[{"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"06","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1710.02741"],"isi":["000466130000009"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00454-018-0035-8","file_date_updated":"2020-07-14T12:47:14Z","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2019","volume":61,"date_updated":"2023-09-07T13:17:36Z","date_created":"2019-02-14T11:54:08Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"683"},{"id":"7944","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Lubiw, Anna","first_name":"Anna","last_name":"Lubiw"},{"full_name":"Masárová, Zuzana","first_name":"Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","page":"880-898","article_type":"original","citation":{"short":"A. Lubiw, Z. Masárová, U. Wagner, Discrete & Computational Geometry 61 (2019) 880–898.","mla":"Lubiw, Anna, et al. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” Discrete & Computational Geometry, vol. 61, no. 4, Springer Nature, 2019, pp. 880–98, doi:10.1007/s00454-018-0035-8.","chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” Discrete & Computational Geometry. Springer Nature, 2019. https://doi.org/10.1007/s00454-018-0035-8.","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete & Computational Geometry. 2019;61(4):880-898. doi:10.1007/s00454-018-0035-8","apa":"Lubiw, A., Masárová, Z., & Wagner, U. (2019). A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-018-0035-8","ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge-labelled triangulations,” Discrete & Computational Geometry, vol. 61, no. 4. Springer Nature, pp. 880–898, 2019.","ista":"Lubiw A, Masárová Z, Wagner U. 2019. A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete & Computational Geometry. 61(4), 880–898."},"publication":"Discrete & Computational Geometry","date_published":"2019-06-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm (with 𝑂(𝑛8) being a crude bound on the run-time) to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of 𝑂(𝑛7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture."}],"intvolume":" 61","ddc":["000"],"title":"A proof of the orbit conjecture for flipping edge-labelled triangulations","status":"public","_id":"5986","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"e1bff88f1d77001b53b78c485ce048d7","date_updated":"2020-07-14T12:47:14Z","date_created":"2019-02-14T11:57:22Z","relation":"main_file","file_id":"5988","content_type":"application/pdf","file_size":556276,"creator":"dernst","access_level":"open_access","file_name":"2018_DiscreteGeometry_Lubiw.pdf"}],"oa_version":"Published Version"},{"file_date_updated":"2020-07-14T12:47:13Z","ec_funded":1,"author":[{"full_name":"Li, Xiang","first_name":"Xiang","last_name":"Li","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","first_name":"Giacomo","full_name":"Bighin, Giacomo"},{"full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"related_material":{"record":[{"id":"8958","relation":"dissertation_contains","status":"public"}]},"date_created":"2019-01-27T22:59:10Z","date_updated":"2023-09-07T13:16:42Z","year":"2019","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"Taylor and Francis","month":"01","publication_identifier":{"issn":["00268976"]},"doi":"10.1080/00268976.2019.1567852","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000474641400008"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Problems involving quantum impurities, in which one or a few particles are interacting with a macroscopic environment, represent a pervasive paradigm, spanning across atomic, molecular, and condensed-matter physics. In this paper we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron–a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon–a quasiparticle formed out of a rotating molecule in a bosonic bath. We benchmark these approaches against established theories, evaluating their accuracy as a function of the impurity-bath coupling.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":1309966,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_MolecularPhysics_Li.pdf","checksum":"178964744b636a6f036372f4f090a657","date_created":"2019-01-29T08:32:57Z","date_updated":"2020-07-14T12:47:13Z","file_id":"5896","relation":"main_file"}],"_id":"5886","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon","ddc":["530"],"day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-01-18T00:00:00Z","publication":"Molecular Physics","citation":{"chicago":"Li, Xiang, Giacomo Bighin, Enderalp Yakaboylu, and Mikhail Lemeshko. “Variational Approaches to Quantum Impurities: From the Fröhlich Polaron to the Angulon.” Molecular Physics. Taylor and Francis, 2019. https://doi.org/10.1080/00268976.2019.1567852.","short":"X. Li, G. Bighin, E. Yakaboylu, M. Lemeshko, Molecular Physics (2019).","mla":"Li, Xiang, et al. “Variational Approaches to Quantum Impurities: From the Fröhlich Polaron to the Angulon.” Molecular Physics, Taylor and Francis, 2019, doi:10.1080/00268976.2019.1567852.","apa":"Li, X., Bighin, G., Yakaboylu, E., & Lemeshko, M. (2019). Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics. Taylor and Francis. https://doi.org/10.1080/00268976.2019.1567852","ieee":"X. Li, G. Bighin, E. Yakaboylu, and M. Lemeshko, “Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon,” Molecular Physics. Taylor and Francis, 2019.","ista":"Li X, Bighin G, Yakaboylu E, Lemeshko M. 2019. Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics.","ama":"Li X, Bighin G, Yakaboylu E, Lemeshko M. Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics. 2019. doi:10.1080/00268976.2019.1567852"}},{"year":"2019","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"first_name":"Kristóf","last_name":"Huszár","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057","full_name":"Huszár, Kristóf"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8032"}]},"date_created":"2019-06-11T20:09:57Z","date_updated":"2023-09-07T13:18:26Z","volume":129,"file_date_updated":"2020-07-14T12:47:33Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1812.05528"]},"oa":1,"quality_controlled":"1","conference":{"start_date":"2019-06-18","location":"Portland, Oregon, United States","end_date":"2019-06-21","name":"SoCG: Symposium on Computational Geometry"},"doi":"10.4230/LIPIcs.SoCG.2019.44","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-104-7"]},"_id":"6556","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"3-manifold triangulations with small treewidth","status":"public","ddc":["516"],"intvolume":" 129","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":905885,"access_level":"open_access","file_name":"2019_LIPIcs-Huszar.pdf","checksum":"29d18c435368468aa85823dabb157e43","date_created":"2019-06-12T06:45:33Z","date_updated":"2020-07-14T12:47:33Z","file_id":"6557","relation":"main_file"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Motivated by fixed-parameter tractable (FPT) problems in computational topology, we consider the treewidth tw(M) of a compact, connected 3-manifold M, defined to be the minimum treewidth of the face pairing graph of any triangulation T of M. In this setting the relationship between the topology of a 3-manifold and its treewidth is of particular interest. First, as a corollary of work of Jaco and Rubinstein, we prove that for any closed, orientable 3-manifold M the treewidth tw(M) is at most 4g(M)-2, where g(M) denotes Heegaard genus of M. In combination with our earlier work with Wagner, this yields that for non-Haken manifolds the Heegaard genus and the treewidth are within a constant factor. Second, we characterize all 3-manifolds of treewidth one: These are precisely the lens spaces and a single other Seifert fibered space. Furthermore, we show that all remaining orientable Seifert fibered spaces over the 2-sphere or a non-orientable surface have treewidth two. In particular, for every spherical 3-manifold we exhibit a triangulation of treewidth at most two. Our results further validate the parameter of treewidth (and other related parameters such as cutwidth or congestion) to be useful for topological computing, and also shed more light on the scope of existing FPT-algorithms in the field."}],"publication":"35th International Symposium on Computational Geometry","citation":{"mla":"Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small Treewidth.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20, doi:10.4230/LIPIcs.SoCG.2019.44.","short":"K. Huszár, J. Spreer, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20.","chicago":"Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small Treewidth.” In 35th International Symposium on Computational Geometry, 129:44:1-44:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPIcs.SoCG.2019.44.","ama":"Huszár K, Spreer J. 3-manifold triangulations with small treewidth. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:44:1-44:20. doi:10.4230/LIPIcs.SoCG.2019.44","ista":"Huszár K, Spreer J. 2019. 3-manifold triangulations with small treewidth. 35th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 44:1-44:20.","apa":"Huszár, K., & Spreer, J. (2019). 3-manifold triangulations with small treewidth. In 35th International Symposium on Computational Geometry (Vol. 129, p. 44:1-44:20). Portland, Oregon, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2019.44","ieee":"K. Huszár and J. Spreer, “3-manifold triangulations with small treewidth,” in 35th International Symposium on Computational Geometry, Portland, Oregon, United States, 2019, vol. 129, p. 44:1-44:20."},"page":"44:1-44:20","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","keyword":["computational 3-manifold topology","fixed-parameter tractability","layered triangulations","structural graph theory","treewidth","cutwidth","Heegaard genus"],"day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"month":"11","publication_identifier":{"issn":["1920-180X"]},"language":[{"iso":"eng"}],"doi":"10.20382/JOGC.V10I2A5","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1712.00434"]},"oa":1,"file_date_updated":"2020-07-14T12:47:49Z","date_updated":"2023-09-07T13:18:26Z","date_created":"2019-11-23T12:14:09Z","volume":10,"author":[{"last_name":"Huszár","first_name":"Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87","full_name":"Huszár, Kristóf"},{"full_name":"Spreer, Jonathan","first_name":"Jonathan","last_name":"Spreer"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"285"},{"relation":"part_of_dissertation","status":"public","id":"8032"}]},"publication_status":"published","publisher":"Computational Geometry Laborartoy","department":[{"_id":"UlWa"}],"year":"2019","day":"01","has_accepted_license":"1","article_processing_charge":"No","date_published":"2019-11-01T00:00:00Z","article_type":"original","page":"70–98","publication":"Journal of Computational Geometry","citation":{"chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry. Computational Geometry Laborartoy, 2019. https://doi.org/10.20382/JOGC.V10I2A5.","short":"K. Huszár, J. Spreer, U. Wagner, Journal of Computational Geometry 10 (2019) 70–98.","mla":"Huszár, Kristóf, et al. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry, vol. 10, no. 2, Computational Geometry Laborartoy, 2019, pp. 70–98, doi:10.20382/JOGC.V10I2A5.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” Journal of Computational Geometry, vol. 10, no. 2. Computational Geometry Laborartoy, pp. 70–98, 2019.","apa":"Huszár, K., Spreer, J., & Wagner, U. (2019). On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. Computational Geometry Laborartoy. https://doi.org/10.20382/JOGC.V10I2A5","ista":"Huszár K, Spreer J, Wagner U. 2019. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 10(2), 70–98.","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 2019;10(2):70–98. doi:10.20382/JOGC.V10I2A5"},"abstract":[{"text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how \"simple\" or \"thin\" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth.\r\nIn view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs).\r\nWe derive these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann, Schultens and Saito by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 18(k+1) (resp. 4(3k+1)).","lang":"eng"}],"issue":"2","type":"journal_article","file":[{"date_created":"2019-11-23T12:35:16Z","date_updated":"2020-07-14T12:47:49Z","checksum":"c872d590d38d538404782bca20c4c3f5","file_id":"7094","relation":"main_file","creator":"khuszar","file_size":857590,"content_type":"application/pdf","file_name":"479-1917-1-PB.pdf","access_level":"open_access"}],"oa_version":"Published Version","ddc":["514"],"title":"On the treewidth of triangulated 3-manifolds","status":"public","intvolume":" 10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7093"},{"date_published":"2019-12-17T00:00:00Z","citation":{"ama":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 2019;10. doi:10.1038/s41467-019-13702-4","ista":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744.","apa":"Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur, N. B., Brugués, J., & Loose, M. (2019). Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13702-4","ieee":"P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur, J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA,” Nature Communications, vol. 10. Springer Nature, 2019.","mla":"Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications, vol. 10, 5744, Springer Nature, 2019, doi:10.1038/s41467-019-13702-4.","short":"P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur, J. Brugués, M. Loose, Nature Communications 10 (2019).","chicago":"Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce, Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13702-4."},"publication":"Nature Communications","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2019_NatureComm_Caldas.pdf","access_level":"open_access","creator":"dernst","file_size":8488733,"content_type":"application/pdf","file_id":"7208","relation":"main_file","date_updated":"2020-07-14T12:47:53Z","date_created":"2019-12-23T07:34:56Z","checksum":"a1b44b427ba341383197790d0e8789fa"}],"_id":"7197","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 10","status":"public","title":"Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA","ddc":["570"],"abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner.","lang":"eng"}],"type":"journal_article","doi":"10.1038/s41467-019-13702-4","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000503009300001"]},"project":[{"call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["2041-1723"]},"month":"12","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8358"}]},"author":[{"full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","first_name":"Paulo R"},{"first_name":"Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Pelegrin, Maria D"},{"last_name":"Pearce","first_name":"Daniel J. G.","full_name":"Pearce, Daniel J. G."},{"orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B","full_name":"Budanur, Nazmi B"},{"last_name":"Brugués","first_name":"Jan","full_name":"Brugués, Jan"},{"full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"volume":10,"date_created":"2019-12-20T12:22:57Z","date_updated":"2023-09-07T13:18:51Z","year":"2019","department":[{"_id":"MaLo"},{"_id":"BjHo"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:53Z","article_number":"5744"},{"month":"04","publication_identifier":{"issn":["2399-3642"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"external_id":{"isi":["000465425700006"],"pmid":["31044163"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s42003-019-0373-y","article_number":"138","file_date_updated":"2020-07-14T12:47:53Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"}],"year":"2019","pmid":1,"date_created":"2019-12-23T13:36:50Z","date_updated":"2023-09-07T13:19:22Z","volume":2,"author":[{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"related_material":{"record":[{"id":"7196","relation":"part_of_dissertation","status":"public"}]},"scopus_import":"1","day":"23","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Communications Biology","citation":{"ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Population structure determines the tradeoff between fixation probability and fixation time,” Communications Biology, vol. 2. Springer Nature, 2019.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2019). Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0373-y","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2019. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2, 138.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2019;2. doi:10.1038/s42003-019-0373-y","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0373-y.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Communications Biology 2 (2019).","mla":"Tkadlec, Josef, et al. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” Communications Biology, vol. 2, 138, Springer Nature, 2019, doi:10.1038/s42003-019-0373-y."},"date_published":"2019-04-23T00:00:00Z","type":"journal_article","abstract":[{"text":"The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these amplifiers of natural selection typically increase fixation time. Here we study population structures that achieve a tradeoff between fixation probability and time. First, we show that no amplifiers can have an asymptotically lower absorption time than the well-mixed population. Then we design population structures that substantially augment the fixation probability with just a minor increase in fixation time. Finally, we show that those structures enable higher effective rate of evolution than the well-mixed population provided that the rate of generating advantageous mutants is relatively low. Our work sheds light on how population structure affects the rate of evolution. Moreover, our structures could be useful for lab-based, medical, or industrial applications of evolutionary optimization.","lang":"eng"}],"ddc":["000"],"status":"public","title":"Population structure determines the tradeoff between fixation probability and fixation time","intvolume":" 2","_id":"7210","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"content_type":"application/pdf","file_size":1670274,"creator":"dernst","file_name":"2019_CommBio_Tkadlec.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:53Z","date_created":"2019-12-23T13:39:30Z","checksum":"d1a69bfe73767e4246f0a38e4e1554dd","relation":"main_file","file_id":"7211"}],"oa_version":"Published Version"},{"doi":"10.1145/3360550","conference":{"end_date":"2019-10-25","start_date":"2019-10-23","location":"Athens, Greece","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.1145/3360550"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1909.00989"]},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"}],"quality_controlled":"1","publication_identifier":{"eissn":["2475-1421"]},"month":"10","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10199"}]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Toman","first_name":"Viktor","orcid":"0000-0001-9036-063X","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","full_name":"Toman, Viktor"}],"volume":3,"date_created":"2021-10-27T14:57:06Z","date_updated":"2023-09-07T13:30:27Z","acknowledgement":"The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n","year":"2019","publisher":"ACM","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication_status":"published","file_date_updated":"2021-11-12T11:41:56Z","article_number":"124","date_published":"2019-10-10T00:00:00Z","citation":{"ista":"Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 124.","apa":"Chatterjee, K., Pavlogiannis, A., & Toman, V. (2019). Value-centric dynamic partial order reduction. In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360550","ieee":"K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Athens, Greece, 2019, vol. 3.","ama":"Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. Vol 3. ACM; 2019. doi:10.1145/3360550","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Vol. 3. ACM, 2019. https://doi.org/10.1145/3360550.","mla":"Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, vol. 3, 124, ACM, 2019, doi:10.1145/3360550.","short":"K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019."},"publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications","has_accepted_license":"1","article_processing_charge":"No","day":"10","keyword":["safety","risk","reliability and quality","software"],"file":[{"relation":"main_file","file_id":"10278","checksum":"2149979c46964c4d117af06ccb6c0834","success":1,"date_created":"2021-11-12T11:41:56Z","date_updated":"2021-11-12T11:41:56Z","access_level":"open_access","file_name":"2019_ACM_Chatterjee.pdf","content_type":"application/pdf","file_size":570829,"creator":"cchlebak"}],"oa_version":"Published Version","_id":"10190","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 3","title":"Value-centric dynamic partial order reduction","ddc":["000"],"status":"public","abstract":[{"lang":"eng","text":"The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning."}],"type":"conference"},{"page":"145-154","citation":{"short":"D.-A. Alistarh, G. Nadiradze, N. Koval, in:, 31st ACM Symposium on Parallelism in Algorithms and Architectures, ACM Press, 2019, pp. 145–154.","mla":"Alistarh, Dan-Adrian, et al. “Efficiency Guarantees for Parallel Incremental Algorithms under Relaxed Schedulers.” 31st ACM Symposium on Parallelism in Algorithms and Architectures, ACM Press, 2019, pp. 145–54, doi:10.1145/3323165.3323201.","chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Nikita Koval. “Efficiency Guarantees for Parallel Incremental Algorithms under Relaxed Schedulers.” In 31st ACM Symposium on Parallelism in Algorithms and Architectures, 145–54. ACM Press, 2019. https://doi.org/10.1145/3323165.3323201.","ama":"Alistarh D-A, Nadiradze G, Koval N. Efficiency guarantees for parallel incremental algorithms under relaxed schedulers. In: 31st ACM Symposium on Parallelism in Algorithms and Architectures. ACM Press; 2019:145-154. doi:10.1145/3323165.3323201","ieee":"D.-A. Alistarh, G. Nadiradze, and N. Koval, “Efficiency guarantees for parallel incremental algorithms under relaxed schedulers,” in 31st ACM Symposium on Parallelism in Algorithms and Architectures, Phoenix, AZ, United States, 2019, pp. 145–154.","apa":"Alistarh, D.-A., Nadiradze, G., & Koval, N. (2019). Efficiency guarantees for parallel incremental algorithms under relaxed schedulers. In 31st ACM Symposium on Parallelism in Algorithms and Architectures (pp. 145–154). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3323165.3323201","ista":"Alistarh D-A, Nadiradze G, Koval N. 2019. Efficiency guarantees for parallel incremental algorithms under relaxed schedulers. 31st ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 145–154."},"publication":"31st ACM Symposium on Parallelism in Algorithms and Architectures","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","status":"public","title":"Efficiency guarantees for parallel incremental algorithms under relaxed schedulers","_id":"6673","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"Several classic problems in graph processing and computational geometry are solved via incremental algorithms, which split computation into a series of small tasks acting on shared state, which gets updated progressively. While the sequential variant of such algorithms usually specifies a fixed (but sometimes random) order in which the tasks should be performed, a standard approach to parallelizing such algorithms is to relax this constraint to allow for out-of-order parallel execution. This is the case for parallel implementations of Dijkstra's single-source shortest-paths (SSSP) algorithm, and for parallel Delaunay mesh triangulation. While many software frameworks parallelize incremental computation in this way, it is still not well understood whether this relaxed ordering approach can still provide any complexity guarantees. In this paper, we address this problem, and analyze the efficiency guarantees provided by a range of incremental algorithms when parallelized via relaxed schedulers. We show that, for algorithms such as Delaunay mesh triangulation and sorting by insertion, schedulers with a maximum relaxation factor of k in terms of the maximum priority inversion allowed will introduce a maximum amount of wasted work of O(łog n poly(k)), where n is the number of tasks to be executed. For SSSP, we show that the additional work is O(poly(k), dmax / wmin), where dmax is the maximum distance between two nodes, and wmin is the minimum such distance. In practical settings where n >> k, this suggests that the overheads of relaxation will be outweighed by the improved scalability of the relaxed scheduler. On the negative side, we provide lower bounds showing that certain algorithms will inherently incur a non-trivial amount of wasted work due to scheduler relaxation, even for relatively benign relaxed schedulers."}],"project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2003.09363","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2003.09363"],"isi":["000507618500018"]},"language":[{"iso":"eng"}],"doi":"10.1145/3323165.3323201","conference":{"start_date":"2019-06-22","location":"Phoenix, AZ, United States","end_date":"2019-06-24","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"publication_identifier":{"isbn":["9781450361842"]},"month":"06","publisher":"ACM Press","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2019","date_updated":"2023-09-07T13:31:39Z","date_created":"2019-07-24T08:59:36Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10429"}]},"author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi","orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","first_name":"Nikita"}],"ec_funded":1},{"article_processing_charge":"No","has_accepted_license":"1","day":"03","scopus_import":"1","date_published":"2019-07-03T00:00:00Z","page":"1035-1050","article_type":"original","citation":{"ista":"Erdem FA, Ilic M, Koppensteiner P, Gołacki J, Lubec G, Freissmuth M, Sandtner W. 2019. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 151(8), 1035–1050.","apa":"Erdem, F. A., Ilic, M., Koppensteiner, P., Gołacki, J., Lubec, G., Freissmuth, M., & Sandtner, W. (2019). A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. Rockefeller University Press. https://doi.org/10.1085/jgp.201912318","ieee":"F. A. Erdem et al., “A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2,” The Journal of General Physiology, vol. 151, no. 8. Rockefeller University Press, pp. 1035–1050, 2019.","ama":"Erdem FA, Ilic M, Koppensteiner P, et al. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 2019;151(8):1035-1050. doi:10.1085/jgp.201912318","chicago":"Erdem, Fatma Asli, Marija Ilic, Peter Koppensteiner, Jakub Gołacki, Gert Lubec, Michael Freissmuth, and Walter Sandtner. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology. Rockefeller University Press, 2019. https://doi.org/10.1085/jgp.201912318.","mla":"Erdem, Fatma Asli, et al. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology, vol. 151, no. 8, Rockefeller University Press, 2019, pp. 1035–50, doi:10.1085/jgp.201912318.","short":"F.A. Erdem, M. Ilic, P. Koppensteiner, J. Gołacki, G. Lubec, M. Freissmuth, W. Sandtner, The Journal of General Physiology 151 (2019) 1035–1050."},"publication":"The Journal of General Physiology","issue":"8","abstract":[{"lang":"eng","text":"Transporters of the solute carrier 6 (SLC6) family translocate their cognate substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4). Here, we posited that the transport cycle of individual SLC6 transporters reflects the physiological requirements they operate under. We tested this hypothesis by analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions in real time by electrophysiological recordings. Contrary to monoamine transporters, both GlyTs were found to have a high transport capacity driven by rapid return of the empty transporter after release of Cl− on the intracellular side. Rapid cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate ions and substrate such that their forward transport mode was maintained even under conditions of elevated intracellular Na+ or Cl−. The most important differences in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1 were governed by transition of the substrate-bound transporter from outward- to inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+ binding (or a related conformational change). Kinetic modeling showed that the kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels required for NMDA receptor activation."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2019_JGP_Erdem.pdf","access_level":"open_access","file_size":2641297,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7450","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-05T07:20:32Z","checksum":"5706b4ccd74ee3e50bf7ecb2a203df71"}],"intvolume":" 151","ddc":["570"],"status":"public","title":"A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7398","publication_identifier":{"eissn":["1540-7748"],"issn":["0022-1295"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1085/jgp.201912318","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"external_id":{"isi":["000478792500008"],"pmid":["31270129"]},"oa":1,"file_date_updated":"2020-07-14T12:47:57Z","volume":151,"date_created":"2020-01-29T16:06:29Z","date_updated":"2023-09-07T14:52:23Z","author":[{"full_name":"Erdem, Fatma Asli","first_name":"Fatma Asli","last_name":"Erdem"},{"first_name":"Marija","last_name":"Ilic","full_name":"Ilic, Marija"},{"full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter"},{"full_name":"Gołacki, Jakub","last_name":"Gołacki","first_name":"Jakub"},{"full_name":"Lubec, Gert","first_name":"Gert","last_name":"Lubec"},{"last_name":"Freissmuth","first_name":"Michael","full_name":"Freissmuth, Michael"},{"full_name":"Sandtner, Walter","first_name":"Walter","last_name":"Sandtner"}],"department":[{"_id":"RySh"}],"publisher":"Rockefeller University Press","publication_status":"published","pmid":1,"year":"2019"},{"month":"09","publication_identifier":{"issn":["1097-2765"]},"doi":"10.1016/j.molcel.2019.07.022","language":[{"iso":"eng"}],"external_id":{"isi":["000486614200006"],"pmid":["31492636"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes","call_identifier":"H2020","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309"}],"file_date_updated":"2020-07-14T12:47:57Z","ec_funded":1,"author":[{"last_name":"Letts","first_name":"James A","orcid":"0000-0002-9864-3586","id":"322DA418-F248-11E8-B48F-1D18A9856A87","full_name":"Letts, James A"},{"id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol","last_name":"Fiedorczuk","full_name":"Fiedorczuk, Karol"},{"first_name":"Gianluca","last_name":"Degliesposti","full_name":"Degliesposti, Gianluca"},{"full_name":"Skehel, Mark","first_name":"Mark","last_name":"Skehel"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"date_updated":"2023-09-07T14:53:06Z","date_created":"2020-01-29T16:02:33Z","volume":75,"year":"2019","pmid":1,"publication_status":"published","publisher":"Cell Press","department":[{"_id":"LeSa"}],"day":"19","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-09-19T00:00:00Z","publication":"Molecular Cell","citation":{"ama":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 2019;75(6):1131-1146.e6. doi:10.1016/j.molcel.2019.07.022","apa":"Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., & Sazanov, L. A. (2019). Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2019.07.022","ieee":"J. A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, and L. A. Sazanov, “Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk,” Molecular Cell, vol. 75, no. 6. Cell Press, p. 1131–1146.e6, 2019.","ista":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. 2019. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 75(6), 1131–1146.e6.","short":"J.A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, L.A. Sazanov, Molecular Cell 75 (2019) 1131–1146.e6.","mla":"Letts, James A., et al. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell, vol. 75, no. 6, Cell Press, 2019, p. 1131–1146.e6, doi:10.1016/j.molcel.2019.07.022.","chicago":"Letts, James A, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, and Leonid A Sazanov. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell. Cell Press, 2019. https://doi.org/10.1016/j.molcel.2019.07.022."},"article_type":"original","page":"1131-1146.e6","abstract":[{"lang":"eng","text":"The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII2. CI shows a transition between “closed” and “open” conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII2, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs."}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":9654895,"file_name":"2019_MolecularCell_Letts.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T10:37:28Z","checksum":"5202f53a237d6650ece038fbf13bdcea","file_id":"7447","relation":"main_file"}],"_id":"7395","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk","intvolume":" 75"},{"title":"NetPyNE, a tool for data-driven multiscale modeling of brain circuits","ddc":["570"],"status":"public","intvolume":" 8","_id":"7405","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"7014189c11c10a12feeeae37f054871d","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T08:41:47Z","relation":"main_file","file_id":"7444","file_size":6182359,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_eLife_DuraBernal.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena.","lang":"eng"}],"article_type":"original","publication":"eLife","citation":{"ama":"Dura-Bernal S, Suter B, Gleeson P, et al. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 2019;8. doi:10.7554/elife.44494","ista":"Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. 2019. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 8, e44494.","apa":"Dura-Bernal, S., Suter, B., Gleeson, P., Cantarelli, M., Quintana, A., Rodriguez, F., … Lytton, W. W. (2019). NetPyNE, a tool for data-driven multiscale modeling of brain circuits. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.44494","ieee":"S. Dura-Bernal et al., “NetPyNE, a tool for data-driven multiscale modeling of brain circuits,” eLife, vol. 8. eLife Sciences Publications, 2019.","mla":"Dura-Bernal, Salvador, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” ELife, vol. 8, e44494, eLife Sciences Publications, 2019, doi:10.7554/elife.44494.","short":"S. Dura-Bernal, B. Suter, P. Gleeson, M. Cantarelli, A. Quintana, F. Rodriguez, D.J. Kedziora, G.L. Chadderdon, C.C. Kerr, S.A. Neymotin, R.A. McDougal, M. Hines, G.M. Shepherd, W.W. Lytton, ELife 8 (2019).","chicago":"Dura-Bernal, Salvador, Benjamin Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.44494."},"date_published":"2019-05-31T00:00:00Z","scopus_import":"1","day":"31","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"eLife Sciences Publications","year":"2019","pmid":1,"date_updated":"2023-09-07T14:27:52Z","date_created":"2020-01-30T09:08:01Z","volume":8,"author":[{"full_name":"Dura-Bernal, Salvador","last_name":"Dura-Bernal","first_name":"Salvador"},{"last_name":"Suter","first_name":"Benjamin","orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","full_name":"Suter, Benjamin"},{"first_name":"Padraig","last_name":"Gleeson","full_name":"Gleeson, Padraig"},{"first_name":"Matteo","last_name":"Cantarelli","full_name":"Cantarelli, Matteo"},{"first_name":"Adrian","last_name":"Quintana","full_name":"Quintana, Adrian"},{"last_name":"Rodriguez","first_name":"Facundo","full_name":"Rodriguez, Facundo"},{"full_name":"Kedziora, David J","first_name":"David J","last_name":"Kedziora"},{"full_name":"Chadderdon, George L","first_name":"George L","last_name":"Chadderdon"},{"first_name":"Cliff C","last_name":"Kerr","full_name":"Kerr, Cliff C"},{"full_name":"Neymotin, Samuel A","first_name":"Samuel A","last_name":"Neymotin"},{"last_name":"McDougal","first_name":"Robert A","full_name":"McDougal, Robert A"},{"full_name":"Hines, Michael","last_name":"Hines","first_name":"Michael"},{"full_name":"Shepherd, Gordon MG","last_name":"Shepherd","first_name":"Gordon MG"},{"last_name":"Lytton","first_name":"William W","full_name":"Lytton, William W"}],"article_number":"e44494","file_date_updated":"2020-07-14T12:47:57Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31025934"],"isi":["000468968400001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/elife.44494","month":"05","publication_identifier":{"issn":["2050-084X"]}},{"oa_version":"Published Version","_id":"7400","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 212","status":"public","title":"Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua","issue":"3","abstract":[{"text":"Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination.","lang":"eng"}],"type":"journal_article","date_published":"2019-07-01T00:00:00Z","citation":{"mla":"Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” Genetics, vol. 212, no. 3, Genetics Society of America, 2019, pp. 815–35, doi:10.1534/genetics.119.302045.","short":"P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O. Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov, J.R. Pannell, Genetics 212 (2019) 815–835.","chicago":"Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez, Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” Genetics. Genetics Society of America, 2019. https://doi.org/10.1534/genetics.119.302045.","ama":"Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 2019;212(3):815-835. doi:10.1534/genetics.119.302045","ista":"Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 212(3), 815–835.","ieee":"P. Veltsos et al., “Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua,” Genetics, vol. 212, no. 3. Genetics Society of America, pp. 815–835, 2019.","apa":"Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle, A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.119.302045"},"publication":"Genetics","page":"815-835","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"first_name":"Paris","last_name":"Veltsos","full_name":"Veltsos, Paris"},{"last_name":"Ridout","first_name":"Kate E.","full_name":"Ridout, Kate E."},{"full_name":"Toups, Melissa A","first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380"},{"full_name":"González-Martínez, Santiago C.","last_name":"González-Martínez","first_name":"Santiago C."},{"full_name":"Muyle, Aline","last_name":"Muyle","first_name":"Aline"},{"full_name":"Emery, Olivier","first_name":"Olivier","last_name":"Emery"},{"first_name":"Pasi","last_name":"Rastas","full_name":"Rastas, Pasi"},{"last_name":"Hudzieczek","first_name":"Vojtech","full_name":"Hudzieczek, Vojtech"},{"first_name":"Roman","last_name":"Hobza","full_name":"Hobza, Roman"},{"last_name":"Vyskot","first_name":"Boris","full_name":"Vyskot, Boris"},{"last_name":"Marais","first_name":"Gabriel A. B.","full_name":"Marais, Gabriel A. B."},{"last_name":"Filatov","first_name":"Dmitry A.","full_name":"Filatov, Dmitry A."},{"full_name":"Pannell, John R.","first_name":"John R.","last_name":"Pannell"}],"volume":212,"date_updated":"2023-09-07T14:49:29Z","date_created":"2020-01-29T16:15:44Z","pmid":1,"year":"2019","publisher":"Genetics Society of America","department":[{"_id":"BeVi"}],"publication_status":"published","ec_funded":1,"doi":"10.1534/genetics.119.302045","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1534/genetics.119.302045","open_access":"1"}],"oa":1,"external_id":{"pmid":["31113811"],"isi":["000474809300015"]},"project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1943-2631"],"issn":["0016-6731"]},"month":"07"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation."}],"issue":"7","status":"public","title":"Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo","intvolume":" 146","_id":"7404","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","scopus_import":"1","day":"04","article_processing_charge":"No","article_type":"original","publication":"Development","citation":{"chicago":"Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.171397.","mla":"Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” Development, vol. 146, no. 7, dev171397, The Company of Biologists, 2019, doi:10.1242/dev.171397.","short":"T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang, M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019).","ista":"Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397.","ieee":"T. Stürner et al., “Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo,” Development, vol. 146, no. 7. The Company of Biologists, 2019.","apa":"Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang, Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. The Company of Biologists. https://doi.org/10.1242/dev.171397","ama":"Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 2019;146(7). doi:10.1242/dev.171397"},"date_published":"2019-04-04T00:00:00Z","article_number":"dev171397","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"The Company of Biologists","year":"2019","pmid":1,"date_created":"2020-01-29T16:27:10Z","date_updated":"2023-09-07T14:47:00Z","volume":146,"author":[{"full_name":"Stürner, Tomke","first_name":"Tomke","last_name":"Stürner"},{"full_name":"Tatarnikova, Anastasia","last_name":"Tatarnikova","first_name":"Anastasia"},{"full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","last_name":"Müller","first_name":"Jan"},{"full_name":"Schaffran, Barbara","first_name":"Barbara","last_name":"Schaffran"},{"full_name":"Cuntz, Hermann","first_name":"Hermann","last_name":"Cuntz"},{"full_name":"Zhang, Yun","last_name":"Zhang","first_name":"Yun"},{"full_name":"Nemethova, Maria","last_name":"Nemethova","first_name":"Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bogdan, Sven","last_name":"Bogdan","first_name":"Sven"},{"first_name":"Vic","last_name":"Small","full_name":"Small, Vic"},{"first_name":"Gaia","last_name":"Tavosanis","full_name":"Tavosanis, Gaia"}],"month":"04","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"isi":1,"quality_controlled":"1","external_id":{"pmid":["30910826"],"isi":["000464583200006"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.171397"}],"language":[{"iso":"eng"}],"doi":"10.1242/dev.171397"},{"oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7402","status":"public","title":"Graph planning with expected finite horizon","abstract":[{"lang":"eng","text":"Graph planning gives rise to fundamental algorithmic questions such as shortest path, traveling salesman problem, etc. A classical problem in discrete planning is to consider a weighted graph and construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary, to represent the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time. Consequently, our polynomial-time algorithm for adversarial stopping time also computes an optimal plan among all possible plans."}],"type":"conference","date_published":"2019-06-01T00:00:00Z","citation":{"ista":"Chatterjee K, Doyen L. 2019. Graph planning with expected finite horizon. 34th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.","apa":"Chatterjee, K., & Doyen, L. (2019). Graph planning with expected finite horizon. In 34th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/lics.2019.8785706","ieee":"K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” in 34th Annual ACM/IEEE Symposium on Logic in Computer Science, Vancouver, BC, Canada, 2019, pp. 1–13.","ama":"Chatterjee K, Doyen L. Graph planning with expected finite horizon. In: 34th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2019:1-13. doi:10.1109/lics.2019.8785706","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” In 34th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. IEEE, 2019. https://doi.org/10.1109/lics.2019.8785706.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13, doi:10.1109/lics.2019.8785706.","short":"K. Chatterjee, L. Doyen, in:, 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13."},"publication":"34th Annual ACM/IEEE Symposium on Logic in Computer Science","page":"1-13","article_processing_charge":"No","day":"01","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"later_version","id":"11402"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"}],"date_created":"2020-01-29T16:18:33Z","date_updated":"2023-09-07T14:48:11Z","year":"2019","publisher":"IEEE","department":[{"_id":"KrCh"}],"publication_status":"published","doi":"10.1109/lics.2019.8785706","conference":{"name":"LICS: Symposium on Logic in Computer Science","end_date":"2019-06-27","start_date":"2019-06-24","location":"Vancouver, BC, Canada"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.03642"}],"external_id":{"arxiv":["1802.03642"],"isi":["000805002800001"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"isbn":["9781728136080"]},"month":"06"},{"file_date_updated":"2020-07-14T12:47:58Z","article_number":"150","author":[{"full_name":"Vukics, A.","first_name":"A.","last_name":"Vukics"},{"full_name":"Dombi, A.","first_name":"A.","last_name":"Dombi"},{"full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"},{"full_name":"Domokos, P.","first_name":"P.","last_name":"Domokos"}],"volume":3,"date_created":"2020-02-05T09:57:57Z","date_updated":"2023-09-07T14:57:39Z","year":"2019","department":[{"_id":"JoFi"}],"publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","publication_status":"published","publication_identifier":{"issn":["2521-327X"]},"month":"06","doi":"10.22331/q-2019-06-03-150","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000469987500004"],"arxiv":["1809.09737"]},"isi":1,"quality_controlled":"1","abstract":[{"text":"We prove that the observable telegraph signal accompanying the bistability in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings model is the finite-size precursor of what in the thermodynamic limit is a genuine first-order phase transition. We construct a finite-size scaling of the system parameters to a well-defined thermodynamic limit, in which the system remains the same microscopic system, but the telegraph signal becomes macroscopic both in its timescale and intensity. The existence of such a finite-size scaling completes and justifies the classification of the photon-blockade-breakdown effect as a first-order dissipative quantum phase transition.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"7483","relation":"main_file","checksum":"26b9ba8f0155d183f1ee55295934a17f","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-11T09:25:23Z","access_level":"open_access","file_name":"2019_Quantum_Vukics.pdf","creator":"dernst","content_type":"application/pdf","file_size":5805248}],"_id":"7451","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 3","status":"public","title":"Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition","ddc":["530"],"has_accepted_license":"1","article_processing_charge":"No","day":"03","date_published":"2019-06-03T00:00:00Z","citation":{"mla":"Vukics, A., et al. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum, vol. 3, 150, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019, doi:10.22331/q-2019-06-03-150.","short":"A. Vukics, A. Dombi, J.M. Fink, P. Domokos, Quantum 3 (2019).","chicago":"Vukics, A., A. Dombi, Johannes M Fink, and P. Domokos. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019. https://doi.org/10.22331/q-2019-06-03-150.","ama":"Vukics A, Dombi A, Fink JM, Domokos P. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 2019;3. doi:10.22331/q-2019-06-03-150","ista":"Vukics A, Dombi A, Fink JM, Domokos P. 2019. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 3, 150.","apa":"Vukics, A., Dombi, A., Fink, J. M., & Domokos, P. (2019). Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 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The method optimizes a Lagrangean relaxation of the original energy minimization problem using a multi plane block-coordinate Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean decomposition. We show empirically that our method outperforms state-of-the-art Lagrangean decomposition based algorithms on some challenging Markov Random Field, multi-label discrete tomography and graph matching problems.","lang":"eng"}],"type":"conference","oa_version":"Preprint","title":"Map inference via block-coordinate Frank-Wolfe algorithm","status":"public","_id":"7468","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","citation":{"ama":"Swoboda P, Kolmogorov V. Map inference via block-coordinate Frank-Wolfe algorithm. 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Phuong and C. Lampert, “Distillation-based training for multi-exit architectures,” in IEEE International Conference on Computer Vision, Seoul, Korea, 2019, vol. 2019–October, pp. 1355–1364.","apa":"Phuong, M., & Lampert, C. (2019). Distillation-based training for multi-exit architectures. In IEEE International Conference on Computer Vision (Vol. 2019–October, pp. 1355–1364). Seoul, Korea: IEEE. https://doi.org/10.1109/ICCV.2019.00144","ista":"Phuong M, Lampert C. 2019. Distillation-based training for multi-exit architectures. IEEE International Conference on Computer Vision. ICCV: International Conference on Computer Vision vol. 2019–October, 1355–1364.","ama":"Phuong M, Lampert C. Distillation-based training for multi-exit architectures. In: IEEE International Conference on Computer Vision. Vol 2019-October. IEEE; 2019:1355-1364. doi:10.1109/ICCV.2019.00144","chicago":"Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” In IEEE International Conference on Computer Vision, 2019–October:1355–64. IEEE, 2019. https://doi.org/10.1109/ICCV.2019.00144.","short":"M. Phuong, C. Lampert, in:, IEEE International Conference on Computer Vision, IEEE, 2019, pp. 1355–1364.","mla":"Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” IEEE International Conference on Computer Vision, vol. 2019–October, IEEE, 2019, pp. 1355–64, doi:10.1109/ICCV.2019.00144."},"publication":"IEEE International Conference on Computer Vision","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:47:59Z","date_created":"2020-02-11T09:06:39Z","checksum":"7b77fb5c2d27c4c37a7612ba46a66117","file_id":"7480","relation":"main_file","creator":"bphuong","file_size":735768,"content_type":"application/pdf","file_name":"main.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","ddc":["000"],"status":"public","title":"Distillation-based training for multi-exit architectures","_id":"7479","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Multi-exit architectures, in which a stack of processing layers is interleaved with early output layers, allow the processing of a test example to stop early and thus save computation time and/or energy. In this work, we propose a new training procedure for multi-exit architectures based on the principle of knowledge distillation. The method encourage searly exits to mimic later, more accurate exits, by matching their output probabilities.\r\nExperiments on CIFAR100 and ImageNet show that distillation-based training significantly improves the accuracy of early exits while maintaining state-of-the-art accuracy for late ones. The method is particularly beneficial when training data is limited and it allows a straightforward extension to semi-supervised learning,i.e. making use of unlabeled data at training time. Moreover, it takes only afew lines to implement and incurs almost no computational overhead at training time, and none at all at test time."}],"type":"conference"},{"type":"conference","abstract":[{"lang":"eng","text":"We present a novel class of convolutional neural networks (CNNs) for set functions,i.e., data indexed with the powerset of a finite set. The convolutions are derivedas linear, shift-equivariant functions for various notions of shifts on set functions.The framework is fundamentally different from graph convolutions based on theLaplacian, as it provides not one but several basic shifts, one for each element inthe ground set. Prototypical experiments with several set function classificationtasks on synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate the potential of our new powerset CNNs."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7542","title":"Powerset convolutional neural networks","status":"public","intvolume":" 32","oa_version":"Published Version","day":"01","article_processing_charge":"No","citation":{"ieee":"C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural networks,” presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.","apa":"Wendler, C., Alistarh, D.-A., & Püschel, M. (2019). Powerset convolutional neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada: Neural Information Processing Systems Foundation.","ista":"Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks. NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938.","ama":"Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks. In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.","chicago":"Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation, 2019.","short":"C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing Systems Foundation, 2019, pp. 927–938.","mla":"Wendler, Chris, et al. Powerset Convolutional Neural Networks. Vol. 32, Neural Information Processing Systems Foundation, 2019, pp. 927–38."},"page":"927-938","date_published":"2019-12-01T00:00:00Z","ec_funded":1,"year":"2019","publication_status":"published","publisher":"Neural Information Processing Systems Foundation","department":[{"_id":"DaAl"}],"author":[{"first_name":"Chris","last_name":"Wendler","full_name":"Wendler, Chris"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Püschel, Markus","first_name":"Markus","last_name":"Püschel"}],"date_created":"2020-02-28T10:03:24Z","date_updated":"2023-09-08T11:13:52Z","volume":32,"month":"12","publication_identifier":{"issn":["1049-5258"]},"external_id":{"arxiv":["1909.02253"],"isi":["000534424300084"]},"oa":1,"main_file_link":[{"url":"http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"conference":{"location":"Vancouver, Canada","start_date":"2019-12-08","end_date":"2019-12-14","name":"NIPS: Conference on Neural Information Processing Systems"},"language":[{"iso":"eng"}]},{"status":"public","title":"Social immunity","publication_status":"published","editor":[{"full_name":"Choe, Jae","first_name":"Jae","last_name":"Choe"}],"department":[{"_id":"SyCr"}],"publisher":"Elsevier","year":"2019","_id":"7513","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2020-02-23T23:00:36Z","date_updated":"2023-09-08T11:12:04Z","oa_version":"None","author":[{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"},{"full_name":"Kutzer, Megan","first_name":"Megan","last_name":"Kutzer","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978"}],"edition":"2","type":"book_chapter","abstract":[{"lang":"eng","text":"Social insects (i.e., ants, termites and the social bees and wasps) protect their colonies from disease using a combination of individual immunity and collectively performed defenses, termed social immunity. The first line of social immune defense is sanitary care, which is performed by colony members to protect their pathogen-exposed nestmates from developing an infection. If sanitary care fails and an infection becomes established, a second line of social immune defense is deployed to stop disease transmission within the colony and to protect the valuable queens, which together with the males are the reproductive individuals of the colony. Insect colonies are separated into these reproductive individuals and the sterile worker force, forming a superorganismal reproductive unit reminiscent of the differentiated germline and soma in a multicellular organism. Ultimately, the social immune response preserves the germline of the superorganism insect colony and increases overall fitness of the colony in case of disease. "}],"isi":1,"quality_controlled":"1","page":"747-755","publication":"Encyclopedia of Animal Behavior","citation":{"mla":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” Encyclopedia of Animal Behavior, edited by Jae Choe, 2nd ed., Elsevier, 2019, pp. 747–55, doi:10.1016/B978-0-12-809633-8.90721-0.","short":"S. Cremer, M. Kutzer, in:, J. Choe (Ed.), Encyclopedia of Animal Behavior, 2nd ed., Elsevier, 2019, pp. 747–755.","chicago":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” In Encyclopedia of Animal Behavior, edited by Jae Choe, 2nd ed., 747–55. Elsevier, 2019. https://doi.org/10.1016/B978-0-12-809633-8.90721-0.","ama":"Cremer S, Kutzer M. Social immunity. In: Choe J, ed. Encyclopedia of Animal Behavior. 2nd ed. Elsevier; 2019:747-755. doi:10.1016/B978-0-12-809633-8.90721-0","ista":"Cremer S, Kutzer M. 2019.Social immunity. In: Encyclopedia of Animal Behavior. , 747–755.","ieee":"S. Cremer and M. Kutzer, “Social immunity,” in Encyclopedia of Animal Behavior, 2nd ed., J. Choe, Ed. Elsevier, 2019, pp. 747–755.","apa":"Cremer, S., & Kutzer, M. (2019). Social immunity. In J. Choe (Ed.), Encyclopedia of Animal Behavior (2nd ed., pp. 747–755). Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.90721-0"},"external_id":{"isi":["000248989500026"]},"language":[{"iso":"eng"}],"date_published":"2019-02-06T00:00:00Z","doi":"10.1016/B978-0-12-809633-8.90721-0","scopus_import":"1","day":"06","month":"02","article_processing_charge":"No","publication_identifier":{"eisbn":["9780128132524"],"isbn":["9780128132517"]}},{"type":"conference","abstract":[{"text":"Bending-active structures are able to efficiently produce complex curved shapes starting from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match the global curvature (i.e., bending requests) of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc that fits a bounding box of 3.90x3.96x3.25 meters.","lang":"eng"}],"status":"public","publication_status":"published","title":"FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels","publisher":"International Center for Numerical Methods in Engineering","department":[{"_id":"BeBi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9261","year":"2019","date_created":"2021-03-21T23:01:21Z","date_updated":"2023-09-08T11:21:54Z","oa_version":"None","author":[{"full_name":"Laccone, Francesco","first_name":"Francesco","last_name":"Laccone"},{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"full_name":"Perez Rodriguez, Jesus","last_name":"Perez Rodriguez","first_name":"Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"},{"full_name":"Ponchio, Federico","first_name":"Federico","last_name":"Ponchio"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"last_name":"Cignoni","first_name":"Paolo","full_name":"Cignoni, Paolo"}],"scopus_import":"1","day":"10","month":"10","publication_identifier":{"isbn":["9788412110104"],"issn":["2518-6582"]},"article_processing_charge":"No","isi":1,"quality_controlled":"1","page":"509-515","publication":"IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE","external_id":{"isi":["000563497600059"]},"citation":{"short":"F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel, P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–515.","mla":"Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–15.","chicago":"Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni, Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” In IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, 509–15. International Center for Numerical Methods in Engineering, 2019.","ama":"Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In: IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. International Center for Numerical Methods in Engineering; 2019:509-515.","apa":"Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel, B., & Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering.","ieee":"F. Laccone et al., “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” in IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, Barcelona, Spain, 2019, pp. 509–515.","ista":"Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B, Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515."},"language":[{"iso":"eng"}],"conference":{"end_date":"2019-10-10","location":"Barcelona, Spain","start_date":"2019-10-07","name":"IASS: International Association for Shell and Spatial Structures"},"date_published":"2019-10-10T00:00:00Z"},{"citation":{"ama":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. Detecting visual relationships using box attention. In: Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00217","ista":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. 2019. Detecting visual relationships using box attention. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 1749–1753.","apa":"Kolesnikov, A., Kuznetsova, A., Lampert, C., & Ferrari, V. (2019). Detecting visual relationships using box attention. In Proceedings of the 2019 International Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00217","ieee":"A. Kolesnikov, A. Kuznetsova, C. Lampert, and V. Ferrari, “Detecting visual relationships using box attention,” in Proceedings of the 2019 International Conference on Computer Vision Workshop, Seoul, South Korea, 2019.","mla":"Kolesnikov, Alexander, et al. “Detecting Visual Relationships Using Box Attention.” Proceedings of the 2019 International Conference on Computer Vision Workshop, 1749–1753, IEEE, 2019, doi:10.1109/ICCVW.2019.00217.","short":"A. Kolesnikov, A. Kuznetsova, C. Lampert, V. Ferrari, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","chicago":"Kolesnikov, Alexander, Alina Kuznetsova, Christoph Lampert, and Vittorio Ferrari. “Detecting Visual Relationships Using Box Attention.” In Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE, 2019. https://doi.org/10.1109/ICCVW.2019.00217."},"publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","title":"Detecting visual relationships using box attention","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7640","oa_version":"Preprint","type":"conference","abstract":[{"text":"We propose a new model for detecting visual relationships, such as \"person riding motorcycle\" or \"bottle on table\". This task is an important step towards comprehensive structured mage understanding, going beyond detecting individual objects. Our main novelty is a Box Attention mechanism that allows to model pairwise interactions between objects using standard object detection pipelines. The resulting model is conceptually clean, expressive and relies on well-justified training and prediction procedures. Moreover, unlike previously proposed approaches, our model does not introduce any additional complex components or hyperparameters on top of those already required by the underlying detection model. We conduct an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating strong quantitative and qualitative results.","lang":"eng"}],"project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1807.02136","open_access":"1"}],"external_id":{"arxiv":["1807.02136"],"isi":["000554591601098"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/ICCVW.2019.00217","conference":{"location":"Seoul, South Korea","start_date":"2019-10-27","end_date":"2019-10-28","name":"ICCVW: International Conference on Computer Vision Workshop"},"publication_identifier":{"isbn":["9781728150239"]},"month":"10","publisher":"IEEE","department":[{"_id":"ChLa"}],"publication_status":"published","year":"2019","date_updated":"2023-09-08T11:18:37Z","date_created":"2020-04-05T22:00:51Z","author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander","full_name":"Kolesnikov, Alexander"},{"last_name":"Kuznetsova","first_name":"Alina","full_name":"Kuznetsova, Alina"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"},{"first_name":"Vittorio","last_name":"Ferrari","full_name":"Ferrari, Vittorio"}],"article_number":"1749-1753","ec_funded":1},{"article_number":"748-752","type":"conference","abstract":[{"text":"Deep neural networks (DNNs) have become increasingly important due to their excellent empirical performance on a wide range of problems. However, regularization is generally achieved by indirect means, largely due to the complex set of functions defined by a network and the difficulty in measuring function complexity. There exists no method in the literature for additive regularization based on a norm of the function, as is classically considered in statistical learning theory. In this work, we study the tractability of function norms for deep neural networks with ReLU activations. We provide, to the best of our knowledge, the first proof in the literature of the NP-hardness of computing function norms of DNNs of 3 or more layers. We also highlight a fundamental difference between shallow and deep networks. In the light on these results, we propose a new regularization strategy based on approximate function norms, and show its efficiency on a segmentation task with a DNN.","lang":"eng"}],"status":"public","publication_status":"published","title":"Function norms for neural networks","publisher":"IEEE","department":[{"_id":"VlKo"}],"year":"2019","_id":"7639","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2020-04-05T22:00:50Z","date_updated":"2023-09-08T11:19:12Z","oa_version":"None","author":[{"full_name":"Rannen-Triki, Amal","last_name":"Rannen-Triki","first_name":"Amal"},{"last_name":"Berman","first_name":"Maxim","full_name":"Berman, Maxim"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"first_name":"Matthew B.","last_name":"Blaschko","full_name":"Blaschko, Matthew B."}],"scopus_import":"1","month":"10","day":"01","publication_identifier":{"isbn":["9781728150239"]},"article_processing_charge":"No","isi":1,"quality_controlled":"1","publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","citation":{"ama":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. Function norms for neural networks. In: Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00097","ieee":"A. Rannen-Triki, M. Berman, V. Kolmogorov, and M. B. Blaschko, “Function norms for neural networks,” in Proceedings of the 2019 International Conference on Computer Vision Workshop, Seoul, South Korea, 2019.","apa":"Rannen-Triki, A., Berman, M., Kolmogorov, V., & Blaschko, M. B. (2019). Function norms for neural networks. In Proceedings of the 2019 International Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00097","ista":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. 2019. Function norms for neural networks. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 748–752.","short":"A. Rannen-Triki, M. Berman, V. Kolmogorov, M.B. Blaschko, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","mla":"Rannen-Triki, Amal, et al. “Function Norms for Neural Networks.” Proceedings of the 2019 International Conference on Computer Vision Workshop, 748–752, IEEE, 2019, doi:10.1109/ICCVW.2019.00097.","chicago":"Rannen-Triki, Amal, Maxim Berman, Vladimir Kolmogorov, and Matthew B. Blaschko. “Function Norms for Neural Networks.” In Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE, 2019. https://doi.org/10.1109/ICCVW.2019.00097."},"external_id":{"isi":["000554591600090"]},"language":[{"iso":"eng"}],"conference":{"name":"ICCVW: International Conference on Computer Vision Workshop","location":"Seoul, South Korea","start_date":"2019-10-27","end_date":"2019-10-28"},"doi":"10.1109/ICCVW.2019.00097","date_published":"2019-10-01T00:00:00Z"},{"date_created":"2020-08-21T04:25:39Z","date_updated":"2023-09-08T11:24:15Z","edition":"4","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"editor":[{"last_name":"Balding","first_name":"David","full_name":"Balding, David"},{"last_name":"Moltke","first_name":"Ida","full_name":"Moltke, Ida"},{"first_name":"John","last_name":"Marioni","full_name":"Marioni, John"}],"publication_status":"published","year":"2019","publication_identifier":{"isbn":["9781119429142"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1002/9781119487845.ch4","quality_controlled":"1","isi":1,"external_id":{"isi":["000261343000003"]},"abstract":[{"text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it.","lang":"eng"}],"type":"book_chapter","oa_version":"None","status":"public","title":"Mathematical models in population genetics","ddc":["576"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8281","article_processing_charge":"No","day":"29","date_published":"2019-07-29T00:00:00Z","page":"115-144","citation":{"apa":"Barton, N. H., & Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4","ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4."},"publication":"Handbook of statistical genomics"},{"abstract":[{"lang":"eng","text":"Denote by ∆N the N-dimensional simplex. A map f : ∆N → Rd is an almost r-embedding if fσ1∩. . .∩fσr = ∅ whenever σ1, . . . , σr are pairwise disjoint faces. A counterexample to the topological Tverberg conjecture asserts that if r is not a prime power and d ≥ 2r + 1, then there is an almost r-embedding ∆(d+1)(r−1) → Rd. This was improved by Blagojevi´c–Frick–Ziegler using a simple construction of higher-dimensional counterexamples by taking k-fold join power of lower-dimensional ones. We improve this further (for d large compared to r): If r is not a prime power and N := (d+ 1)r−r l\r\nd + 2 r + 1 m−2, then there is an almost r-embedding ∆N → Rd. For the r-fold van Kampen–Flores conjecture we also produce counterexamples which are stronger than previously known. Our proof is based on generalizations of the Mabillard–Wagner theorem on construction of almost r-embeddings from equivariant maps, and of the Ozaydin theorem on existence of equivariant maps. "}],"type":"preprint","article_number":"1908.08731","related_material":{"record":[{"id":"8156","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","last_name":"Avvakumov"},{"last_name":"Karasev","first_name":"R.","full_name":"Karasev, R."},{"last_name":"Skopenkov","first_name":"A.","full_name":"Skopenkov, A."}],"oa_version":"Preprint","date_created":"2020-07-30T10:45:34Z","date_updated":"2023-09-08T11:20:02Z","_id":"8184","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","acknowledgement":"We would like to thank F. Frick for helpful discussions","publisher":"arXiv","department":[{"_id":"UlWa"}],"title":"Stronger counterexamples to the topological Tverberg conjecture","status":"public","publication_status":"submitted","article_processing_charge":"No","month":"08","day":"23","date_published":"2019-08-23T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000986519600004"],"arxiv":["1908.08731"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.08731"}],"citation":{"chicago":"Avvakumov, Sergey, R. Karasev, and A. Skopenkov. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv. arXiv, n.d.","mla":"Avvakumov, Sergey, et al. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv, 1908.08731, arXiv.","short":"S. Avvakumov, R. Karasev, A. Skopenkov, ArXiv (n.d.).","ista":"Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv, 1908.08731.","ieee":"S. Avvakumov, R. Karasev, and A. Skopenkov, “Stronger counterexamples to the topological Tverberg conjecture,” arXiv. arXiv.","apa":"Avvakumov, S., Karasev, R., & Skopenkov, A. (n.d.). Stronger counterexamples to the topological Tverberg conjecture. arXiv. arXiv.","ama":"Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv."},"publication":"arXiv","project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312","call_identifier":"FWF","name":"Algorithms for Embeddings and Homotopy Theory"}],"isi":1},{"month":"04","publication_identifier":{"issn":["03029743"],"isbn":["9783030172589"],"eissn":["16113349"]},"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2018/426","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"conference":{"name":"PKC: Public-Key Cryptograhy","start_date":"2019-04-14","location":"Beijing, China","end_date":"2019-04-17"},"doi":"10.1007/978-3-030-17259-6_11","language":[{"iso":"eng"}],"ec_funded":1,"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"author":[{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg","full_name":"Fuchsbauer, Georg"},{"last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"first_name":"Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10035"}]},"date_created":"2019-05-13T08:13:46Z","date_updated":"2023-09-08T11:33:20Z","volume":11443,"scopus_import":"1","day":"06","article_processing_charge":"No","citation":{"mla":"Fuchsbauer, Georg, et al. Adaptively Secure Proxy Re-Encryption. Vol. 11443, Springer Nature, 2019, pp. 317–46, doi:10.1007/978-3-030-17259-6_11.","short":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, Springer Nature, 2019, pp. 317–346.","chicago":"Fuchsbauer, Georg, Chethan Kamath Hosdurg, Karen Klein, and Krzysztof Z Pietrzak. “Adaptively Secure Proxy Re-Encryption,” 11443:317–46. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17259-6_11.","ama":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. Adaptively secure proxy re-encryption. In: Vol 11443. Springer Nature; 2019:317-346. doi:10.1007/978-3-030-17259-6_11","ista":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. 2019. Adaptively secure proxy re-encryption. PKC: Public-Key Cryptograhy, LNCS, vol. 11443, 317–346.","apa":"Fuchsbauer, G., Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2019). Adaptively secure proxy re-encryption (Vol. 11443, pp. 317–346). Presented at the PKC: Public-Key Cryptograhy, Beijing, China: Springer Nature. https://doi.org/10.1007/978-3-030-17259-6_11","ieee":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “Adaptively secure proxy re-encryption,” presented at the PKC: Public-Key Cryptograhy, Beijing, China, 2019, vol. 11443, pp. 317–346."},"page":"317-346","date_published":"2019-04-06T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key 𝑝𝑘′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under 𝑝𝑘′ without having to know the underlying message, while transformations from 𝑝𝑘′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure.\r\n\r\nAll existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in Open image in new window , rendering the result meaningless already for moderate Open image in new window .\r\n\r\nJafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications.\r\n\r\nOur results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14)."}],"_id":"6430","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Adaptively secure proxy re-encryption","status":"public","intvolume":" 11443","oa_version":"Preprint"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-08916-5","quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000459704600001"]},"month":"02","publication_identifier":{"issn":["2041-1723"]},"date_updated":"2023-09-08T11:39:02Z","date_created":"2019-03-05T13:18:30Z","volume":10,"author":[{"first_name":"Jonathan","last_name":"Mayzel","full_name":"Mayzel, Jonathan"},{"full_name":"Steinberg, Victor","first_name":"Victor","last_name":"Steinberg"},{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","first_name":"Atul"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"BjHo"}],"year":"2019","file_date_updated":"2020-07-14T12:47:18Z","ec_funded":1,"article_number":"937","date_published":"2019-02-26T00:00:00Z","publication":"Nature Communications","citation":{"short":"J. Mayzel, V. Steinberg, A. Varshney, Nature Communications 10 (2019).","mla":"Mayzel, Jonathan, et al. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications, vol. 10, 937, Springer Nature, 2019, doi:10.1038/s41467-019-08916-5.","chicago":"Mayzel, Jonathan, Victor Steinberg, and Atul Varshney. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-08916-5.","ama":"Mayzel J, Steinberg V, Varshney A. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 2019;10. doi:10.1038/s41467-019-08916-5","ieee":"J. Mayzel, V. Steinberg, and A. Varshney, “Stokes flow analogous to viscous electron current in graphene,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Mayzel, J., Steinberg, V., & Varshney, A. (2019). Stokes flow analogous to viscous electron current in graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-08916-5","ista":"Mayzel J, Steinberg V, Varshney A. 2019. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 10, 937."},"day":"26","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"checksum":"61192fc49e0d44907c2a4fe384e4b97f","date_created":"2019-03-05T13:33:04Z","date_updated":"2020-07-14T12:47:18Z","relation":"main_file","file_id":"6070","content_type":"application/pdf","file_size":2646391,"creator":"dernst","access_level":"open_access","file_name":"2019_NatureComm_Mayzel.pdf"}],"title":"Stokes flow analogous to viscous electron current in graphene","status":"public","ddc":["530","532"],"intvolume":" 10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6069","abstract":[{"lang":"eng","text":"Electron transport in two-dimensional conducting materials such as graphene, with dominant electron–electron interaction, exhibits unusual vortex flow that leads to a nonlocal current-field relation (negative resistance), distinct from the classical Ohm’s law. The transport behavior of these materials is best described by low Reynolds number hydrodynamics, where the constitutive pressure–speed relation is Stoke’s law. Here we report evidence of such vortices observed in a viscous flow of Newtonian fluid in a microfluidic device consisting of a rectangular cavity—analogous to the electronic system. We extend our experimental observations to elliptic cavities of different eccentricities, and validate them by numerically solving bi-harmonic equation obtained for the viscous flow with no-slip boundary conditions. We verify the existence of a predicted threshold at which vortices appear. Strikingly, we find that a two-dimensional theoretical model captures the essential features of three-dimensional Stokes flow in experiments."}],"type":"journal_article"},{"month":"02","publication_identifier":{"issn":["2041-1723"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000458175300001"],"arxiv":["1902.03763"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.1038/s41467-019-08551-0","language":[{"iso":"eng"}],"article_number":"652","file_date_updated":"2020-07-14T12:47:17Z","ec_funded":1,"year":"2019","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Springer Nature","author":[{"first_name":"Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"date_updated":"2023-09-08T11:39:54Z","date_created":"2019-02-15T07:10:46Z","volume":10,"scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"No","publication":"Nature Communications","citation":{"ama":"Varshney A, Steinberg V. Elastic alfven waves in elastic turbulence. Nature Communications. 2019;10. doi:10.1038/s41467-019-08551-0","apa":"Varshney, A., & Steinberg, V. (2019). Elastic alfven waves in elastic turbulence. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-08551-0","ieee":"A. Varshney and V. Steinberg, “Elastic alfven waves in elastic turbulence,” Nature Communications, vol. 10. Springer Nature, 2019.","ista":"Varshney A, Steinberg V. 2019. Elastic alfven waves in elastic turbulence. Nature Communications. 10, 652.","short":"A. Varshney, V. Steinberg, Nature Communications 10 (2019).","mla":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” Nature Communications, vol. 10, 652, Springer Nature, 2019, doi:10.1038/s41467-019-08551-0.","chicago":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-08551-0."},"article_type":"original","date_published":"2019-02-08T00:00:00Z","type":"journal_article","abstract":[{"text":"Speed of sound waves in gases and liquids are governed by the compressibility of the medium. There exists another type of non-dispersive wave where the wave speed depends on stress instead of elasticity of the medium. A well-known example is the Alfven wave, which propagates through plasma permeated by a magnetic field with the speed determined by magnetic tension. An elastic analogue of Alfven waves has been predicted in a flow of dilute polymer solution where the elastic stress of the stretching polymers determines the elastic wave speed. Here we present quantitative evidence of elastic Alfven waves in elastic turbulence of a viscoelastic creeping flow between two obstacles in channel flow. The key finding in the experimental proof is a nonlinear dependence of the elastic wave speed cel on the Weissenberg number Wi, which deviates from predictions based on a model of linear polymer elasticity.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6014","ddc":["530"],"status":"public","title":"Elastic alfven waves in elastic turbulence","intvolume":" 10","file":[{"relation":"main_file","file_id":"6015","checksum":"d3acf07eaad95ec040d8e8565fc9ac37","date_created":"2019-02-15T07:15:00Z","date_updated":"2020-07-14T12:47:17Z","access_level":"open_access","file_name":"2019_NatureComm_Varshney.pdf","file_size":1331490,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version"},{"department":[{"_id":"SiHi"}],"publisher":"Elsevier","publication_status":"published","year":"2019","volume":15,"date_updated":"2023-09-08T11:38:04Z","date_created":"2019-05-14T11:47:40Z","author":[{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole"},{"full_name":"Sotiropoulou, Panagiota A.","first_name":"Panagiota A.","last_name":"Sotiropoulou"},{"full_name":"Heller, Gerwin","last_name":"Heller","first_name":"Gerwin"},{"first_name":"Beate M.","last_name":"Lichtenberger","full_name":"Lichtenberger, Beate M."},{"first_name":"Martin","last_name":"Holcmann","full_name":"Holcmann, Martin"},{"first_name":"Bahar","last_name":"Camurdanoglu","full_name":"Camurdanoglu, Bahar"},{"last_name":"Baykuscheva-Gentscheva","first_name":"Temenuschka","full_name":"Baykuscheva-Gentscheva, Temenuschka"},{"full_name":"Blanpain, Cedric","last_name":"Blanpain","first_name":"Cedric"},{"full_name":"Sibilia, Maria","first_name":"Maria","last_name":"Sibilia"}],"file_date_updated":"2020-07-14T12:47:30Z","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000470104600022"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.isci.2019.04.018","publication_identifier":{"issn":["2589-0042"]},"month":"05","intvolume":" 15","status":"public","title":"EGFR controls hair shaft differentiation in a p53-independent manner","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6451","file":[{"relation":"main_file","file_id":"6452","checksum":"a9ad2296726c9474ad5860c9c2f53622","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-14T11:51:51Z","access_level":"open_access","file_name":"2019_iScience_Amberg.pdf","file_size":8365970,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Epidermal growth factor receptor (EGFR) signaling controls skin development and homeostasis inmice and humans, and its deficiency causes severe skin inflammation, which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle stem cells. Expression and alternative splicing analysisof RNA sequencing data from interfollicular epidermis and outer root sheath indicate that EGFR con-trols genes involved in epidermal differentiation and also in centrosome function, DNA damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions in proliferative epidermal compartments, aswell asp53-independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1 protein specifically in the innermost epithelial hair layers, resulting in disorganizationof medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomousEGFR functions in the epidermis."}],"page":"243-256","citation":{"ista":"Amberg N, Sotiropoulou PA, Heller G, Lichtenberger BM, Holcmann M, Camurdanoglu B, Baykuscheva-Gentscheva T, Blanpain C, Sibilia M. 2019. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 15, 243–256.","apa":"Amberg, N., Sotiropoulou, P. A., Heller, G., Lichtenberger, B. M., Holcmann, M., Camurdanoglu, B., … Sibilia, M. (2019). EGFR controls hair shaft differentiation in a p53-independent manner. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.04.018","ieee":"N. Amberg et al., “EGFR controls hair shaft differentiation in a p53-independent manner,” iScience, vol. 15. Elsevier, pp. 243–256, 2019.","ama":"Amberg N, Sotiropoulou PA, Heller G, et al. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 2019;15:243-256. doi:10.1016/j.isci.2019.04.018","chicago":"Amberg, Nicole, Panagiota A. Sotiropoulou, Gerwin Heller, Beate M. Lichtenberger, Martin Holcmann, Bahar Camurdanoglu, Temenuschka Baykuscheva-Gentscheva, Cedric Blanpain, and Maria Sibilia. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.04.018.","mla":"Amberg, Nicole, et al. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience, vol. 15, Elsevier, 2019, pp. 243–56, doi:10.1016/j.isci.2019.04.018.","short":"N. Amberg, P.A. Sotiropoulou, G. Heller, B.M. Lichtenberger, M. Holcmann, B. Camurdanoglu, T. Baykuscheva-Gentscheva, C. Blanpain, M. Sibilia, IScience 15 (2019) 243–256."},"publication":"iScience","date_published":"2019-05-31T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"31"},{"type":"journal_article","issue":"3","abstract":[{"text":"We study effects of a bounded and compactly supported perturbation on multidimensional continuum random Schrödinger operators in the region of complete localisation. Our main emphasis is on Anderson orthogonality for random Schrödinger operators. Among others, we prove that Anderson orthogonality does occur for Fermi energies in the region of complete localisation with a non-zero probability. This partially confirms recent non-rigorous findings [V. Khemani et al., Nature Phys. 11 (2015), 560–565]. The spectral shift function plays an important role in our analysis of Anderson orthogonality. We identify it with the index of the corresponding pair of spectral projections and explore the consequences thereof. All our results rely on the main technical estimate of this paper which guarantees separate exponential decay of the disorder-averaged Schatten p-norm of χa(f(H)−f(Hτ))χb in a and b. Here, Hτ is a perturbation of the random Schrödinger operator H, χa is the multiplication operator corresponding to the indicator function of a unit cube centred about a∈Rd, and f is in a suitable class of functions of bounded variation with distributional derivative supported in the region of complete localisation for H.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10879","intvolume":" 9","status":"public","title":"Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function","oa_version":"Preprint","scopus_import":"1","keyword":["Random Schrödinger operators","spectral shift function","Anderson orthogonality"],"article_processing_charge":"No","day":"01","citation":{"chicago":"Dietlein, Adrian M, Martin Gebert, and Peter Müller. “Perturbations of Continuum Random Schrödinger Operators with Applications to Anderson Orthogonality and the Spectral Shift Function.” Journal of Spectral Theory. European Mathematical Society Publishing House, 2019. https://doi.org/10.4171/jst/267.","mla":"Dietlein, Adrian M., et al. “Perturbations of Continuum Random Schrödinger Operators with Applications to Anderson Orthogonality and the Spectral Shift Function.” Journal of Spectral Theory, vol. 9, no. 3, European Mathematical Society Publishing House, 2019, pp. 921–65, doi:10.4171/jst/267.","short":"A.M. Dietlein, M. Gebert, P. Müller, Journal of Spectral Theory 9 (2019) 921–965.","ista":"Dietlein AM, Gebert M, Müller P. 2019. Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function. Journal of Spectral Theory. 9(3), 921–965.","ieee":"A. M. Dietlein, M. Gebert, and P. Müller, “Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function,” Journal of Spectral Theory, vol. 9, no. 3. European Mathematical Society Publishing House, pp. 921–965, 2019.","apa":"Dietlein, A. M., Gebert, M., & Müller, P. (2019). Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function. Journal of Spectral Theory. European Mathematical Society Publishing House. https://doi.org/10.4171/jst/267","ama":"Dietlein AM, Gebert M, Müller P. Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function. Journal of Spectral Theory. 2019;9(3):921-965. doi:10.4171/jst/267"},"publication":"Journal of Spectral Theory","page":"921-965","article_type":"original","date_published":"2019-03-01T00:00:00Z","year":"2019","acknowledgement":"M.G. was supported by the DFG under grant GE 2871/1-1.","department":[{"_id":"LaEr"}],"publisher":"European Mathematical Society Publishing House","publication_status":"published","author":[{"id":"317CB464-F248-11E8-B48F-1D18A9856A87","last_name":"Dietlein","first_name":"Adrian M","full_name":"Dietlein, Adrian M"},{"full_name":"Gebert, Martin","last_name":"Gebert","first_name":"Martin"},{"last_name":"Müller","first_name":"Peter","full_name":"Müller, Peter"}],"volume":9,"date_created":"2022-03-18T12:36:42Z","date_updated":"2023-09-08T11:35:31Z","publication_identifier":{"issn":["1664-039X"]},"month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1701.02956","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1701.02956"],"isi":["000484709400006"]},"quality_controlled":"1","isi":1,"doi":"10.4171/jst/267","language":[{"iso":"eng"}]},{"oa_version":"Preprint","status":"public","title":"A mean-field model with discontinuous coefficients for neurons with spatial interaction","intvolume":" 39","_id":"10878","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Starting from a microscopic model for a system of neurons evolving in time which individually follow a stochastic integrate-and-fire type model, we study a mean-field limit of the system. Our model is described by a system of SDEs with discontinuous coefficients for the action potential of each neuron and takes into account the (random) spatial configuration of neurons allowing the interaction to depend on it. In the limit as the number of particles tends to infinity, we obtain a nonlinear Fokker-Planck type PDE in two variables, with derivatives only with respect to one variable and discontinuous coefficients. We also study strong well-posedness of the system of SDEs and prove the existence and uniqueness of a weak measure-valued solution to the PDE, obtained as the limit of the laws of the empirical measures for the system of particles.","lang":"eng"}],"issue":"6","type":"journal_article","date_published":"2019-06-01T00:00:00Z","article_type":"original","page":"3037-3067","publication":"Discrete and Continuous Dynamical Systems","citation":{"short":"F. Flandoli, E. Priola, G.A. Zanco, Discrete and Continuous Dynamical Systems 39 (2019) 3037–3067.","mla":"Flandoli, Franco, et al. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” Discrete and Continuous Dynamical Systems, vol. 39, no. 6, American Institute of Mathematical Sciences, 2019, pp. 3037–67, doi:10.3934/dcds.2019126.","chicago":"Flandoli, Franco, Enrico Priola, and Giovanni A Zanco. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” Discrete and Continuous Dynamical Systems. American Institute of Mathematical Sciences, 2019. https://doi.org/10.3934/dcds.2019126.","ama":"Flandoli F, Priola E, Zanco GA. A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. 2019;39(6):3037-3067. doi:10.3934/dcds.2019126","apa":"Flandoli, F., Priola, E., & Zanco, G. A. (2019). A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. American Institute of Mathematical Sciences. https://doi.org/10.3934/dcds.2019126","ieee":"F. Flandoli, E. Priola, and G. A. Zanco, “A mean-field model with discontinuous coefficients for neurons with spatial interaction,” Discrete and Continuous Dynamical Systems, vol. 39, no. 6. American Institute of Mathematical Sciences, pp. 3037–3067, 2019.","ista":"Flandoli F, Priola E, Zanco GA. 2019. A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. 39(6), 3037–3067."},"day":"01","article_processing_charge":"No","keyword":["Applied Mathematics","Discrete Mathematics and Combinatorics","Analysis"],"scopus_import":"1","date_updated":"2023-09-08T11:34:45Z","date_created":"2022-03-18T12:33:34Z","volume":39,"author":[{"full_name":"Flandoli, Franco","first_name":"Franco","last_name":"Flandoli"},{"last_name":"Priola","first_name":"Enrico","full_name":"Priola, Enrico"},{"first_name":"Giovanni A","last_name":"Zanco","id":"47491882-F248-11E8-B48F-1D18A9856A87","full_name":"Zanco, Giovanni A"}],"publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"American Institute of Mathematical Sciences","year":"2019","acknowledgement":"The second author has been partially supported by INdAM through the GNAMPA Research\r\nProject (2017) “Sistemi stocastici singolari: buona posizione e problemi di controllo”. The third\r\nauthor was partly funded by the Austrian Science Fund (FWF) project F 65.","language":[{"iso":"eng"}],"doi":"10.3934/dcds.2019126","quality_controlled":"1","isi":1,"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"main_file_link":[{"url":"https://arxiv.org/abs/1708.04156","open_access":"1"}],"oa":1,"external_id":{"isi":["000459954800003"],"arxiv":["1708.04156"]},"month":"06","publication_identifier":{"issn":["1553-5231"]}},{"publication_identifier":{"isbn":["9781450362177"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1145/3293611.3331581","conference":{"name":"PODC: Symposium on Principles of Distributed Computing","start_date":"2019-07-29","location":"Toronto, ON, Canada","end_date":"2019-08-02"},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1905.03012"],"isi":["000570442000037"]},"main_file_link":[{"url":"https://arxiv.org/abs/1905.03012","open_access":"1"}],"ec_funded":1,"date_updated":"2023-09-08T11:37:22Z","date_created":"2019-10-08T12:57:14Z","author":[{"full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho","last_name":"Foerster"},{"first_name":"Janne","last_name":"Korhonen","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne"},{"first_name":"Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"}],"department":[{"_id":"DaAl"}],"publisher":"ACM","publication_status":"published","year":"2019","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-08-01T00:00:00Z","page":"259-261","citation":{"mla":"Foerster, Klaus-Tycho, et al. “Does Preprocessing Help under Congestion?” Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–61, doi:10.1145/3293611.3331581.","short":"K.-T. Foerster, J. Korhonen, J. Rybicki, S. Schmid, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–261.","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Joel Rybicki, and Stefan Schmid. “Does Preprocessing Help under Congestion?” In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, 259–61. ACM, 2019. https://doi.org/10.1145/3293611.3331581.","ama":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. Does preprocessing help under congestion? In: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. ACM; 2019:259-261. doi:10.1145/3293611.3331581","ista":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. 2019. Does preprocessing help under congestion? Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 259–261.","ieee":"K.-T. Foerster, J. Korhonen, J. Rybicki, and S. Schmid, “Does preprocessing help under congestion?,” in Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, Toronto, ON, Canada, 2019, pp. 259–261.","apa":"Foerster, K.-T., Korhonen, J., Rybicki, J., & Schmid, S. (2019). Does preprocessing help under congestion? In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing (pp. 259–261). Toronto, ON, Canada: ACM. https://doi.org/10.1145/3293611.3331581"},"publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing","abstract":[{"lang":"eng","text":"This paper investigates the power of preprocessing in the CONGEST model. Schmid and Suomela (ACM HotSDN 2013) introduced the SUPPORTED CONGEST model to study the application of distributed algorithms in Software-Defined Networks (SDNs). In this paper, we show that a large class of lower bounds in the CONGEST model still hold in the SUPPORTED model, highlighting the robustness of these bounds. This also raises the question how much does\r\npreprocessing help in the CONGEST model."}],"type":"conference","oa_version":"Preprint","title":"Does preprocessing help under congestion?","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6935"},{"date_published":"2019-02-01T00:00:00Z","citation":{"chicago":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.","mla":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics, vol. 65, no. 1, Springer, 2019, pp. 133–38, doi:10.1007/s00294-018-0879-8.","short":"N. Nikolic, Current Genetics 65 (2019) 133–138.","ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","ieee":"N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1. Springer, pp. 133–138, 2019.","apa":"Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. Springer. https://doi.org/10.1007/s00294-018-0879-8","ama":"Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 2019;65(1):133-138. doi:10.1007/s00294-018-0879-8"},"publication":"Current Genetics","page":"133-138","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","file":[{"creator":"dernst","file_size":776399,"content_type":"application/pdf","file_name":"2019_CurrentGenetics_Nikolic.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:47Z","date_created":"2019-02-06T07:50:58Z","checksum":"6779708b0b632a1a6ed28c56f5161142","file_id":"5930","relation":"main_file"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"138","intvolume":" 65","status":"public","title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","ddc":["570"],"issue":"1","abstract":[{"text":"Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin–antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche.","lang":"eng"}],"type":"journal_article","doi":"10.1007/s00294-018-0879-8","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000456958800017"]},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"quality_controlled":"1","month":"02","author":[{"orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela"}],"volume":65,"date_created":"2018-12-11T11:44:50Z","date_updated":"2023-09-08T13:23:42Z","year":"2019","publisher":"Springer","department":[{"_id":"CaGu"}],"publication_status":"published","publist_id":"7785","ec_funded":1,"file_date_updated":"2020-07-14T12:44:47Z"},{"page":"257 - 311","citation":{"mla":"Fischer, Julian L., and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations, vol. 266, no. 1, Elsevier, 2019, pp. 257–311, doi:10.1016/j.jde.2018.07.045.","short":"J.L. Fischer, O. Kneuss, Journal of Differential Equations 266 (2019) 257–311.","chicago":"Fischer, Julian L, and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.07.045.","ama":"Fischer JL, Kneuss O. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 2019;266(1):257-311. doi:10.1016/j.jde.2018.07.045","ista":"Fischer JL, Kneuss O. 2019. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 266(1), 257–311.","ieee":"J. L. Fischer and O. Kneuss, “Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity,” Journal of Differential Equations, vol. 266, no. 1. Elsevier, pp. 257–311, 2019.","apa":"Fischer, J. L., & Kneuss, O. (2019). Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.07.045"},"publication":"Journal of Differential Equations","date_published":"2019-01-05T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"05","intvolume":" 266","status":"public","title":"Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity","_id":"151","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"text":"We construct planar bi-Sobolev mappings whose local volume distortion is bounded from below by a given function f∈Lp with p>1. More precisely, for any 1<q<(p+1)/2 we construct W1,q-bi-Sobolev maps with identity boundary conditions; for f∈L∞, we provide bi-Lipschitz maps. The basic building block of our construction are bi-Lipschitz maps which stretch a given compact subset of the unit square by a given factor while preserving the boundary. The construction of these stretching maps relies on a slight strengthening of the celebrated covering result of Alberti, Csörnyei, and Preiss for measurable planar sets in the case of compact sets. We apply our result to a model functional in nonlinear elasticity, the integrand of which features fast blowup as the Jacobian determinant of the deformation becomes small. For such functionals, the derivation of the equilibrium equations for minimizers requires an additional regularization of test functions, which our maps provide.","lang":"eng"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1408.1587"],"isi":["000449108500010"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1408.1587","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jde.2018.07.045","month":"01","department":[{"_id":"JuFi"}],"publisher":"Elsevier","publication_status":"published","year":"2019","volume":266,"date_created":"2018-12-11T11:44:54Z","date_updated":"2023-09-08T13:25:35Z","author":[{"last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"full_name":"Kneuss, Olivier","last_name":"Kneuss","first_name":"Olivier"}],"publist_id":"7770"},{"month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000462680200002"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"doi":"10.1111/jnc.14601","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:45Z","ec_funded":1,"year":"2019","acknowledgement":" This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung \r\nn[f+b] (C13-002) to SH; a program grant from the Human Frontiers Science Program (RGP0053/2014) to SH; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No 618444 to SH, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro)to SH.\r\n","publication_status":"published","publisher":"Wiley","department":[{"_id":"SiHi"}],"author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole","last_name":"Amberg","full_name":"Amberg, Nicole"},{"first_name":"Susanne","last_name":"Laukoter","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"date_updated":"2023-09-11T13:40:26Z","date_created":"2018-12-11T11:44:14Z","volume":149,"scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Journal of Neurochemistry","citation":{"chicago":"Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14601.","mla":"Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry, vol. 149, no. 1, Wiley, 2019, pp. 12–26, doi:10.1111/jnc.14601.","short":"N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019) 12–26.","ista":"Amberg N, Laukoter S, Hippenmeyer S. 2019. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 149(1), 12–26.","apa":"Amberg, N., Laukoter, S., & Hippenmeyer, S. (2019). Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14601","ieee":"N. Amberg, S. Laukoter, and S. Hippenmeyer, “Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex,” Journal of Neurochemistry, vol. 149, no. 1. Wiley, pp. 12–26, 2019.","ama":"Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 2019;149(1):12-26. doi:10.1111/jnc.14601"},"article_type":"review","page":"12-26","date_published":"2019-04-01T00:00:00Z","type":"journal_article","abstract":[{"text":"The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons and glial cells which emerge from distinct neural stem cell (NSC) lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells (RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development. This article is protected by copyright. All rights reserved.","lang":"eng"}],"issue":"1","_id":"27","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex","ddc":["570"],"intvolume":" 149","oa_version":"Published Version","file":[{"checksum":"db027721a95d36f5de36aadcd0bdf7e6","date_created":"2020-01-07T13:35:52Z","date_updated":"2020-07-14T12:45:45Z","file_id":"7239","relation":"main_file","creator":"kschuh","file_size":889709,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_Wiley_Amberg.pdf"}]},{"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)"}],"external_id":{"isi":["000457468300011"],"pmid":["30559456"]},"oa":1,"acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41556-018-0247-4","month":"02","publication_identifier":{"issn":["14657392"]},"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publisher":"Nature Publishing Group","year":"2019","pmid":1,"date_created":"2018-12-30T22:59:15Z","date_updated":"2023-09-11T14:03:28Z","volume":21,"author":[{"full_name":"Petridou, Nicoletta","first_name":"Nicoletta","last_name":"Petridou","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"full_name":"Salbreux, Guillaume","first_name":"Guillaume","last_name":"Salbreux"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/"}]},"file_date_updated":"2020-10-21T07:18:35Z","ec_funded":1,"article_type":"original","page":"169–178","publication":"Nature Cell Biology","citation":{"chicago":"Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology. Nature Publishing Group, 2019. https://doi.org/10.1038/s41556-018-0247-4.","mla":"Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology, vol. 21, Nature Publishing Group, 2019, pp. 169–178, doi:10.1038/s41556-018-0247-4.","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178.","ista":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 21, 169–178.","apa":"Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0247-4","ieee":"N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg, “Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling,” Nature Cell Biology, vol. 21. Nature Publishing Group, pp. 169–178, 2019.","ama":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 2019;21:169–178. doi:10.1038/s41556-018-0247-4"},"date_published":"2019-02-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","status":"public","ddc":["570"],"intvolume":" 21","_id":"5789","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","file":[{"checksum":"e38523787b3bc84006f2793de99ad70f","success":1,"date_updated":"2020-10-21T07:18:35Z","date_created":"2020-10-21T07:18:35Z","relation":"main_file","file_id":"8685","content_type":"application/pdf","file_size":71590590,"creator":"dernst","access_level":"open_access","file_name":"2018_NatureCellBio_Petridou_accepted.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis."}]},{"oa_version":"Published Version","intvolume":" 116","title":"Harmonic dynamics of the Abelian sandpile","status":"public","_id":"196","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"8","abstract":[{"lang":"eng","text":"The abelian sandpile serves as a model to study self-organized criticality, a phenomenon occurring in biological, physical and social processes. The identity of the abelian group is a fractal composed of self-similar patches, and its limit is subject of extensive collaborative research. Here, we analyze the evolution of the sandpile identity under harmonic fields of different orders. We show that this evolution corresponds to periodic cycles through the abelian group characterized by the smooth transformation and apparent conservation of the patches constituting the identity. The dynamics induced by second and third order harmonics resemble smooth stretchings, respectively translations, of the identity, while the ones induced by fourth order harmonics resemble magnifications and rotations. Starting with order three, the dynamics pass through extended regions of seemingly random configurations which spontaneously reassemble into accentuated patterns. We show that the space of harmonic functions projects to the extended analogue of the sandpile group, thus providing a set of universal coordinates identifying configurations between different domains. Since the original sandpile group is a subgroup of the extended one, this directly implies that it admits a natural renormalization. Furthermore, we show that the harmonic fields can be induced by simple Markov processes, and that the corresponding stochastic dynamics show remarkable robustness over hundreds of periods. Finally, we encode information into seemingly random configurations, and decode this information with an algorithm requiring minimal prior knowledge. Our results suggest that harmonic fields might split the sandpile group into sub-sets showing different critical coefficients, and that it might be possible to extend the fractal structure of the identity beyond the boundaries of its domain. "}],"type":"journal_article","date_published":"2019-02-19T00:00:00Z","page":"2821-2830","article_type":"original","citation":{"short":"M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.","mla":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences, vol. 116, no. 8, National Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.","chicago":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.","ama":"Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116","apa":"Lang, M., & Shkolnikov, M. (2019). Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1812015116","ieee":"M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings of the National Academy of Sciences, vol. 116, no. 8. National Academy of Sciences, pp. 2821–2830, 2019.","ista":"Lang M, Shkolnikov M. 2019. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 116(8), 2821–2830."},"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","day":"19","scopus_import":"1","volume":116,"date_created":"2018-12-11T11:45:08Z","date_updated":"2023-09-11T14:09:34Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/"}]},"author":[{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","last_name":"Lang"},{"id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","first_name":"Mikhail","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail"}],"publisher":"National Academy of Sciences","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"TaHa"}],"publication_status":"published","pmid":1,"acknowledgement":"M.L. is grateful to the members of the C Guet and G Tkacik groups for valuable comments and support. M.S. is grateful to Nikita Kalinin for inspiring communications.\r\n","year":"2019","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1812015116","quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1812015116"}],"oa":1,"external_id":{"arxiv":["1806.10823"],"isi":["000459074400013"],"pmid":[" 30728300"]},"publication_identifier":{"eissn":["1091-6490"]},"month":"02"},{"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"10","page":"602-614","article_type":"original","citation":{"chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8sm01956h.","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.","ieee":"B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019.","apa":"Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","ama":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h"},"publication":"Soft Matter","date_published":"2019-01-10T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion.","lang":"eng"}],"intvolume":" 15","title":"Limiting shapes of confined lipid vesicles","ddc":["530"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5817","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"8641","date_updated":"2020-10-09T11:00:05Z","date_created":"2020-10-09T11:00:05Z","checksum":"614c337d6424ccd3d48d1b1f9513510d","success":1,"file_name":"lmt_sftmtr_V8.pdf","access_level":"open_access","content_type":"application/pdf","file_size":5370762,"creator":"bkavcic"}],"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"month":"01","isi":1,"quality_controlled":"1","external_id":{"isi":["000457329700003"],"pmid":["30629082"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1039/c8sm01956h","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","file_date_updated":"2020-10-09T11:00:05Z","publisher":"Royal Society of Chemistry","department":[{"_id":"GaTk"}],"publication_status":"published","pmid":1,"year":"2019","volume":15,"date_created":"2019-01-11T07:37:47Z","date_updated":"2023-09-13T08:47:16Z","author":[{"last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor"},{"last_name":"Sakashita","first_name":"A.","full_name":"Sakashita, A."},{"first_name":"H.","last_name":"Noguchi","full_name":"Noguchi, H."},{"full_name":"Ziherl, P.","first_name":"P.","last_name":"Ziherl"}]},{"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2019-02-01T00:00:00Z","publication":"Calculus of Variations and Partial Differential Equations","citation":{"ama":"Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 2019;58(1). doi:10.1007/s00526-018-1456-1","ista":"Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.","apa":"Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1","ieee":"M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1. Springer, 2019.","mla":"Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1, 19, Springer, 2019, doi:10.1007/s00526-018-1456-1.","short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019).","chicago":"Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations. Springer, 2019. https://doi.org/10.1007/s00526-018-1456-1."},"article_type":"original","abstract":[{"lang":"eng","text":"We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5895","date_updated":"2020-07-14T12:47:55Z","date_created":"2019-01-28T15:37:11Z","checksum":"ba05ac2d69de4c58d2cd338b63512798","file_name":"2018_Calculus_Erbar.pdf","access_level":"open_access","file_size":645565,"content_type":"application/pdf","creator":"dernst"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"73","status":"public","ddc":["510"],"title":"On the geometry of geodesics in discrete optimal transport","intvolume":" 58","month":"02","publication_identifier":{"issn":["09442669"]},"doi":"10.1007/s00526-018-1456-1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1805.06040"],"isi":["000452849400001"]},"isi":1,"quality_controlled":"1","project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","grant_number":" F06504","_id":"260482E2-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"file_date_updated":"2020-07-14T12:47:55Z","ec_funded":1,"article_number":"19","author":[{"last_name":"Erbar","first_name":"Matthias","full_name":"Erbar, Matthias"},{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"},{"last_name":"Wirth","first_name":"Melchior","full_name":"Wirth, Melchior"}],"date_created":"2018-12-11T11:44:29Z","date_updated":"2023-09-13T09:12:35Z","volume":58,"year":"2019","publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"Springer"},{"scopus_import":1,"day":"01","publication":"ACM Transactions on Algorithms","citation":{"chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms. ACM, 2019. https://doi.org/10.1145/3344549.","short":"H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019).","mla":"Akitaya, Hugo, et al. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms, vol. 15, no. 4, 50, ACM, 2019, doi:10.1145/3344549.","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2019). Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3344549","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” ACM Transactions on Algorithms, vol. 15, no. 4. ACM, 2019.","ista":"Akitaya H, Fulek R, Tóth C. 2019. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 15(4), 50.","ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 2019;15(4). doi:10.1145/3344549"},"article_type":"original","date_published":"2019-10-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold 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 the same point or overlapping arcs due to data compression or low resolution. This raises the computational problem of deciding whether a given map ϕ : G → M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖ is the unform norm.\r\nA polynomial-time algorithm for recognizing weak embeddings has recently been found by Fulek and Kynčl. It reduces the problem to solving a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where ω ∈ [2,2.373) 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: We perform a sequence of local operations that gradually “untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak embedding. It combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.\r\n"}],"issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6982","status":"public","title":"Recognizing weak embeddings of graphs","intvolume":" 15","oa_version":"Preprint","month":"10","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1709.09209","open_access":"1"}],"external_id":{"arxiv":["1709.09209"]},"quality_controlled":"1","project":[{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}],"doi":"10.1145/3344549","language":[{"iso":"eng"}],"article_number":"50","year":"2019","publication_status":"published","publisher":"ACM","department":[{"_id":"UlWa"}],"author":[{"first_name":"Hugo","last_name":"Akitaya","full_name":"Akitaya, Hugo"},{"first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Tóth, Csaba","first_name":"Csaba","last_name":"Tóth"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"309"}]},"date_updated":"2023-09-15T12:19:31Z","date_created":"2019-11-04T15:45:17Z","volume":15},{"day":"30","article_processing_charge":"No","has_accepted_license":"1","date_published":"2019-09-30T00:00:00Z","page":"132","citation":{"mla":"Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid Systems. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6894.","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6894.","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:10.15479/AT:ISTA:6894","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","apa":"Giacobbe, M. (2019). Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6894","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019."},"abstract":[{"text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"checksum":"773beaf4a85dc2acc2c12b578fbe1965","date_created":"2019-09-27T14:15:05Z","date_updated":"2020-07-14T12:47:43Z","file_id":"6916","relation":"main_file","creator":"mgiacobbe","content_type":"application/pdf","file_size":4100685,"access_level":"open_access","file_name":"giacobbe_thesis.pdf"},{"creator":"mgiacobbe","file_size":7959732,"content_type":"application/gzip","access_level":"closed","file_name":"giacobbe_thesis_src.tar.gz","checksum":"97f1c3da71feefd27e6e625d32b4c75b","date_updated":"2020-07-14T12:47:43Z","date_created":"2019-09-27T14:22:04Z","file_id":"6917","relation":"source_file"}],"oa_version":"Published Version","status":"public","ddc":["000"],"title":"Automatic time-unbounded reachability analysis of hybrid systems","_id":"6894","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"09","publication_identifier":{"eissn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6894","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:47:43Z","date_created":"2019-09-22T14:08:44Z","date_updated":"2023-09-19T09:30:43Z","author":[{"first_name":"Mirco","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco"}],"related_material":{"record":[{"id":"631","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"647"},{"status":"public","relation":"part_of_dissertation","id":"140"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","year":"2019"},{"oa":1,"citation":{"chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019).","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"doi":"10.5061/dryad.2kb6fh4","date_published":"2019-01-09T00:00:00Z","month":"01","day":"09","article_processing_charge":"No","title":"Data from: The consequences of an introgression event","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","year":"2019","_id":"9805","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-06T12:03:50Z","date_updated":"2023-09-19T10:06:07Z","oa_version":"Published Version","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"id":"40","relation":"used_in_publication","status":"public"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}]},{"publist_id":"8048","ec_funded":1,"file_date_updated":"2020-10-02T09:33:28Z","author":[{"last_name":"Trébuchet","first_name":"Guillaume","full_name":"Trébuchet, Guillaume"},{"full_name":"Cattenoz, Pierre B","first_name":"Pierre B","last_name":"Cattenoz"},{"first_name":"János","last_name":"Zsámboki","full_name":"Zsámboki, János"},{"full_name":"Mazaud, David","last_name":"Mazaud","first_name":"David"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"},{"full_name":"Fanto, Manolis","first_name":"Manolis","last_name":"Fanto"},{"first_name":"Angela","last_name":"Giangrande","full_name":"Giangrande, Angela"}],"volume":39,"date_updated":"2023-09-19T10:10:55Z","date_created":"2018-12-11T11:44:07Z","pmid":1,"year":"2019","acknowledgement":"This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC) and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques), and G.T. by governmental and ARC fellowships. This work was also supported by grants from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM. We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant, R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC for reagents and flies. We also thank all of the laboratory members for comments on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and antibody facilities for technical assistance; and D. Dembele for help with statistics. In addition, we thank Alison Brewer for help with Luciferase assays.","department":[{"_id":"DaSi"}],"publisher":"Society for Neuroscience","publication_status":"published","month":"01","doi":"10.1523/JNEUROSCI.1059-18.2018","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["30504274"],"isi":["000455189900006"]},"project":[{"_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions"}],"quality_controlled":"1","isi":1,"issue":"2","abstract":[{"text":"Despite their different origins, Drosophila glia and hemocytes are related cell populations that provide an immune function. Drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. Drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, the Drosophila immune cells within (glia) and outside the nervous system (hemocytes) require the same transcription factor Glide/Gcm for their development. This raises the issue of how do glia specifically differentiate in the nervous system and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how does one factor trigger different fates. In Drosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the Glide/Gcm transcription factor, glia originate from the ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2019_JournNeuroscience_Trebuchet.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":9455414,"file_id":"8596","relation":"main_file","date_updated":"2020-10-02T09:33:28Z","date_created":"2020-10-02T09:33:28Z","success":1,"checksum":"8f6925eb4cd1e8747d8ea25929c68de6"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8","intvolume":" 39","ddc":["570"],"status":"public","title":"The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate","article_processing_charge":"No","has_accepted_license":"1","day":"09","scopus_import":"1","date_published":"2019-01-09T00:00:00Z","citation":{"ama":"Trébuchet G, Cattenoz PB, Zsámboki J, et al. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 2019;39(2):238-255. doi:10.1523/JNEUROSCI.1059-18.2018","apa":"Trébuchet, G., Cattenoz, P. B., Zsámboki, J., Mazaud, D., Siekhaus, D. E., Fanto, M., & Giangrande, A. (2019). The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1059-18.2018","ieee":"G. Trébuchet et al., “The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate,” Journal of Neuroscience, vol. 39, no. 2. Society for Neuroscience, pp. 238–255, 2019.","ista":"Trébuchet G, Cattenoz PB, Zsámboki J, Mazaud D, Siekhaus DE, Fanto M, Giangrande A. 2019. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 39(2), 238–255.","short":"G. Trébuchet, P.B. Cattenoz, J. Zsámboki, D. Mazaud, D.E. Siekhaus, M. Fanto, A. Giangrande, Journal of Neuroscience 39 (2019) 238–255.","mla":"Trébuchet, Guillaume, et al. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience, vol. 39, no. 2, Society for Neuroscience, 2019, pp. 238–55, doi:10.1523/JNEUROSCI.1059-18.2018.","chicago":"Trébuchet, Guillaume, Pierre B Cattenoz, János Zsámboki, David Mazaud, Daria E Siekhaus, Manolis Fanto, and Angela Giangrande. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience. Society for Neuroscience, 2019. https://doi.org/10.1523/JNEUROSCI.1059-18.2018."},"publication":"Journal of Neuroscience","page":"238-255","article_type":"original"},{"volume":99,"date_created":"2018-12-11T11:44:06Z","date_updated":"2023-09-19T10:13:08Z","author":[{"first_name":"Iordan V","last_name":"Ganev","id":"447491B8-F248-11E8-B48F-1D18A9856A87","full_name":"Ganev, Iordan V"}],"publisher":"Wiley","department":[{"_id":"TaHa"}],"publication_status":"published","year":"2019","publist_id":"8052","file_date_updated":"2020-07-14T12:46:35Z","language":[{"iso":"eng"}],"doi":"10.1112/jlms.12193","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000470025900008"]},"month":"06","file":[{"file_size":431754,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2019_Wiley_Ganev.pdf","checksum":"1be56239b2cd740a0e9a084f773c22f6","date_updated":"2020-07-14T12:46:35Z","date_created":"2020-01-07T13:31:53Z","relation":"main_file","file_id":"7238"}],"oa_version":"Published Version","intvolume":" 99","title":"The wonderful compactification for quantum groups","ddc":["510"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5","issue":"3","abstract":[{"lang":"eng","text":"In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2."}],"type":"journal_article","date_published":"2019-06-01T00:00:00Z","page":"778-806","citation":{"ama":"Ganev IV. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 2019;99(3):778-806. doi:10.1112/jlms.12193","ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806.","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 778–806, 2019.","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12193","mla":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:10.1112/jlms.12193.","short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.","chicago":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12193."},"publication":"Journal of the London Mathematical Society","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1"},{"file_date_updated":"2020-07-14T12:47:51Z","related_material":{"record":[{"id":"1346","status":"public","relation":"part_of_dissertation"},{"id":"6377","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"449"}]},"author":[{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","first_name":"Mina K","full_name":"Vasileva, Mina K"}],"date_updated":"2023-09-19T10:39:33Z","date_created":"2019-12-11T21:24:39Z","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","publication_identifier":{"eissn":["2663-337X"]},"month":"12","doi":"10.15479/AT:ISTA:7172","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"degree_awarded":"PhD","oa":1,"abstract":[{"lang":"eng","text":"The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.\r\nThe first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.\r\nThe second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.\r\nThe third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.\r\nIn the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.\r\nIn the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2019-12-12T09:32:36Z","date_updated":"2020-07-14T12:47:51Z","checksum":"ef981c1a3b1d9da0edcbedcff4970d37","file_id":"7175","relation":"source_file","creator":"mvasilev","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":20454014,"file_name":"Thesis_Mina_final_upload_7.docx","access_level":"closed"},{"file_size":11565025,"content_type":"application/pdf","creator":"mvasilev","file_name":"Thesis_Mina_final_upload_7.pdf","access_level":"open_access","date_created":"2019-12-12T09:33:10Z","date_updated":"2020-07-14T12:47:51Z","checksum":"3882c4585e46c9cfb486e4225cad54ab","relation":"main_file","file_id":"7176"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7172","status":"public","title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","ddc":["570"],"article_processing_charge":"No","has_accepted_license":"1","day":"12","date_published":"2019-12-12T00:00:00Z","citation":{"mla":"Vasileva, Mina K. Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7172.","short":"M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019.","chicago":"Vasileva, Mina K. “Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7172.","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:10.15479/AT:ISTA:7172","ista":"Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ieee":"M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019.","apa":"Vasileva, M. K. (2019). Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7172"},"page":"192"},{"file_date_updated":"2020-07-14T12:47:19Z","article_number":"e0212699","volume":14,"date_updated":"2023-09-19T14:46:47Z","date_created":"2019-03-10T22:59:21Z","author":[{"full_name":"Goudarzi, Mohammad","first_name":"Mohammad","last_name":"Goudarzi","id":"3384113A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Boquet-Pujadas, Aleix","last_name":"Boquet-Pujadas","first_name":"Aleix"},{"full_name":"Olivo-Marin, Jean Christophe","first_name":"Jean Christophe","last_name":"Olivo-Marin"},{"full_name":"Raz, Erez","first_name":"Erez","last_name":"Raz"}],"publisher":"Public Library of Science","department":[{"_id":"Bio"}],"publication_status":"published","year":"2019","month":"02","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0212699","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000459712100022"]},"issue":"2","abstract":[{"text":"Blebs are cellular protrusions observed in migrating cells and in cells undergoing spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm during bleb formation and the concurrent changes in cell volume using zebrafish primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation occurs concomitantly with cytoplasmic inflow into it and that during this process the total cell volume does not change. We thus show that bleb formation in primordial germ cells results primarily from redistribution of material within the cell rather than being driven by flow of water from an external source.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2019_PLoSOne_Goudarzi.pdf","access_level":"open_access","creator":"dernst","file_size":2967731,"content_type":"application/pdf","file_id":"6096","relation":"main_file","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-11T16:09:23Z","checksum":"b885de050ed4bb3c86f706487a47197f"}],"oa_version":"Published Version","intvolume":" 14","ddc":["570"],"status":"public","title":"Fluid dynamics during bleb formation in migrating cells in vivo","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6093","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1","date_published":"2019-02-26T00:00:00Z","citation":{"ama":"Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. 2019;14(2). doi:10.1371/journal.pone.0212699","ista":"Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. 2019. Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. 14(2), e0212699.","ieee":"M. Goudarzi, A. Boquet-Pujadas, J. C. Olivo-Marin, and E. Raz, “Fluid dynamics during bleb formation in migrating cells in vivo,” PLOS ONE, vol. 14, no. 2. Public Library of Science, 2019.","apa":"Goudarzi, M., Boquet-Pujadas, A., Olivo-Marin, J. C., & Raz, E. (2019). Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0212699","mla":"Goudarzi, Mohammad, et al. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” PLOS ONE, vol. 14, no. 2, e0212699, Public Library of Science, 2019, doi:10.1371/journal.pone.0212699.","short":"M. Goudarzi, A. Boquet-Pujadas, J.C. Olivo-Marin, E. Raz, PLOS ONE 14 (2019).","chicago":"Goudarzi, Mohammad, Aleix Boquet-Pujadas, Jean Christophe Olivo-Marin, and Erez Raz. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” PLOS ONE. Public Library of Science, 2019. https://doi.org/10.1371/journal.pone.0212699."},"publication":"PLOS ONE"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:6473","language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"05","year":"2019","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1576"},{"id":"6900","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","status":"public","id":"281"},{"relation":"dissertation_contains","status":"public","id":"2016"}]},"author":[{"full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A","last_name":"Cepeda Humerez","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-05-21T00:11:23Z","date_updated":"2023-09-19T15:13:26Z","file_date_updated":"2020-07-14T12:47:31Z","citation":{"chicago":"Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473.","mla":"Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473.","short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.","ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","apa":"Cepeda Humerez, S. A. (2019). Estimating information flow in single cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6473","ama":"Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473"},"page":"135","date_published":"2019-05-23T00:00:00Z","keyword":["Information estimation","Time-series","data analysis"],"article_processing_charge":"No","has_accepted_license":"1","day":"23","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6473","ddc":["004"],"status":"public","title":"Estimating information flow in single cells","oa_version":"Published Version","file":[{"file_id":"6480","relation":"source_file","checksum":"75f9184c1346e10a5de5f9cc7338309a","date_created":"2019-05-23T11:18:16Z","date_updated":"2020-07-14T12:47:31Z","access_level":"closed","file_name":"Thesis_Cepeda.zip","creator":"scepeda","content_type":"application/zip","file_size":23937464},{"checksum":"afdc0633ddbd71d5b13550d7fb4f4454","date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-23T11:18:13Z","relation":"main_file","file_id":"6481","content_type":"application/pdf","file_size":16646985,"creator":"scepeda","access_level":"open_access","file_name":"CepedaThesis.pdf"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. "}]},{"has_accepted_license":"1","article_processing_charge":"No","day":"11","date_published":"2019-03-11T00:00:00Z","page":"189","citation":{"ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019."},"abstract":[{"lang":"eng","text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"file_size":20995465,"content_type":"application/pdf","creator":"rprizak","access_level":"open_access","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","checksum":"e60a72de35d270b31f1a23d50f224ec0","date_created":"2019-03-06T16:05:07Z","date_updated":"2020-07-14T12:47:18Z","relation":"main_file","file_id":"6072"},{"title":"Latex files","file_id":"6073","relation":"source_file","date_created":"2019-03-06T16:09:39Z","date_updated":"2020-07-14T12:47:18Z","checksum":"67c2630333d05ebafef5f018863a8465","file_name":"thesis_v2_merge.zip","access_level":"closed","creator":"rprizak","content_type":"application/zip","file_size":85705272}],"oa_version":"Published Version","title":"Coevolution of transcription factors and their binding sites in sequence space","status":"public","ddc":["576"],"_id":"6071","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"month":"03","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"doi":"10.15479/at:ista:th6071","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"oa":1,"file_date_updated":"2020-07-14T12:47:18Z","date_updated":"2023-09-22T10:00:48Z","date_created":"2019-03-06T16:16:10Z","related_material":{"record":[{"id":"1358","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"955"}]},"author":[{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publication_status":"published","year":"2019"}]