[{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer Aided Verification"},"type":"conference","_id":"8272","department":[{"_id":"KrCh"}],"file_date_updated":"2020-08-17T11:32:44Z","ddc":["000"],"date_updated":"2023-10-03T11:36:13Z","intvolume":" 12225","month":"07","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"volume":12225,"related_material":{"record":[{"status":"public","id":"12738","relation":"later_version"}]},"language":[{"iso":"eng"}],"file":[{"file_id":"8276","checksum":"093d4788d7d5b2ce0ffe64fbe7820043","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-08-17T11:32:44Z","file_name":"2020_LNCS_CAV_Chatterjee.pdf","creator":"dernst","date_updated":"2020-08-17T11:32:44Z","file_size":625056}],"publication_status":"published","publication_identifier":{"issn":["03029743"],"isbn":["9783030532901"],"eissn":["16113349"]},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"title":"Stochastic games with lexicographic reachability-safety objectives","external_id":{"isi":["000695272500021"],"arxiv":["2005.04018"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Katoen","full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P"},{"first_name":"Maximilian","last_name":"Weininger","full_name":"Weininger, Maximilian"},{"first_name":"Tobias","full_name":"Winkler, Tobias","last_name":"Winkler"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21.","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in International Conference on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.","ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: International Conference on Computer Aided Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21","apa":"Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In International Conference on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature. https://doi.org/10.1007/978-3-030-53291-8_21","chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In International Conference on Computer Aided Verification, 12225:398–420. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21.","ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2020-08-16T22:00:58Z","date_published":"2020-07-14T00:00:00Z","doi":"10.1007/978-3-030-53291-8_21","page":"398-420","publication":"International Conference on Computer Aided Verification","day":"14","year":"2020","has_accepted_license":"1","isi":1},{"page":"145-161","date_published":"2020-02-27T00:00:00Z","doi":"10.1016/bs.mcb.2020.01.006","date_created":"2020-03-08T23:00:47Z","isi":1,"year":"2020","day":"27","publication":"Methods in Cell Biology","quality_controlled":"1","publisher":"Elsevier","oa":1,"author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"external_id":{"isi":["000611826500008"]},"article_processing_charge":"No","editor":[{"last_name":"Tran","full_name":"Tran, Phong ","first_name":"Phong "}],"title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","citation":{"short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161.","ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.","apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier. https://doi.org/10.1016/bs.mcb.2020.01.006","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006.","ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.","chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61. Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"volume":158,"related_material":{"record":[{"id":"8358","status":"public","relation":"part_of_dissertation"}]},"ec_funded":1,"publication_identifier":{"issn":["0091679X"]},"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["Methods in Cell Biology"],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1101/839571","open_access":"1"}],"month":"02","intvolume":" 158","abstract":[{"lang":"eng","text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material."}],"oa_version":"Preprint","department":[{"_id":"MaLo"}],"date_updated":"2023-10-04T09:50:24Z","type":"book_chapter","status":"public","_id":"7572"},{"project":[{"call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","name":"Self-Organization of the Bacterial Cell"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","name":"Reconstitution of bacterial cell wall sythesis","grant_number":"LT000824/2016"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020. https://doi.org/10.1038/s41564-019-0657-5.","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5","ieee":"N. S. Baranova et al., “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology, vol. 5. Springer Nature, pp. 407–417, 2020.","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology, vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S."},{"orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Víctor M.","last_name":"Hernández-Rocamora","full_name":"Hernández-Rocamora, Víctor M."},{"first_name":"Carlos","last_name":"Alfonso","full_name":"Alfonso, Carlos"},{"id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","first_name":"Maria D","last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D"},{"first_name":"Germán","last_name":"Rivas","full_name":"Rivas, Germán"},{"last_name":"Vollmer","full_name":"Vollmer, Waldemar","first_name":"Waldemar"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"external_id":{"pmid":["31959972"],"isi":["000508584700007"]},"article_processing_charge":"No","title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"year":"2020","day":"20","publication":"Nature Microbiology","page":"407-417","date_published":"2020-01-20T00:00:00Z","doi":"10.1038/s41564-019-0657-5","date_created":"2020-01-28T16:14:41Z","_id":"7387","type":"journal_article","article_type":"letter_note","status":"public","date_updated":"2023-10-06T12:22:38Z","department":[{"_id":"MaLo"}],"abstract":[{"lang":"eng","text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site."}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://europepmc.org/article/PMC/7048620"}],"month":"01","intvolume":" 5","publication_identifier":{"issn":["2058-5276"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":5,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/"}],"record":[{"id":"14280","status":"public","relation":"dissertation_contains"}]},"ec_funded":1},{"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8164","creator":"mwintrae","date_updated":"2020-07-24T07:09:06Z","file_size":1476072,"date_created":"2020-07-24T07:09:06Z","file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1588-2896"],"issn":["0081-6906"]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"2","volume":57,"oa_version":"Published Version","abstract":[{"text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.","lang":"eng"}],"intvolume":" 57","month":"07","scopus_import":"1","ddc":["510"],"date_updated":"2023-10-10T13:05:27Z","file_date_updated":"2020-07-24T07:09:06Z","department":[{"_id":"HeEd"}],"_id":"8163","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","publication":"Studia Scientiarum Mathematicarum Hungarica","day":"24","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-07-24T07:09:18Z","date_published":"2020-07-24T00:00:00Z","doi":"10.1556/012.2020.57.2.1454","page":"193-199","acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","oa":1,"publisher":"Akadémiai Kiadó","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199.","chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó, 2020. https://doi.org/10.1556/012.2020.57.2.1454.","apa":"Vegter, G., & Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó. https://doi.org/10.1556/012.2020.57.2.1454","ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 2020;57(2):193-199. doi:10.1556/012.2020.57.2.1454","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020.","short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199.","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454."},"title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","external_id":{"isi":["000570978400005"]},"article_processing_charge":"No","author":[{"full_name":"Vegter, Gert","last_name":"Vegter","first_name":"Gert"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z00342"}]},{"citation":{"mla":"Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:10.29252/ijmsi.15.2.117.","ieee":"A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020.","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.","apa":"Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117","ama":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117","chicago":"Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.","ista":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1805.10672"]},"article_processing_charge":"No","author":[{"last_name":"Shakiba","full_name":"Shakiba, A.","first_name":"A."},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady"},{"first_name":"M.R.","full_name":"Hooshmandasl, M.R.","last_name":"Hooshmandasl"},{"first_name":"M.","full_name":"Alambardar Meybodi, M.","last_name":"Alambardar Meybodi"}],"title":"A note on belief structures and s-approximation spaces","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"year":"2020","has_accepted_license":"1","publication":"Iranian Journal of Mathematical Sciences and Informatics","day":"01","page":"117-128","date_created":"2020-10-18T22:01:36Z","doi":"10.29252/ijmsi.15.2.117","date_published":"2020-10-01T00:00:00Z","acknowledgement":"We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences.","oa":1,"quality_controlled":"1","publisher":"Iranian Academic Center for Education, Culture and Research","date_updated":"2023-10-16T09:25:00Z","ddc":["000"],"file_date_updated":"2020-10-19T11:14:20Z","department":[{"_id":"KrCh"}],"_id":"8671","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2008-9473"],"issn":["1735-4463"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2020_ijmsi_Shakiba_accepted.pdf","date_created":"2020-10-19T11:14:20Z","file_size":261688,"date_updated":"2020-10-19T11:14:20Z","creator":"dernst","success":1,"file_id":"8676","checksum":"f299661a6d51cda6d255a76be696f48d","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"volume":15,"issue":"2","abstract":[{"lang":"eng","text":"We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. "}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 15","month":"10"},{"file_date_updated":"2020-09-21T13:15:02Z","department":[{"_id":"JaMa"}],"date_updated":"2023-10-16T09:22:50Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"6359","volume":25,"publication_status":"published","publication_identifier":{"eissn":["1083-6489"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":273042,"date_updated":"2020-09-21T13:15:02Z","file_name":"2020_EJournProbab_Dareiotis.pdf","date_created":"2020-09-21T13:15:02Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8549","checksum":"8e7c42e72596f6889d786e8e8b89994f"}],"scopus_import":"1","intvolume":" 25","month":"07","abstract":[{"text":"The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","external_id":{"arxiv":["1812.04583"],"isi":["000550150700001"]},"author":[{"first_name":"Konstantinos","last_name":"Dareiotis","full_name":"Dareiotis, Konstantinos"},{"last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"}],"title":"On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift","citation":{"chicago":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP479.","ista":"Dareiotis K, Gerencser M. 2020. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 25, 82.","mla":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability, vol. 25, 82, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP479.","apa":"Dareiotis, K., & Gerencser, M. (2020). On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP479","ama":"Dareiotis K, Gerencser M. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP479","short":"K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020).","ieee":"K. Dareiotis and M. Gerencser, “On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"82","date_created":"2019-04-30T07:40:17Z","date_published":"2020-07-16T00:00:00Z","doi":"10.1214/20-EJP479","year":"2020","isi":1,"has_accepted_license":"1","publication":"Electronic Journal of Probability","day":"16","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1"},{"ddc":["000"],"date_updated":"2023-10-16T10:04:02Z","supervisor":[{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"department":[{"_id":"ChLa"}],"file_date_updated":"2020-09-14T13:39:17Z","_id":"8390","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_name":"2020_Thesis_Royer.pdf","date_created":"2020-09-14T13:39:14Z","creator":"dernst","file_size":30224591,"date_updated":"2020-09-14T13:39:14Z","success":1,"checksum":"c914d2f88846032f3d8507734861b6ee","file_id":"8391","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"checksum":"ae98fb35d912cff84a89035ae5794d3c","file_id":"8392","relation":"main_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"thesis_sources.zip","date_created":"2020-09-14T13:39:17Z","creator":"dernst","file_size":74227627,"date_updated":"2020-09-14T13:39:17Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-007-7"]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"relation":"part_of_dissertation","id":"7936","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7937"},{"relation":"part_of_dissertation","id":"8193","status":"public"},{"status":"public","id":"8092","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"911","status":"public"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"abstract":[{"text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. ","lang":"eng"}],"month":"09","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390","mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria.","chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390."},"title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","article_processing_charge":"No","author":[{"orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","last_name":"Royer","first_name":"Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87"}],"day":"14","year":"2020","has_accepted_license":"1","date_created":"2020-09-14T13:42:09Z","doi":"10.15479/AT:ISTA:8390","date_published":"2020-09-14T00:00:00Z","page":"197","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","oa":1,"publisher":"Institute of Science and Technology Austria"},{"page":"7498-7507","date_created":"2020-07-31T16:53:49Z","date_published":"2020-07-01T00:00:00Z","doi":"10.1109/CVPR42600.2020.00752","year":"2020","has_accepted_license":"1","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","day":"01","oa":1,"publisher":"IEEE","quality_controlled":"1","article_processing_charge":"No","external_id":{"arxiv":["2004.04180"]},"author":[{"id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445","last_name":"Henderson"},{"first_name":"Vagia","last_name":"Tsiminaki","full_name":"Tsiminaki, Vagia"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"title":"Leveraging 2D data to learn textured 3D mesh generation","citation":{"ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507.","chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 7498–7507. IEEE, 2020. https://doi.org/10.1109/CVPR42600.2020.00752.","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.","ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Virtual, 2020, pp. 7498–7507.","apa":"Henderson, P. M., Tsiminaki, V., & Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 7498–7507). Virtual: IEEE. https://doi.org/10.1109/CVPR42600.2020.00752","ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2020:7498-7507. doi:10.1109/CVPR42600.2020.00752","mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–507, doi:10.1109/CVPR42600.2020.00752."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publication_identifier":{"eisbn":["9781728171685"],"eissn":["2575-7075"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-07-31T16:57:12Z","file_name":"paper.pdf","date_updated":"2020-07-31T16:57:12Z","file_size":10262773,"creator":"phenders","file_id":"8187","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"main_file_link":[{"open_access":"1","url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf"}],"scopus_import":"1","month":"07","abstract":[{"text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes.","lang":"eng"}],"oa_version":"Submitted Version","file_date_updated":"2020-07-31T16:57:12Z","department":[{"_id":"ChLa"}],"date_updated":"2023-10-17T07:37:11Z","ddc":["004"],"conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","start_date":"2020-06-14","location":"Virtual","end_date":"2020-06-19"},"type":"conference","status":"public","_id":"8186"},{"_id":"7416","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-10-17T09:01:48Z","department":[{"_id":"JiFr"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements."}],"intvolume":" 15","month":"01","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1559-2324"]},"issue":"1","volume":15,"article_number":"1687175","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 15(1), 1687175.","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior. Taylor & Francis, 2020. https://doi.org/10.1080/15592324.2019.1687175.","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687175","apa":"Sinclair, S. A., & Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2019.1687175","short":"S.A. Sinclair, U. Krämer, Plant Signaling & Behavior 15 (2020).","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” Plant Signaling & Behavior, vol. 15, no. 1. Taylor & Francis, 2020.","mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior, vol. 15, no. 1, 1687175, Taylor & Francis, 2020, doi:10.1080/15592324.2019.1687175."},"title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","external_id":{"pmid":["31696764"],"isi":["000494909300001"]},"article_processing_charge":"No","author":[{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A","orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A","last_name":"Sinclair"},{"full_name":"Krämer, U.","last_name":"Krämer","first_name":"U."}],"oa":1,"publisher":"Taylor & Francis","quality_controlled":"1","publication":"Plant Signaling & Behavior","day":"01","year":"2020","isi":1,"date_created":"2020-01-30T10:12:04Z","doi":"10.1080/15592324.2019.1687175","date_published":"2020-01-01T00:00:00Z"},{"issue":"1","volume":16,"related_material":{"record":[{"id":"9723","status":"deleted","relation":"research_data"}]},"publication_status":"published","publication_identifier":{"issn":["1553-7374"]},"language":[{"iso":"eng"}],"file":[{"checksum":"a297f54d1fef0efe4789ca00f37f241e","file_id":"7484","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2020_PLOSPatho_Dick.pdf","date_created":"2020-02-11T10:07:28Z","file_size":4551246,"date_updated":"2020-07-14T12:47:59Z","creator":"dernst"}],"scopus_import":"1","intvolume":" 16","month":"01","abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"FlSc"}],"date_updated":"2023-10-17T12:29:34Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"7464","date_created":"2020-02-06T18:47:17Z","date_published":"2020-01-27T00:00:00Z","doi":"10.1371/journal.ppat.1008277","year":"2020","has_accepted_license":"1","isi":1,"publication":"PLOS Pathogens","day":"27","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","article_processing_charge":"No","external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"author":[{"first_name":"Robert A.","full_name":"Dick, Robert A.","last_name":"Dick"},{"first_name":"Chaoyi","full_name":"Xu, Chaoyi","last_name":"Xu"},{"full_name":"Morado, Dustin R.","last_name":"Morado","first_name":"Dustin R."},{"last_name":"Kravchuk","orcid":"0000-0001-9523-9089","full_name":"Kravchuk, Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","first_name":"Vladyslav"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"full_name":"Lyddon, Terri D.","last_name":"Lyddon","first_name":"Terri D."},{"last_name":"Broad","full_name":"Broad, Arianna M.","first_name":"Arianna M."},{"first_name":"J. Ryan","last_name":"Feathers","full_name":"Feathers, J. Ryan"},{"full_name":"Johnson, Marc C.","last_name":"Johnson","first_name":"Marc C."},{"full_name":"Vogt, Volker M.","last_name":"Vogt","first_name":"Volker M."},{"full_name":"Perilla, Juan R.","last_name":"Perilla","first_name":"Juan R."},{"last_name":"Briggs","full_name":"Briggs, John A. G.","first_name":"John A. G."},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","citation":{"ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","ieee":"R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol. 16, no. 1. Public Library of Science, 2020.","ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"article_number":"e1008277"}]