[{"scopus_import":1,"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"alternative_title":["MIMB"],"intvolume":"      1771","day":"01","oa_version":"None","_id":"305","citation":{"ista":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.","ieee":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” <i>Methods in Molecular Biology</i>, vol. 1771. Springer, pp. 183–202, 2018.","short":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.","mla":"Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” <i>Methods in Molecular Biology</i>, vol. 1771, Springer, 2018, pp. 183–202, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7792-5_15\">10.1007/978-1-4939-7792-5_15</a>.","ama":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. <i>Methods in Molecular Biology</i>. 2018;1771:183-202. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7792-5_15\">10.1007/978-1-4939-7792-5_15</a>","apa":"Misun, P., Birchler, A., Lang, M., Hierlemann, A., &#38; Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. <i>Methods in Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/978-1-4939-7792-5_15\">https://doi.org/10.1007/978-1-4939-7792-5_15</a>","chicago":"Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” <i>Methods in Molecular Biology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-7792-5_15\">https://doi.org/10.1007/978-1-4939-7792-5_15</a>."},"quality_controlled":"1","publist_id":"7574","publisher":"Springer","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Methods in Molecular Biology","date_published":"2018-01-01T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"Fabrication and operation of microfluidic hanging drop networks","author":[{"full_name":"Misun, Patrick","last_name":"Misun","first_name":"Patrick"},{"full_name":"Birchler, Axel","first_name":"Axel","last_name":"Birchler"},{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","last_name":"Lang"},{"full_name":"Hierlemann, Andreas","last_name":"Hierlemann","first_name":"Andreas"},{"last_name":"Frey","first_name":"Olivier","full_name":"Frey, Olivier"}],"date_created":"2018-12-11T11:45:43Z","date_updated":"2021-01-12T07:40:42Z","abstract":[{"text":"The hanging-drop network (HDN) is a technology platform based on a completely open microfluidic network at the bottom of an inverted, surface-patterned substrate. The platform is predominantly used for the formation, culturing, and interaction of self-assembled spherical microtissues (spheroids) under precisely controlled flow conditions. Here, we describe design, fabrication, and operation of microfluidic hanging-drop networks.","lang":"eng"}],"acknowledgement":"This work was financially supported by FP7 of the EU through the project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS” (contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss National Science Foundation for Olivier Frey. The research leading to these results also received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE, ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members of the Guet and Tkačik groups, IST Austria, for valuable comments and support.","type":"journal_article","volume":1771,"ec_funded":1,"status":"public","year":"2018","language":[{"iso":"eng"}],"page":"183 - 202","doi":"10.1007/978-1-4939-7792-5_15","month":"01"},{"volume":4,"status":"public","ec_funded":1,"type":"journal_article","month":"04","year":"2018","oa":1,"file":[{"file_id":"5929","access_level":"open_access","creator":"dernst","date_created":"2019-02-06T07:36:24Z","relation":"main_file","file_name":"2018_Heliyon_DeMartino.pdf","date_updated":"2020-07-14T12:45:59Z","file_size":994490,"content_type":"application/pdf","checksum":"67010cf5e3b3e0637c659371714a715a"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"4","doi":"10.1016/j.heliyon.2018.e00596","has_accepted_license":"1","citation":{"chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” <i>Heliyon</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.heliyon.2018.e00596\">https://doi.org/10.1016/j.heliyon.2018.e00596</a>.","apa":"De Martino, A., &#38; De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. <i>Heliyon</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.heliyon.2018.e00596\">https://doi.org/10.1016/j.heliyon.2018.e00596</a>","ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. <i>Heliyon</i>. 2018;4(4). doi:<a href=\"https://doi.org/10.1016/j.heliyon.2018.e00596\">10.1016/j.heliyon.2018.e00596</a>","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” <i>Heliyon</i>, vol. 4, no. 4. Elsevier, 2018.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” <i>Heliyon</i>, vol. 4, no. 4, e00596, Elsevier, 2018, doi:<a href=\"https://doi.org/10.1016/j.heliyon.2018.e00596\">10.1016/j.heliyon.2018.e00596</a>.","ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596."},"quality_controlled":"1","ddc":["530"],"publisher":"Elsevier","scopus_import":1,"intvolume":"         4","department":[{"_id":"GaTk"}],"day":"01","_id":"306","oa_version":"Published Version","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:45:44Z","title":"An introduction to the maximum entropy approach and its application to inference problems in biology","author":[{"last_name":"De Martino","first_name":"Andrea","full_name":"De Martino, Andrea"},{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","first_name":"Daniele","orcid":"0000-0002-5214-4706"}],"date_updated":"2024-10-09T20:58:19Z","abstract":[{"lang":"eng","text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file_date_updated":"2020-07-14T12:45:59Z","publication":"Heliyon","date_published":"2018-04-01T00:00:00Z","article_number":"e00596","corr_author":"1"},{"issue":"4","doi":"10.1103/PhysRevA.97.043812","language":[{"iso":"eng"}],"oa":1,"year":"2018","arxiv":1,"isi":1,"month":"04","type":"journal_article","acknowledgement":"The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE).","status":"public","volume":97,"article_number":" 043812 ","date_published":"2018-04-09T00:00:00Z","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. "}],"main_file_link":[{"url":"https://arxiv.org/abs/1712.10127","open_access":"1"}],"date_updated":"2023-09-13T09:00:41Z","title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","author":[{"last_name":"Redchenko","first_name":"Elena","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Makarov","first_name":"Alexander","full_name":"Makarov, Alexander"},{"last_name":"Yudson","first_name":"Vladimir","full_name":"Yudson, Vladimir"}],"external_id":{"isi":["000429454000015"],"arxiv":["1712.10127"]},"date_created":"2018-12-11T11:45:44Z","oa_version":"Submitted Version","article_processing_charge":"No","_id":"307","day":"09","department":[{"_id":"JoFi"}],"intvolume":"        97","article_type":"original","scopus_import":"1","publisher":"American Physical Society","publist_id":"7572","citation":{"apa":"Redchenko, E., Makarov, A., &#38; Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.97.043812\">https://doi.org/10.1103/PhysRevA.97.043812</a>","ama":"Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2018;97(4). doi:<a href=\"https://doi.org/10.1103/PhysRevA.97.043812\">10.1103/PhysRevA.97.043812</a>","chicago":"Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevA.97.043812\">https://doi.org/10.1103/PhysRevA.97.043812</a>.","ista":"Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field.  Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812.","short":"E. Redchenko, A. Makarov, V. Yudson,  Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","mla":"Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevA.97.043812\">10.1103/PhysRevA.97.043812</a>.","ieee":"E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” <i> Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 97, no. 4. American Physical Society, 2018."},"quality_controlled":"1"},{"abstract":[{"text":"Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2018.04.002"}],"date_updated":"2024-10-22T10:12:36Z","title":"Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration","author":[{"id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","full_name":"Ratheesh, Aparna","orcid":"0000-0001-7190-0776","first_name":"Aparna","last_name":"Ratheesh"},{"full_name":"Biebl, Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Biebl"},{"full_name":"Smutny, Michael","first_name":"Michael","last_name":"Smutny"},{"first_name":"Jana","last_name":"Veselá","id":"433253EE-F248-11E8-B48F-1D18A9856A87","full_name":"Veselá, Jana"},{"first_name":"Ekaterina","last_name":"Papusheva","full_name":"Papusheva, Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila","last_name":"György","first_name":"Attila","orcid":"0000-0002-1819-198X"},{"last_name":"Casano","first_name":"Alessandra M","orcid":"0000-0002-6009-6804","full_name":"Casano, Alessandra M","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353"}],"date_created":"2018-12-11T11:45:44Z","external_id":{"pmid":["29738712"],"isi":["000432461400009"]},"project":[{"grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","date_published":"2018-05-07T00:00:00Z","publication":"Developmental Cell","publication_status":"published","pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","acknowledged_ssus":[{"_id":"SSU"}],"citation":{"chicago":"Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” <i>Developmental Cell</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.04.002\">https://doi.org/10.1016/j.devcel.2018.04.002</a>.","apa":"Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2018.04.002\">https://doi.org/10.1016/j.devcel.2018.04.002</a>","ama":"Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. <i>Developmental Cell</i>. 2018;45(3):331-346. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.04.002\">10.1016/j.devcel.2018.04.002</a>","ieee":"A. Ratheesh <i>et al.</i>, “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” <i>Developmental Cell</i>, vol. 45, no. 3. Elsevier, pp. 331–346, 2018.","short":"A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346.","mla":"Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” <i>Developmental Cell</i>, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.04.002\">10.1016/j.devcel.2018.04.002</a>.","ista":"Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346."},"quality_controlled":"1","article_processing_charge":"No","oa_version":"Published Version","_id":"308","day":"07","department":[{"_id":"DaSi"},{"_id":"CaHe"},{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"MiSi"}],"intvolume":"        45","scopus_import":"1","article_type":"original","isi":1,"month":"05","page":"331 - 346","related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/","relation":"press_release","description":"News on IST Homepage"}]},"doi":"10.1016/j.devcel.2018.04.002","issue":"3","language":[{"iso":"eng"}],"oa":1,"year":"2018","ec_funded":1,"status":"public","volume":45,"type":"journal_article"},{"day":"01","_id":"309","article_processing_charge":"No","oa_version":"Preprint","scopus_import":"1","department":[{"_id":"UlWa"}],"publisher":"ACM","publist_id":"7556","citation":{"ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA, 2018, pp. 274–292.","short":"H. Akitaya, R. Fulek, C. Tóth, in:, ACM, 2018, pp. 274–292.","mla":"Akitaya, Hugo, et al. <i>Recognizing Weak Embeddings of Graphs</i>. ACM, 2018, pp. 274–92, doi:<a href=\"https://doi.org/10.1137/1.9781611975031.20\">10.1137/1.9781611975031.20</a>.","ista":"Akitaya H, Fulek R, Tóth C. 2018. Recognizing weak embeddings of graphs. SODA: Symposium on Discrete Algorithms, 274–292.","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs,” 274–92. ACM, 2018. <a href=\"https://doi.org/10.1137/1.9781611975031.20\">https://doi.org/10.1137/1.9781611975031.20</a>.","ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. In: ACM; 2018:274-292. doi:<a href=\"https://doi.org/10.1137/1.9781611975031.20\">10.1137/1.9781611975031.20</a>","apa":"Akitaya, H., Fulek, R., &#38; Tóth, C. (2018). Recognizing weak embeddings of graphs (pp. 274–292). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA: ACM. <a href=\"https://doi.org/10.1137/1.9781611975031.20\">https://doi.org/10.1137/1.9781611975031.20</a>"},"quality_controlled":"1","date_published":"2018-01-01T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","date_updated":"2025-04-14T13:52:37Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09209"}],"abstract":[{"text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ' : G ! M of a graph G into a 2manifold M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to a common node or arc, due to data compression or low resolution. This raises the computational problem of deciding whether a given map ' : G ! M comes from an embedding. A map ' : G ! M is a weak embedding if it can be perturbed into an embedding ψ: G ! M with k' \"k < \" for every &quot; &gt; 0. A polynomial-time algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl [14], which reduces to solving a system of linear equations over Z2. It runs in O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler than [14]: We perform a sequence of local operations that gradually &quot;untangles&quot; the image '(G) into an embedding (G), or reports that ' is not a weak embedding. It generalizes a recent technique developed for the case that G is a cycle and the embedding is a simple polygon [1], and combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.","lang":"eng"}],"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"date_created":"2018-12-11T11:45:45Z","external_id":{"arxiv":["1709.09209"],"isi":["000483921200021"]},"title":"Recognizing weak embeddings of graphs","author":[{"full_name":"Akitaya, Hugo","last_name":"Akitaya","first_name":"Hugo"},{"last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Csaba","last_name":"Tóth","full_name":"Tóth, Csaba"}],"type":"conference","acknowledgement":"∗Research supported in part by the NSF awards CCF-1422311 and CCF-1423615, and the Science Without Borders program. The second author gratefully acknowledges support from Austrian Science Fund (FWF): M2281-N35.","status":"public","doi":"10.1137/1.9781611975031.20","related_material":{"record":[{"relation":"later_version","id":"6982","status":"public"}]},"conference":{"start_date":"2018-01-07","name":"SODA: Symposium on Discrete Algorithms","end_date":"2018-01-10","location":"New Orleans, LA, USA"},"page":"274 - 292","year":"2018","oa":1,"language":[{"iso":"eng"}],"isi":1,"arxiv":1,"month":"01"},{"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/243816v2.full"}],"date_updated":"2025-05-05T13:48:04Z","abstract":[{"lang":"eng","text":"Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus."}],"project":[{"name":"Human Brain Project Specific Grant Agreement 2","grant_number":"785907","call_identifier":"H2020","_id":"26436750-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Ferrari","first_name":"Ulisse","full_name":"Ferrari, Ulisse"},{"last_name":"Deny","first_name":"Stephane","full_name":"Deny, Stephane"},{"full_name":"Chalk, Matthew J","first_name":"Matthew J","last_name":"Chalk"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"full_name":"Mora, Thierry","first_name":"Thierry","last_name":"Mora"}],"title":"Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons","external_id":{"isi":["000447486100004"]},"date_created":"2018-12-11T11:44:15Z","date_published":"2018-10-17T00:00:00Z","article_number":"042410","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Physical Review E","publisher":"American Physical Society","publist_id":"8024","citation":{"ista":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410.","mla":"Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” <i>Physical Review E</i>, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.042410\">10.1103/PhysRevE.98.042410</a>.","short":"U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018).","ieee":"U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” <i>Physical Review E</i>, vol. 98, no. 4. American Physical Society, 2018.","ama":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. <i>Physical Review E</i>. 2018;98(4). doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.042410\">10.1103/PhysRevE.98.042410</a>","apa":"Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., &#38; Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.98.042410\">https://doi.org/10.1103/PhysRevE.98.042410</a>","chicago":"Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” <i>Physical Review E</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevE.98.042410\">https://doi.org/10.1103/PhysRevE.98.042410</a>."},"quality_controlled":"1","day":"17","article_processing_charge":"No","oa_version":"Preprint","_id":"31","scopus_import":"1","article_type":"original","department":[{"_id":"GaTk"}],"intvolume":"        98","isi":1,"month":"10","doi":"10.1103/PhysRevE.98.042410","issue":"4","oa":1,"year":"2018","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2470-0045"]},"ec_funded":1,"status":"public","volume":98,"type":"journal_article","acknowledgement":"This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013)."},{"year":"2018","oa":1,"language":[{"iso":"eng"}],"doi":"10.1137/1.9781611975031.151","page":"2341 - 2356","conference":{"name":"SODA: Symposium on Discrete Algorithms","location":"New Orleans, Louisiana, United States","end_date":"2018-01-10","start_date":"2018-01-07"},"month":"01","isi":1,"arxiv":1,"type":"conference","status":"public","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2018-01-01T00:00:00Z","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:45:45Z","external_id":{"arxiv":["1711.09148"],"isi":["000483921200152"]},"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvorák, Wolfgang","last_name":"Dvorák","first_name":"Wolfgang"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"title":"Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter","date_updated":"2025-04-14T13:51:04Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09148"}],"abstract":[{"lang":"eng","text":"A model of computation that is widely used in the formal analysis of reactive systems is symbolic algorithms. In this model the access to the input graph is restricted to consist of symbolic operations, which are expensive in comparison to the standard RAM operations. We give lower bounds on the number of symbolic operations for basic graph problems such as the computation of the strongly connected components and of the approximate diameter as well as for fundamental problems in model checking such as safety, liveness, and coliveness. Our lower bounds are linear in the number of vertices of the graph, even for constant-diameter graphs. For none of these problems lower bounds on the number of symbolic operations were known before. The lower bounds show an interesting separation of these problems from the reachability problem, which can be solved with O(D) symbolic operations, where D is the diameter of the graph. Additionally we present an approximation algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve a (1 +ϵ)-approximation for any constant &gt; 0. This compares to O(n/D) symbolic steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation. Finally we also give a refined analysis of the strongly connected components algorithms of [15], showing that it uses an optimal number of symbolic steps that is proportional to the sum of the diameters of the strongly connected components."}],"scopus_import":"1","department":[{"_id":"KrCh"}],"day":"01","_id":"310","article_processing_charge":"No","oa_version":"Preprint","citation":{"apa":"Chatterjee, K., Dvorák, W., Henzinger, M., &#38; Loitzenbauer, V. (2018). Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. <a href=\"https://doi.org/10.1137/1.9781611975031.151\">https://doi.org/10.1137/1.9781611975031.151</a>","ama":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. In: ACM; 2018:2341-2356. doi:<a href=\"https://doi.org/10.1137/1.9781611975031.151\">10.1137/1.9781611975031.151</a>","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Veronika Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. <a href=\"https://doi.org/10.1137/1.9781611975031.151\">https://doi.org/10.1137/1.9781611975031.151</a>.","ista":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. 2018. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.","mla":"Chatterjee, Krishnendu, et al. <i>Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter</i>. ACM, 2018, pp. 2341–56, doi:<a href=\"https://doi.org/10.1137/1.9781611975031.151\">10.1137/1.9781611975031.151</a>.","short":"K. Chatterjee, W. Dvorák, M. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356.","ieee":"K. Chatterjee, W. Dvorák, M. Henzinger, and V. Loitzenbauer, “Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States, 2018, pp. 2341–2356."},"quality_controlled":"1","publisher":"ACM","publist_id":"7555"},{"day":"25","_id":"314","article_processing_charge":"No","oa_version":"Published Version","scopus_import":"1","article_type":"letter_note","intvolume":"         6","department":[{"_id":"AnKi"}],"publisher":"Cell Press","publist_id":"7551","citation":{"ista":"Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402.","ieee":"G. Bauer <i>et al.</i>, “The science of living matter for tomorrow,” <i>Cell Systems</i>, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","mla":"Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” <i>Cell Systems</i>, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:<a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">10.1016/j.cels.2018.04.003</a>.","short":"G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402.","ama":"Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. <i>Cell Systems</i>. 2018;6(4):400-402. doi:<a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">10.1016/j.cels.2018.04.003</a>","apa":"Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">https://doi.org/10.1016/j.cels.2018.04.003</a>","chicago":"Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” <i>Cell Systems</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">https://doi.org/10.1016/j.cels.2018.04.003</a>."},"quality_controlled":"1","date_published":"2018-04-25T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"publication_status":"published","publication":"Cell Systems","date_updated":"2023-09-19T10:11:25Z","main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2018.04.003","open_access":"1"}],"abstract":[{"lang":"eng","text":"The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations."}],"date_created":"2018-12-11T11:45:46Z","external_id":{"isi":["000432192100003"],"pmid":["29698645"]},"title":"The science of living matter for tomorrow","author":[{"full_name":"Bauer, Guntram","last_name":"Bauer","first_name":"Guntram"},{"last_name":"Fakhri","first_name":"Nikta","full_name":"Fakhri, Nikta"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva"},{"full_name":"Kondev, Jané","first_name":"Jané","last_name":"Kondev"},{"full_name":"Kruse, Karsten","last_name":"Kruse","first_name":"Karsten"},{"full_name":"Noji, Hiroyuki","first_name":"Hiroyuki","last_name":"Noji"},{"full_name":"Riveline, Daniel","first_name":"Daniel","last_name":"Riveline"},{"first_name":"Timothy","last_name":"Saunders","full_name":"Saunders, Timothy"},{"last_name":"Thatta","first_name":"Mukund","full_name":"Thatta, Mukund"},{"last_name":"Wieschaus","first_name":"Eric","full_name":"Wieschaus, Eric"}],"type":"journal_article","publication_identifier":{"eissn":["2405-4712"]},"status":"public","volume":6,"issue":"4","doi":"10.1016/j.cels.2018.04.003","page":"400 - 402","year":"2018","oa":1,"language":[{"iso":"eng"}],"isi":1,"month":"04"},{"volume":16,"status":"public","publication_identifier":{"issn":["1544-9173"]},"type":"journal_article","month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"file_name":"2017_PLOS_Polechova.pdf","date_updated":"2020-07-14T12:46:01Z","file_size":6968201,"content_type":"application/pdf","checksum":"908c52751bba30c55ed36789e5e4c84d","relation":"main_file","date_created":"2019-01-22T08:30:03Z","creator":"dernst","access_level":"open_access","file_id":"5870"}],"oa":1,"year":"2018","related_material":{"record":[{"status":"public","id":"9839","relation":"research_data"}]},"has_accepted_license":"1","doi":"10.1371/journal.pbio.2005372","issue":"6","ddc":["576"],"citation":{"ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” <i>PLoS Biology</i>, vol. 16, no. 6. Public Library of Science, 2018.","short":"J. Polechova, PLoS Biology 16 (2018).","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” <i>PLoS Biology</i>, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005372\">10.1371/journal.pbio.2005372</a>.","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” <i>PLoS Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005372\">https://doi.org/10.1371/journal.pbio.2005372</a>.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. <i>PLoS Biology</i>. 2018;16(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005372\">10.1371/journal.pbio.2005372</a>","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005372\">https://doi.org/10.1371/journal.pbio.2005372</a>"},"quality_controlled":"1","publisher":"Public Library of Science","publist_id":"7550","department":[{"_id":"NiBa"}],"intvolume":"        16","scopus_import":"1","oa_version":"Published Version","article_processing_charge":"No","_id":"315","day":"15","title":"Is the sky the limit? On the expansion threshold of a species’ range","author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112"}],"date_created":"2018-12-11T11:45:46Z","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"date_updated":"2025-07-10T11:52:27Z","file_date_updated":"2020-07-14T12:46:01Z","publication":"PLoS Biology","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e2005372","date_published":"2018-06-15T00:00:00Z"},{"type":"journal_article","volume":209,"status":"public","ec_funded":1,"year":"2018","oa":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.300748","issue":"3","page":"861-883","related_material":{"record":[{"relation":"research_data","status":"public","id":"9813"}],"link":[{"url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","relation":"press_release","description":"News on IST Homepage"}]},"month":"07","isi":1,"article_type":"original","scopus_import":"1","intvolume":"       209","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"day":"01","_id":"316","article_processing_charge":"No","oa_version":"Preprint","quality_controlled":"1","citation":{"mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” <i>Genetics</i>, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:<a href=\"https://doi.org/10.1534/genetics.118.300748\">10.1534/genetics.118.300748</a>.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” <i>Genetics</i>, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.300748\">https://doi.org/10.1534/genetics.118.300748</a>.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.300748\">https://doi.org/10.1534/genetics.118.300748</a>","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. <i>Genetics</i>. 2018;209(3):861-883. doi:<a href=\"https://doi.org/10.1534/genetics.118.300748\">10.1534/genetics.118.300748</a>"},"publisher":"Genetics Society of America","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","publication":"Genetics","date_published":"2018-07-01T00:00:00Z","project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"date_created":"2018-12-11T11:45:47Z","external_id":{"isi":["000437171700017"]},"author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bodova, Katarina","orcid":"0000-0002-7214-0171","last_name":"Bodova","first_name":"Katarina"},{"last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","first_name":"Melinda"}],"title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","date_updated":"2025-04-15T06:50:00Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/node/80098.abstract"}],"abstract":[{"text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants.","lang":"eng"}]},{"type":"journal_article","volume":8,"pubrep_id":"1016","status":"public","file":[{"creator":"system","access_level":"open_access","file_id":"5256","date_updated":"2020-07-14T12:46:02Z","file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf","file_size":1850530,"checksum":"20af238ca4ba6491b77270be8d826bf5","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:17:04Z"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","oa":1,"doi":"10.1038/s41598-018-24004-y","issue":"1","has_accepted_license":"1","month":"04","isi":1,"intvolume":"         8","department":[{"_id":"GeKa"}],"scopus_import":"1","_id":"317","article_processing_charge":"No","oa_version":"Published Version","day":"09","ddc":["539"],"citation":{"ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018.","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” <i>Scientific Reports</i>, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-24004-y\">10.1038/s41598-018-24004-y</a>.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018).","ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-24004-y\">https://doi.org/10.1038/s41598-018-24004-y</a>.","ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-24004-y\">10.1038/s41598-018-24004-y</a>","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., &#38; Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-24004-y\">https://doi.org/10.1038/s41598-018-24004-y</a>"},"quality_controlled":"1","publisher":"Nature Publishing Group","publist_id":"7548","publication":"Scientific Reports","file_date_updated":"2020-07-14T12:46:02Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","article_number":"5690","corr_author":"1","date_published":"2018-04-09T00:00:00Z","external_id":{"isi":["000429404300013"]},"date_created":"2018-12-11T11:45:47Z","title":"Palladium gates for reproducible quantum dots in silicon","author":[{"last_name":"Brauns","first_name":"Matthias","full_name":"Brauns, Matthias","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amitonov, Sergey","first_name":"Sergey","last_name":"Amitonov"},{"full_name":"Spruijtenburg, Paul","first_name":"Paul","last_name":"Spruijtenburg"},{"first_name":"Floris","last_name":"Zwanenburg","full_name":"Zwanenburg, Floris"}],"abstract":[{"lang":"eng","text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack."}],"date_updated":"2024-10-09T20:58:34Z"},{"date_created":"2018-12-11T11:45:47Z","external_id":{"pmid":["29486189"],"isi":["000426150700002"]},"title":"A fat lot of good for wound healing","author":[{"id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","full_name":"Casano, Alessandra M","orcid":"0000-0002-6009-6804","last_name":"Casano","first_name":"Alessandra M"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"date_updated":"2024-10-09T20:58:17Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29486189","open_access":"1"}],"abstract":[{"text":"The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"publication_status":"published","publication":"Developmental Cell","date_published":"2018-02-26T00:00:00Z","corr_author":"1","citation":{"ieee":"A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” <i>Developmental Cell</i>, vol. 44, no. 4. Cell Press, pp. 405–406, 2018.","short":"A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406.","mla":"Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.” <i>Developmental Cell</i>, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">10.1016/j.devcel.2018.02.009</a>.","ista":"Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental Cell. 44(4), 405–406.","chicago":"Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound Healing.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">https://doi.org/10.1016/j.devcel.2018.02.009</a>.","ama":"Casano AM, Sixt MK. A fat lot of good for wound healing. <i>Developmental Cell</i>. 2018;44(4):405-406. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">10.1016/j.devcel.2018.02.009</a>","apa":"Casano, A. M., &#38; Sixt, M. K. (2018). A fat lot of good for wound healing. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">https://doi.org/10.1016/j.devcel.2018.02.009</a>"},"quality_controlled":"1","publist_id":"7547","publisher":"Cell Press","scopus_import":"1","intvolume":"        44","department":[{"_id":"MiSi"}],"day":"26","_id":"318","article_processing_charge":"No","oa_version":"Published Version","month":"02","isi":1,"year":"2018","oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2018.02.009","issue":"4","page":"405 - 406","volume":44,"status":"public","acknowledgement":"Short Survey","type":"journal_article"},{"file":[{"relation":"main_file","date_created":"2018-12-17T12:42:57Z","date_updated":"2020-07-14T12:46:03Z","file_name":"2018_CellReports_Chen.pdf","content_type":"application/pdf","checksum":"d9f74277fd57176e04732707d575cf08","file_size":4461997,"file_id":"5703","creator":"dernst","access_level":"open_access"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"year":"2018","oa":1,"issue":"4","doi":"10.1016/j.celrep.2018.09.066","page":"852 - 861.e7","has_accepted_license":"1","month":"10","isi":1,"acknowledgement":"This work was supported by Deutsche Forschungsgemeinschaft (DFG) grant KU2569/1-1 (to M.K.); DFG project EXC307Centre for Integrative Neuroscience (CIN), including grant Pool Project 2011-12 (jointly to M.K. and I.E.); and the Charitable Hertie Foundation (to I.E.). CIN is an Excellence Cluster funded by the DFG within the framework of the Excellence Initiative for 2008–2018. M.K. is supported by the Tistou & Charlotte Kerstan Foundation.","type":"journal_article","volume":25,"status":"public","publication":"Cell Reports","file_date_updated":"2020-07-14T12:46:03Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","date_published":"2018-10-23T00:00:00Z","external_id":{"isi":["000448219500005"]},"date_created":"2018-12-11T11:44:16Z","title":"In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2","author":[{"full_name":"Chen, Ting","first_name":"Ting","last_name":"Chen"},{"full_name":"Kula, Bartosz","first_name":"Bartosz","last_name":"Kula"},{"last_name":"Nagy","first_name":"Balint","orcid":"0000-0002-4002-4686","full_name":"Nagy, Balint","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2"},{"last_name":"Barzan","first_name":"Ruxandra","full_name":"Barzan, Ruxandra"},{"last_name":"Gall","first_name":"Andrea","full_name":"Gall, Andrea"},{"full_name":"Ehrlich, Ingrid","first_name":"Ingrid","last_name":"Ehrlich"},{"last_name":"Kukley","first_name":"Maria","full_name":"Kukley, Maria"}],"abstract":[{"lang":"eng","text":"The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in vivo during the peak of myelination by targeting the GluA2 subunit. Expression of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered proliferation of OPCs and reduced their differentiation into oligodendrocytes. Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit (C-tail), a modification designed to affect the interaction between GluA2 and AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs, decreased the differentiation of OPCs without affecting their proliferation. These findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs, as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in the mouse corpus callosum, are important for balancing the response of OPCs to proliferation and differentiation cues. In the brain, oligodendrocyte precursor cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC synapses alters proliferation and differentiation of OPCs. This expands the traditional view of synaptic transmission by suggesting neurons also use synapses to modulate behavior of glia."}],"date_updated":"2023-09-11T14:13:32Z","intvolume":"        25","department":[{"_id":"SaSi"}],"scopus_import":"1","_id":"32","article_processing_charge":"No","oa_version":"Published Version","day":"23","ddc":["570"],"citation":{"chicago":"Chen, Ting, Bartosz Kula, Balint Nagy, Ruxandra Barzan, Andrea Gall, Ingrid Ehrlich, and Maria Kukley. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” <i>Cell Reports</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">https://doi.org/10.1016/j.celrep.2018.09.066</a>.","ama":"Chen T, Kula B, Nagy B, et al. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. <i>Cell Reports</i>. 2018;25(4):852-861.e7. doi:<a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">10.1016/j.celrep.2018.09.066</a>","apa":"Chen, T., Kula, B., Nagy, B., Barzan, R., Gall, A., Ehrlich, I., &#38; Kukley, M. (2018). In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">https://doi.org/10.1016/j.celrep.2018.09.066</a>","ieee":"T. Chen <i>et al.</i>, “In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2,” <i>Cell Reports</i>, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018.","short":"T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell Reports 25 (2018) 852–861.e7.","mla":"Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” <i>Cell Reports</i>, vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:<a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">10.1016/j.celrep.2018.09.066</a>.","ista":"Chen T, Kula B, Nagy B, Barzan R, Gall A, Ehrlich I, Kukley M. 2018. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. 25(4), 852–861.e7."},"quality_controlled":"1","publisher":"Elsevier","publist_id":"8023"},{"month":"04","isi":1,"file":[{"file_id":"5690","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2018-12-17T10:37:50Z","checksum":"76070f3729f9c603e1080d0151aa2b11","content_type":"application/pdf","file_size":3180444,"file_name":"2018_Neuron_Hu.pdf","date_updated":"2020-07-14T12:46:03Z"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","oa":1,"issue":"1","doi":"10.1016/j.neuron.2018.02.024","has_accepted_license":"1","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/"}]},"page":"156 - 165","volume":98,"status":"public","ec_funded":1,"type":"journal_article","external_id":{"isi":["000429192100016"]},"date_created":"2018-12-11T11:45:48Z","title":"Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons","author":[{"full_name":"Hu, Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua","last_name":"Hu"},{"first_name":"Fabian","last_name":"Roth","full_name":"Roth, Fabian"},{"orcid":"0000-0001-7577-1676","first_name":"David H","last_name":"Vandael","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"project":[{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"},{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses"},{"call_identifier":"FWF","grant_number":"Z00312","name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. "}],"date_updated":"2025-04-15T08:29:04Z","file_date_updated":"2020-07-14T12:46:03Z","publication":"Neuron","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","corr_author":"1","date_published":"2018-04-04T00:00:00Z","ddc":["570"],"quality_controlled":"1","citation":{"apa":"Hu, H., Roth, F., Vandael, D. H., &#38; Jonas, P. M. (2018). Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">https://doi.org/10.1016/j.neuron.2018.02.024</a>","ama":"Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. <i>Neuron</i>. 2018;98(1):156-165. doi:<a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">10.1016/j.neuron.2018.02.024</a>","chicago":"Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” <i>Neuron</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">https://doi.org/10.1016/j.neuron.2018.02.024</a>.","ista":"Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 98(1), 156–165.","ieee":"H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons,” <i>Neuron</i>, vol. 98, no. 1. Elsevier, pp. 156–165, 2018.","short":"H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.","mla":"Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” <i>Neuron</i>, vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:<a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">10.1016/j.neuron.2018.02.024</a>."},"publisher":"Elsevier","publist_id":"7545","intvolume":"        98","department":[{"_id":"PeJo"}],"scopus_import":"1","_id":"320","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","day":"04"},{"page":"1029 - 1031","has_accepted_license":"1","issue":"5","doi":"10.1109/TPAMI.2018.2804998","file":[{"creator":"dernst","access_level":"open_access","file_id":"7835","checksum":"b19c75da06faf3291a3ca47dfa50ef63","file_size":141724,"content_type":"application/pdf","file_name":"2018_IEEE_Darrell.pdf","date_updated":"2020-07-14T12:46:03Z","relation":"main_file","date_created":"2020-05-14T12:50:48Z"}],"language":[{"iso":"eng"}],"oa":1,"year":"2018","isi":1,"month":"05","type":"journal_article","status":"public","volume":40,"corr_author":"1","date_published":"2018-05-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:03Z","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The twelve papers in this special section focus on learning systems with shared information for computer vision and multimedia communication analysis. In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes containing a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with shared information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different levels of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems.","lang":"eng"}],"date_updated":"2024-10-09T20:58:26Z","title":"Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis","author":[{"full_name":"Darrell, Trevor","last_name":"Darrell","first_name":"Trevor"},{"first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"last_name":"Sebe","first_name":"Nico","full_name":"Sebe, Nico"},{"last_name":"Wu","first_name":"Ying","full_name":"Wu, Ying"},{"full_name":"Yan, Yan","last_name":"Yan","first_name":"Yan"}],"date_created":"2018-12-11T11:45:48Z","external_id":{"isi":["000428901200001"]},"oa_version":"Published Version","article_processing_charge":"No","_id":"321","day":"01","department":[{"_id":"ChLa"}],"intvolume":"        40","article_type":"original","scopus_import":"1","publist_id":"7544","publisher":"IEEE","ddc":["000"],"citation":{"ista":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. 2018. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(5), 1029–1031.","mla":"Darrell, Trevor, et al. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 5, IEEE, 2018, pp. 1029–31, doi:<a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">10.1109/TPAMI.2018.2804998</a>.","short":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, Y. Yan, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1029–1031.","ieee":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, and Y. Yan, “Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 5. IEEE, pp. 1029–1031, 2018.","ama":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2018;40(5):1029-1031. doi:<a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">10.1109/TPAMI.2018.2804998</a>","apa":"Darrell, T., Lampert, C., Sebe, N., Wu, Y., &#38; Yan, Y. (2018). Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">https://doi.org/10.1109/TPAMI.2018.2804998</a>","chicago":"Darrell, Trevor, Christoph Lampert, Nico Sebe, Ying Wu, and Yan Yan. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">https://doi.org/10.1109/TPAMI.2018.2804998</a>."},"quality_controlled":"1"},{"main_file_link":[{"url":"https://arxiv.org/abs/1412.7211","open_access":"1"}],"date_updated":"2025-04-14T09:12:46Z","abstract":[{"lang":"eng","text":"We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework."}],"project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","call_identifier":"FP7"}],"author":[{"full_name":"Ganev, Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87","first_name":"Iordan V","last_name":"Ganev"}],"title":"Quantizations of multiplicative hypertoric varieties at a root of unity","date_created":"2018-12-11T11:45:49Z","external_id":{"isi":["000433270600005"],"arxiv":["1412.7211"]},"date_published":"2018-07-15T00:00:00Z","corr_author":"1","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Journal of Algebra","publisher":"World Scientific Publishing","publist_id":"7543","quality_controlled":"1","citation":{"ieee":"I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root of unity,” <i>Journal of Algebra</i>, vol. 506. World Scientific Publishing, pp. 92–128, 2018.","short":"I.V. Ganev, Journal of Algebra 506 (2018) 92–128.","mla":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” <i>Journal of Algebra</i>, vol. 506, World Scientific Publishing, 2018, pp. 92–128, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">10.1016/j.jalgebra.2018.03.015</a>.","ista":"Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 506, 92–128.","chicago":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” <i>Journal of Algebra</i>. World Scientific Publishing, 2018. <a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">https://doi.org/10.1016/j.jalgebra.2018.03.015</a>.","apa":"Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at a root of unity. <i>Journal of Algebra</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">https://doi.org/10.1016/j.jalgebra.2018.03.015</a>","ama":"Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of unity. <i>Journal of Algebra</i>. 2018;506:92-128. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">10.1016/j.jalgebra.2018.03.015</a>"},"day":"15","oa_version":"Preprint","article_processing_charge":"No","_id":"322","scopus_import":"1","department":[{"_id":"TaHa"}],"intvolume":"       506","arxiv":1,"isi":1,"month":"07","page":"92 - 128","doi":"10.1016/j.jalgebra.2018.03.015","oa":1,"year":"2018","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","volume":506,"type":"journal_article","acknowledgement":"National Science Foundation: Graduate Research Fellowship and grant No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project and providing guidance throughout, particularly for the formulation of Frobenius quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and constant encouragement, and for suggesting the term ‘hypertoric quantum group.’ Many results appearing in the current paper were proven independently by Nicholas Cooney; the author is grateful to Nicholas for sharing his insight on various topics, including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating the definition of multiplicative hypertoric varieties, as well as the content of Remark 2.14. The author also benefited immensely from the close reading and detailed comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_number":"34","date_published":"2018-01-01T00:00:00Z","external_id":{"arxiv":["1709.04037"]},"date_created":"2018-12-11T11:45:50Z","title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","author":[{"full_name":"Agrawal, Sheshansh","last_name":"Agrawal","first_name":"Sheshansh"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novotny","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr"}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"abstract":[{"text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach.","lang":"eng"}],"date_updated":"2024-10-21T06:02:40Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.04037"}],"intvolume":"         2","department":[{"_id":"KrCh"}],"scopus_import":"1","_id":"325","oa_version":"Preprint","day":"01","citation":{"ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:<a href=\"https://doi.org/10.1145/3158122\">10.1145/3158122</a>","apa":"Agrawal, S., Chatterjee, K., &#38; Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. <a href=\"https://doi.org/10.1145/3158122\">https://doi.org/10.1145/3158122</a>","chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. <a href=\"https://doi.org/10.1145/3158122\">https://doi.org/10.1145/3158122</a>.","ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","mla":"Agrawal, Sheshansh, et al. <i>Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs</i>. Vol. 2, no. POPL, 34, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3158122\">10.1145/3158122</a>.","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL."},"quality_controlled":"1","publisher":"ACM","publist_id":"7540","language":[{"iso":"eng"}],"year":"2018","oa":1,"doi":"10.1145/3158122","issue":"POPL","conference":{"start_date":"2018-01-07","name":"POPL: Principles of Programming Languages","location":"Los Angeles, CA, USA","end_date":"2018-01-13"},"month":"01","arxiv":1,"type":"conference","volume":2,"status":"public"},{"day":"07","article_processing_charge":"No","oa_version":"Published Version","_id":"326","scopus_import":"1","department":[{"_id":"RySh"}],"intvolume":"        47","acknowledged_ssus":[{"_id":"EM-Fac"}],"publist_id":"7539","publisher":"Wiley","citation":{"short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” <i>European Journal of Neuroscience</i>, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:<a href=\"https://doi.org/10.1111/ejn.13901\">10.1111/ejn.13901</a>.","ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” <i>European Journal of Neuroscience</i>, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018.","ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” <i>European Journal of Neuroscience</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/ejn.13901\">https://doi.org/10.1111/ejn.13901</a>.","apa":"Sawada, K., Kawakami, R., Shigemoto, R., &#38; Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. <i>European Journal of Neuroscience</i>. Wiley. <a href=\"https://doi.org/10.1111/ejn.13901\">https://doi.org/10.1111/ejn.13901</a>","ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. <i>European Journal of Neuroscience</i>. 2018;47(9):1033-1042. doi:<a href=\"https://doi.org/10.1111/ejn.13901\">10.1111/ejn.13901</a>"},"quality_controlled":"1","ddc":["570"],"date_published":"2018-03-07T00:00:00Z","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"European Journal of Neuroscience","file_date_updated":"2020-07-14T12:46:06Z","date_updated":"2023-09-19T09:58:40Z","abstract":[{"lang":"eng","text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites."}],"author":[{"first_name":"Kazuaki","last_name":"Sawada","full_name":"Sawada, Kazuaki"},{"first_name":"Ryosuke","last_name":"Kawakami","full_name":"Kawakami, Ryosuke"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi"},{"full_name":"Nemoto, Tomomi","last_name":"Nemoto","first_name":"Tomomi"}],"title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","external_id":{"isi":["000431496400001"]},"date_created":"2018-12-11T11:45:50Z","type":"journal_article","status":"public","volume":47,"has_accepted_license":"1","page":"1033 - 1042","doi":"10.1111/ejn.13901","issue":"9","oa":1,"year":"2018","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"file":[{"file_id":"5721","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2018-12-17T16:16:50Z","file_name":"2018_EJN_Sawada.pdf","date_updated":"2020-07-14T12:46:06Z","checksum":"98e901d8229e44aa8f3b51d248dedd09","content_type":"application/pdf","file_size":4850261}],"language":[{"iso":"eng"}],"isi":1,"month":"03"},{"oa_version":"Preprint","article_processing_charge":"No","_id":"327","day":"19","department":[{"_id":"MaSe"}],"intvolume":"        97","scopus_import":"1","publisher":"American Physical Society","publist_id":"7538","citation":{"ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307.","ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” <i>Physical Review B</i>, vol. 97, no. 10. American Physical Society, 2018.","mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” <i>Physical Review B</i>, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">10.1103/PhysRevB.97.104307</a>.","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., &#38; Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">https://doi.org/10.1103/PhysRevB.97.104307</a>","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. <i>Physical Review B</i>. 2018;97(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">10.1103/PhysRevB.97.104307</a>","chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">https://doi.org/10.1103/PhysRevB.97.104307</a>."},"quality_controlled":"1","article_number":"104307","date_published":"2018-03-19T00:00:00Z","publication":"Physical Review B","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations."}],"main_file_link":[{"url":"https://arxiv.org/abs/1706.05026","open_access":"1"}],"date_updated":"2025-06-04T07:50:22Z","title":"Slow dynamics in translation-invariant quantum lattice models","author":[{"first_name":"Alexios","last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Žnidarič","first_name":"Marko","full_name":"Žnidarič, Marko"},{"first_name":"Mariya","last_name":"Medvedyeva","full_name":"Medvedyeva, Mariya"},{"full_name":"Abanin, Dmitry","first_name":"Dmitry","last_name":"Abanin"},{"last_name":"Prosen","first_name":"Tomaž","full_name":"Prosen, Tomaž"},{"full_name":"Papić, Zlatko","first_name":"Zlatko","last_name":"Papić"}],"external_id":{"isi":["000427798800005"],"arxiv":["1706.05026"]},"date_created":"2018-12-11T11:45:50Z","type":"journal_article","acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","status":"public","volume":97,"doi":"10.1103/PhysRevB.97.104307","issue":"10","language":[{"iso":"eng"}],"oa":1,"year":"2018","arxiv":1,"isi":1,"month":"03"},{"month":"03","arxiv":1,"isi":1,"language":[{"iso":"eng"}],"oa":1,"year":"2018","issue":"12","doi":"10.1103/PhysRevLett.120.124501","volume":120,"ec_funded":1,"status":"public","acknowledgement":"The authors thank Philipp Maier and the IST Austria workshop for their dedicated technical support.","type":"journal_article","author":[{"first_name":"George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H"},{"first_name":"Jose M","last_name":"Lopez Alonso","orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"title":"Exceeding the asymptotic limit of polymer drag reduction","date_created":"2018-12-11T11:45:51Z","external_id":{"isi":["000427804000005"],"arxiv":["1703.06271"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"The drag of turbulent flows can be drastically decreased by adding small amounts of high molecular weight polymers. While drag reduction initially increases with polymer concentration, it eventually saturates to what is known as the maximum drag reduction (MDR) asymptote; this asymptote is generally attributed to the dynamics being reduced to a marginal yet persistent state of subdued turbulent motion. Contrary to this accepted view, we show that, for an appropriate choice of parameters, polymers can reduce the drag beyond the suggested asymptotic limit, eliminating turbulence and giving way to laminar flow. At higher polymer concentrations, however, the laminar state becomes unstable, resulting in a fluctuating flow with the characteristic drag of the MDR asymptote. Our findings indicate that the asymptotic state is hence dynamically disconnected from ordinary turbulence. © 2018 American Physical Society."}],"main_file_link":[{"url":"https://arxiv.org/abs/1703.06271","open_access":"1"}],"date_updated":"2025-06-04T07:52:00Z","publication":"Physical Review Letters","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","corr_author":"1","article_number":"124501","date_published":"2018-03-19T00:00:00Z","citation":{"ista":"Choueiri GH, Lopez Alonso JM, Hof B. 2018. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 120(12), 124501.","mla":"Choueiri, George H., et al. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” <i>Physical Review Letters</i>, vol. 120, no. 12, 124501, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">10.1103/PhysRevLett.120.124501</a>.","short":"G.H. Choueiri, J.M. Lopez Alonso, B. Hof, Physical Review Letters 120 (2018).","ieee":"G. H. Choueiri, J. M. Lopez Alonso, and B. Hof, “Exceeding the asymptotic limit of polymer drag reduction,” <i>Physical Review Letters</i>, vol. 120, no. 12. American Physical Society, 2018.","ama":"Choueiri GH, Lopez Alonso JM, Hof B. Exceeding the asymptotic limit of polymer drag reduction. <i>Physical Review Letters</i>. 2018;120(12). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">10.1103/PhysRevLett.120.124501</a>","apa":"Choueiri, G. H., Lopez Alonso, J. M., &#38; Hof, B. (2018). Exceeding the asymptotic limit of polymer drag reduction. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">https://doi.org/10.1103/PhysRevLett.120.124501</a>","chicago":"Choueiri, George H, Jose M Lopez Alonso, and Björn Hof. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">https://doi.org/10.1103/PhysRevLett.120.124501</a>."},"quality_controlled":"1","publist_id":"7537","publisher":"American Physical Society","acknowledged_ssus":[{"_id":"SSU"}],"department":[{"_id":"BjHo"}],"intvolume":"       120","scopus_import":"1","article_processing_charge":"No","oa_version":"Preprint","_id":"328","day":"19"}]