2020-07-14T12:47:50Z"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","publication_status":"published","status":"public","month":"06","page":"95","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Mckenzie","full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine"}],"department":[{"_id":"HaJa"}],"date_updated":"2024-03-25T23:30:11Z","doi":"10.15479/at:ista:7132","year":"2019"},{"publication":"2019 IEEE International Symposium on Information Theory","publication_identifier":{"isbn":["9781538692912"]},"arxiv":1,"language":[{"iso":"eng"}],"day":"01","scopus_import":"1","date_published":"2019-07-01T00:00:00Z","_id":"7136","abstract":[{"text":"It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X<i are ϵ-close to be nearly flat (only a constant factor away). The argument is combinatorial (based on simplex coverings).\r\nThis result may be used as a generic tool for \\emph{exhibiting block-source structures}. We demonstrate this by reproving the fundamental converter due to Nisan and Zuckermann (\\emph{J. Computer and System Sciences, 1996}), which shows that sampling blocks from a min-entropy source roughly preserves the entropy rate. Our bound implies, only by straightforward chain rules, an additive loss of o(1) (for sufficiently many samples), which qualitatively meets the first tighter analysis of this problem due to Vadhan (\\emph{CRYPTO'03}), obtained by large deviation techniques. ","lang":"eng"}],"type":"conference","oa_version":"Preprint","isi":1,"conference":{"start_date":"2019-07-07","location":"Paris, France","end_date":"2019-07-12","name":"ISIT: International Symposium on Information Theory"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000489100301043"],"arxiv":["1702.08476"]},"article_number":"8849240","department":[{"_id":"KrPi"}],"author":[{"first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skórski, Maciej","last_name":"Skórski"}],"month":"07","year":"2019","date_updated":"2023-09-06T11:15:41Z","doi":"10.1109/isit.2019.8849240","publisher":"IEEE","oa":1,"citation":{"ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: <i>2019 IEEE International Symposium on Information Theory</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/isit.2019.8849240\">10.1109/isit.2019.8849240</a>","apa":"Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In <i>2019 IEEE International Symposium on Information Theory</i>. Paris, France: IEEE. <a href=\"https://doi.org/10.1109/isit.2019.8849240\">https://doi.org/10.1109/isit.2019.8849240</a>","ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in <i>2019 IEEE International Symposium on Information Theory</i>, Paris, France, 2019.","ista":"Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240.","mla":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” <i>2019 IEEE International Symposium on Information Theory</i>, 8849240, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/isit.2019.8849240\">10.1109/isit.2019.8849240</a>.","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In <i>2019 IEEE International Symposium on Information Theory</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/isit.2019.8849240\">https://doi.org/10.1109/isit.2019.8849240</a>.","short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019."},"main_file_link":[{"url":"https://arxiv.org/abs/1702.08476","open_access":"1"}],"quality_controlled":"1","date_created":"2019-11-28T10:19:21Z","publication_status":"published","status":"public","title":"Strong chain rules for min-entropy under few bits spoiled","article_processing_charge":"No"},{"article_type":"original","title":"Defying gravity: a plant's quest for moisture","article_processing_charge":"No","status":"public","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1038/s41422-019-0254-4","open_access":"1"}],"quality_controlled":"1","date_created":"2019-12-02T12:30:48Z","publisher":"Springer Nature","oa":1,"citation":{"ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” <i>Cell Research</i>, vol. 29. Springer Nature, pp. 965–966, 2019.","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966.","ama":"Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. <i>Cell Research</i>. 2019;29:965-966. doi:<a href=\"https://doi.org/10.1038/s41422-019-0254-4\">10.1038/s41422-019-0254-4</a>","apa":"Sinclair, S. A., &#38; Friml, J. (2019). Defying gravity: a plant’s quest for moisture. <i>Cell Research</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41422-019-0254-4\">https://doi.org/10.1038/s41422-019-0254-4</a>","short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.","chicago":"Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” <i>Cell Research</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41422-019-0254-4\">https://doi.org/10.1038/s41422-019-0254-4</a>.","mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” <i>Cell Research</i>, vol. 29, Springer Nature, 2019, pp. 965–66, doi:<a href=\"https://doi.org/10.1038/s41422-019-0254-4\">10.1038/s41422-019-0254-4</a>."},"doi":"10.1038/s41422-019-0254-4","date_updated":"2023-09-06T11:20:58Z","year":"2019","month":"12","department":[{"_id":"JiFr"}],"pmid":1,"author":[{"last_name":"Sinclair","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"965-966","external_id":{"isi":["000500749600001"],"pmid":["31745287"]},"isi":1,"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content.","lang":"eng"}],"volume":29,"_id":"7143","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","intvolume":"        29","day":"01","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1748-7838"],"issn":["1001-0602"]},"publication":"Cell Research"},{"status":"public","publication_status":"published","article_processing_charge":"No","title":"End-to-end correlated subgap states in hybrid nanowires","article_type":"original","oa":1,"citation":{"mla":"Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” <i>Physical Review B</i>, vol. 100, no. 20, 205412, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevb.100.205412\">10.1103/physrevb.100.205412</a>.","chicago":"Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski, J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevb.100.205412\">https://doi.org/10.1103/physrevb.100.205412</a>.","short":"G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski, J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P. Higginbotham, Physical Review B 100 (2019).","apa":"Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski, F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap states in hybrid nanowires. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.100.205412\">https://doi.org/10.1103/physrevb.100.205412</a>","ama":"Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap states in hybrid nanowires. <i>Physical Review B</i>. 2019;100(20). doi:<a href=\"https://doi.org/10.1103/physrevb.100.205412\">10.1103/physrevb.100.205412</a>","ista":"Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.","ieee":"G. L. R. Anselmetti <i>et al.</i>, “End-to-end correlated subgap states in hybrid nanowires,” <i>Physical Review B</i>, vol. 100, no. 20. American Physical Society, 2019."},"publisher":"American Physical Society","date_created":"2019-12-04T16:02:25Z","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1908.05549","open_access":"1"}],"year":"2019","date_updated":"2024-02-28T13:13:51Z","doi":"10.1103/physrevb.100.205412","external_id":{"isi":["000495967500006"],"arxiv":["1908.05549"]},"article_number":"205412","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Anselmetti","full_name":"Anselmetti, G. L. R.","first_name":"G. L. R."},{"last_name":"Martinez","full_name":"Martinez, E. A.","first_name":"E. A."},{"full_name":"Ménard, G. C.","last_name":"Ménard","first_name":"G. C."},{"first_name":"D.","last_name":"Puglia","full_name":"Puglia, D."},{"full_name":"Malinowski, F. K.","last_name":"Malinowski","first_name":"F. K."},{"first_name":"J. S.","full_name":"Lee, J. S.","last_name":"Lee"},{"full_name":"Choi, S.","last_name":"Choi","first_name":"S."},{"last_name":"Pendharkar","full_name":"Pendharkar, M.","first_name":"M."},{"first_name":"C. J.","full_name":"Palmstrøm, C. J.","last_name":"Palmstrøm"},{"first_name":"C. M.","full_name":"Marcus, C. M.","last_name":"Marcus"},{"first_name":"L.","last_name":"Casparis","full_name":"Casparis, L."},{"first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","last_name":"Higginbotham"}],"department":[{"_id":"AnHi"}],"month":"11","oa_version":"Preprint","type":"journal_article","issue":"20","isi":1,"_id":"7145","volume":100,"abstract":[{"lang":"eng","text":"End-to-end correlated bound states are investigated in superconductor-semiconductor hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently identified from each wire end, and a cross-correlation function is computed that counts end-to-end coincidences, averaging over thousands of subgap features. Strong correlations in a short, 300-nm device are reduced by a factor of 4 in a long, 900-nm device. In addition, subgap conductance distributions are investigated, and correlations between the left and right distributions are identified based on their mutual information."}],"intvolume":"       100","scopus_import":"1","date_published":"2019-11-15T00:00:00Z","publication":"Physical Review B","arxiv":1,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"day":"15"},{"title":"Molecular and evolutionary dynamics of animal sex-chromosome turnover","article_processing_charge":"No","article_type":"original","ec_funded":1,"publication_status":"published","status":"public","quality_controlled":"1","date_created":"2019-12-04T16:05:25Z","publisher":"Springer Nature","citation":{"chicago":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41559-019-1050-8\">https://doi.org/10.1038/s41559-019-1050-8</a>.","mla":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12, Springer Nature, 2019, pp. 1632–41, doi:<a href=\"https://doi.org/10.1038/s41559-019-1050-8\">10.1038/s41559-019-1050-8</a>.","short":"B. Vicoso, Nature Ecology &#38; Evolution 3 (2019) 1632–1641.","ama":"Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover. <i>Nature Ecology &#38; Evolution</i>. 2019;3(12):1632-1641. doi:<a href=\"https://doi.org/10.1038/s41559-019-1050-8\">10.1038/s41559-019-1050-8</a>","apa":"Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-019-1050-8\">https://doi.org/10.1038/s41559-019-1050-8</a>","ieee":"B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,” <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12. Springer Nature, pp. 1632–1641, 2019.","ista":"Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology &#38; Evolution. 3(12), 1632–1641."},"date_updated":"2023-09-06T11:18:59Z","doi":"10.1038/s41559-019-1050-8","year":"2019","month":"11","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"1632-1641","external_id":{"isi":["000500728800009"]},"department":[{"_id":"BeVi"}],"author":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"issue":"12","isi":1,"oa_version":"None","type":"journal_article","volume":3,"abstract":[{"lang":"eng","text":"Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity."}],"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"_id":"7146","intvolume":"         3","scopus_import":"1","date_published":"2019-11-25T00:00:00Z","language":[{"iso":"eng"}],"day":"25","publication":"Nature Ecology & Evolution","publication_identifier":{"issn":["2397-334X"]}},{"alternative_title":["LNCS"],"scopus_import":"1","intvolume":"     11773","date_published":"2019-09-17T00:00:00Z","publication":"17th International Conference on Computational Methods in Systems Biology","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030313036","9783030313043"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"day":"17","type":"conference","oa_version":"None","isi":1,"conference":{"location":"Trieste, Italy","start_date":"2019-09-18","name":"CMSB: Computational Methods in Systems Biology","end_date":"2019-09-20"},"project":[{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture"}],"_id":"7147","volume":11773,"abstract":[{"text":"The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions.","lang":"eng"}],"year":"2019","date_updated":"2023-09-06T11:18:08Z","doi":"10.1007/978-3-030-31304-3_9","page":"155-187","external_id":{"isi":["000557875100009"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"full_name":"Igler, Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"},{"last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana"},{"first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali","last_name":"Sezgin"}],"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"month":"09","status":"public","publication_status":"published","article_processing_charge":"No","title":"Transient memory in gene regulation","citation":{"chicago":"Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In <i>17th International Conference on Computational Methods in Systems Biology</i>, 11773:155–87. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">https://doi.org/10.1007/978-3-030-31304-3_9</a>.","mla":"Guet, Calin C., et al. “Transient Memory in Gene Regulation.” <i>17th International Conference on Computational Methods in Systems Biology</i>, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:<a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">10.1007/978-3-030-31304-3_9</a>.","short":"C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187.","apa":"Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., &#38; Sezgin, A. (2019). Transient memory in gene regulation. In <i>17th International Conference on Computational Methods in Systems Biology</i> (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">https://doi.org/10.1007/978-3-030-31304-3_9</a>","ama":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: <i>17th International Conference on Computational Methods in Systems Biology</i>. Vol 11773. Springer Nature; 2019:155-187. doi:<a href=\"https://doi.org/10.1007/978-3-030-31304-3_9\">10.1007/978-3-030-31304-3_9</a>","ista":"Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory in gene regulation. 17th International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773, 155–187.","ieee":"C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in <i>17th International Conference on Computational Methods in Systems Biology</i>, Trieste, Italy, 2019, vol. 11773, pp. 155–187."},"publisher":"Springer Nature","date_created":"2019-12-04T16:07:50Z","quality_controlled":"1"}]