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M., Richter, B., & Lee, O. (2019). Graphs with at most one crossing. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2019.06.031"},"arxiv":1,"author":[{"first_name":"André ","last_name":"Silva","full_name":"Silva, André "},{"orcid":"0000-0003-2401-8670","full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara","first_name":"Alan M","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Richter, Bruce","first_name":"Bruce","last_name":"Richter"},{"full_name":"Lee, Orlando","last_name":"Lee","first_name":"Orlando"}],"month":"11","_id":"6638","language":[{"iso":"eng"}],"issue":"11","page":"3201-3207","date_updated":"2023-08-29T06:31:41Z","day":"01","publication_identifier":{"issn":["0012-365X"]},"external_id":{"arxiv":["1901.09955"],"isi":["000486358100025"]},"isi":1,"doi":"10.1016/j.disc.2019.06.031","title":"Graphs with at most one crossing","article_processing_charge":"No","oa":1,"ec_funded":1,"year":"2019","date_created":"2019-07-14T21:59:20Z","scopus_import":"1","oa_version":"Preprint","intvolume":" 342","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Discrete Mathematics","date_published":"2019-11-01T00:00:00Z","status":"public","abstract":[{"text":"The crossing number of a graph G is the least number of crossings over all possible drawings of G. We present a structural characterization of graphs with crossing number one.","lang":"eng"}],"publisher":"Elsevier","publication_status":"published","quality_controlled":"1","project":[{"name":"Reglas de Conectividad funcional en el hipocampo","_id":"26366136-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"}],"department":[{"_id":"UlWa"}],"type":"journal_article","volume":342,"main_file_link":[{"url":"https://arxiv.org/abs/1901.09955","open_access":"1"}]},{"day":"21","date_updated":"2024-02-28T13:01:28Z","title":"On diffusive variants of some classical viscoelastic rate-type models","doi":"10.1063/1.5109493","isi":1,"external_id":{"isi":["000479303100002"],"arxiv":["1902.07983"]},"oa":1,"article_processing_charge":"No","conference":{"location":"Zlin, Czech Republic","name":"8th International Conference on Novel Trends in Rheology","start_date":"2019-07-30","end_date":"2019-07-31"},"year":"2019","arxiv":1,"citation":{"mla":"Dostalík, Mark, et al. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” AIP Conference Proceedings, vol. 2107, 020002, AIP Publishing, 2019, doi:10.1063/1.5109493.","short":"M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing, 2019.","chicago":"Dostalík, Mark, Vít Pruša, and Tomas Skrivan. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” In AIP Conference Proceedings, Vol. 2107. AIP Publishing, 2019. https://doi.org/10.1063/1.5109493.","ieee":"M. Dostalík, V. Pruša, and T. Skrivan, “On diffusive variants of some classical viscoelastic rate-type models,” in AIP Conference Proceedings, Zlin, Czech Republic, 2019, vol. 2107.","ista":"Dostalík M, Pruša V, Skrivan T. 2019. On diffusive variants of some classical viscoelastic rate-type models. AIP Conference Proceedings. 8th International Conference on Novel Trends in Rheology vol. 2107, 020002.","apa":"Dostalík, M., Pruša, V., & Skrivan, T. (2019). On diffusive variants of some classical viscoelastic rate-type models. In AIP Conference Proceedings (Vol. 2107). Zlin, Czech Republic: AIP Publishing. https://doi.org/10.1063/1.5109493","ama":"Dostalík M, Pruša V, Skrivan T. On diffusive variants of some classical viscoelastic rate-type models. In: AIP Conference Proceedings. Vol 2107. AIP Publishing; 2019. doi:10.1063/1.5109493"},"month":"05","article_number":"020002","author":[{"full_name":"Dostalík, Mark","last_name":"Dostalík","first_name":"Mark"},{"first_name":"Vít","last_name":"Pruša","full_name":"Pruša, Vít"},{"full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Skrivan"}],"_id":"6642","language":[{"iso":"eng"}],"publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"ChWo"}],"quality_controlled":"1","volume":2107,"type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07983"}],"scopus_import":"1","date_created":"2019-07-15T10:07:09Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2107","abstract":[{"lang":"eng","text":"We present a thermodynamically based approach to the design of models for viscoelastic fluids with stress diffusion effect. In particular, we show how to add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus, FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that the resulting models with the added stress diffusion term are thermodynamically consistent in the sense that they obey the first and the second law of thermodynamics. We point out the potential applications of the provided thermodynamical background in the study of flows of fluids described by the proposed models."}],"date_published":"2019-05-21T00:00:00Z","status":"public","publication":"AIP Conference Proceedings"},{"citation":{"mla":"Khatoniar, Mandeep, et al. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” CLEO: Applications and Technology, paper JTu2A.52, Optica Publishing Group, 2019, doi:10.1364/cleo_at.2019.jtu2a.52.","short":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, V. Menon, in:, CLEO: Applications and Technology, Optica Publishing Group, 2019.","ieee":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, and V. Menon, “Room temperature control of valley coherence in bilayer WS2 exciton polaritons,” in CLEO: Applications and Technology, San Jose, CA, United States, 2019.","chicago":"Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan Ghaemi, and Vinod Menon. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” In CLEO: Applications and Technology. Optica Publishing Group, 2019. https://doi.org/10.1364/cleo_at.2019.jtu2a.52.","apa":"Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., & Menon, V. (2019). Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In CLEO: Applications and Technology. San Jose, CA, United States: Optica Publishing Group. https://doi.org/10.1364/cleo_at.2019.jtu2a.52","ista":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. 2019. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. CLEO: Applications and Technology. CLEO: Conference on Lasers and Electro-Optics, paper JTu2A.52.","ama":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In: CLEO: Applications and Technology. 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Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38.","ieee":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 38:1-38:13.","mla":"Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13, doi:10.4230/LIPICS.SOCG.2019.38.","short":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13.","ama":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:38:1-38:13. doi:10.4230/LIPICS.SOCG.2019.38","ista":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2019. The crossing Tverberg theorem. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 38:1-38:13.","apa":"Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2019). The crossing Tverberg theorem. In 35th International Symposium on Computational Geometry (Vol. 129, p. 38:1-38:13). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.38"},"conference":{"start_date":"2019-06-18","end_date":"2019-06-21","location":"Portland, OR, United States","name":"SoCG 2019: Symposium on Computational Geometry"},"related_material":{"record":[{"relation":"later_version","id":"13974","status":"public"}]},"has_accepted_license":"1","year":"2019","oa":1,"doi":"10.4230/LIPICS.SOCG.2019.38","title":"The crossing Tverberg theorem","external_id":{"arxiv":["1812.04911"]},"day":"01","publication_identifier":{"isbn":["9783959771047"],"issn":["1868-8969"]},"date_updated":"2023-12-13T12:03:35Z","abstract":[{"lang":"eng","text":"The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2."}],"publication":"35th International Symposium on Computational Geometry","date_published":"2019-06-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 129","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_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"date_created":"2019-07-17T10:35:04Z","type":"conference","volume":129,"department":[{"_id":"UlWa"}],"quality_controlled":"1","project":[{"grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"type":"conference","volume":129,"department":[{"_id":"HeEd"}],"quality_controlled":"1","project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF"}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","abstract":[{"text":"Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory\r\nneeded for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.","lang":"eng"}],"publication":"35th International Symposium on Computational Geometry","status":"public","date_published":"2019-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 129","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_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"date_created":"2019-07-17T10:36:09Z","conference":{"location":"Portland, OR, United States","name":"SoCG 2019: Symposium on Computational Geometry","start_date":"2019-06-18","end_date":"2019-06-21"},"has_accepted_license":"1","year":"2019","oa":1,"doi":"10.4230/LIPICS.SOCG.2019.31","title":"Topological data analysis in information space","external_id":{"arxiv":["1903.08510"]},"day":"01","publication_identifier":{"isbn":["9783959771047"]},"date_updated":"2021-01-12T08:08:23Z","page":"31:1-31:14","language":[{"iso":"eng"}],"_id":"6648","file":[{"file_name":"2019_LIPICS_Edelsbrunner.pdf","relation":"main_file","creator":"dernst","checksum":"8ec8720730d4c789bf7b06540f1c29f4","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:35Z","date_created":"2019-07-24T06:40:01Z","file_size":1355179,"file_id":"6666"}],"author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Virk, Ziga","last_name":"Virk","first_name":"Ziga"},{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:35Z","month":"06","ddc":["510"],"arxiv":1,"citation":{"short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14.","mla":"Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14, doi:10.4230/LIPICS.SOCG.2019.31.","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information space,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 31:1-31:14.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data Analysis in Information Space.” In 35th International Symposium on Computational Geometry, 129:31:1-31:14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.31.","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2019). Topological data analysis in information space. In 35th International Symposium on Computational Geometry (Vol. 129, p. 31:1-31:14). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.31","ista":"Edelsbrunner H, Virk Z, Wagner H. 2019. Topological data analysis in information space. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 31:1-31:14.","ama":"Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information space. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:31:1-31:14. doi:10.4230/LIPICS.SOCG.2019.31"}},{"abstract":[{"text":"We propose a novel technique for the automatic design of molds to cast highly complex shapes. The technique generates composite, two-piece molds. Each mold piece is made up of a hard plastic shell and a flexible silicone part. Thanks to the thin, soft, and smartly shaped silicone part, which is kept in place by a hard plastic shell, we can cast objects of unprecedented complexity. An innovative algorithm based on a volumetric analysis defines the layout of the internal cuts in the silicone mold part. Our approach can robustly handle thin protruding features and intertwined topologies that have caused previous methods to fail. We compare our results with state of the art techniques, and we demonstrate the casting of shapes with extremely complex geometry.","lang":"eng"}],"date_published":"2019-07-01T00:00:00Z","status":"public","publication":"ACM Transactions on Graphics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 38","oa_version":"Submitted Version","scopus_import":"1","date_created":"2019-07-19T06:18:15Z","volume":38,"type":"journal_article","department":[{"_id":"BeBi"}],"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020"}],"quality_controlled":"1","publication_status":"published","publisher":"ACM","issue":"4","_id":"6650","language":[{"iso":"eng"}],"article_number":"110","file_date_updated":"2020-07-14T12:47:35Z","month":"07","file":[{"checksum":"b4562af94672b44d2a501046427412af","creator":"dernst","file_name":"2019_ACM_Alderighi_AuthorVersion.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2019-07-19T06:18:53Z","date_updated":"2020-07-14T12:47:35Z","access_level":"open_access","file_id":"6651","file_size":74316182}],"author":[{"first_name":"Thomas","last_name":"Alderighi","full_name":"Alderighi, Thomas"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"last_name":"Giorgi","first_name":"Daniela","full_name":"Giorgi, Daniela"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"full_name":"Cignoni, Paolo","first_name":"Paolo","last_name":"Cignoni"},{"full_name":"Pietroni, Nico","first_name":"Nico","last_name":"Pietroni"}],"citation":{"ama":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. Volume-aware design of composite molds. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322981","ista":"Alderighi T, Malomo L, Giorgi D, Bickel B, Cignoni P, Pietroni N. 2019. Volume-aware design of composite molds. ACM Transactions on Graphics. 38(4), 110.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Bickel, B., Cignoni, P., & Pietroni, N. (2019). Volume-aware design of composite molds. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322981","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322981.","ieee":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, and N. Pietroni, “Volume-aware design of composite molds,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","short":"T. Alderighi, L. Malomo, D. Giorgi, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 38 (2019).","mla":"Alderighi, Thomas, et al. “Volume-Aware Design of Composite Molds.” ACM Transactions on Graphics, vol. 38, no. 4, 110, ACM, 2019, doi:10.1145/3306346.3322981."},"ddc":["000"],"related_material":{"link":[{"description":"YouTube Video","relation":"supplementary_material","url":"https://youtu.be/SO349S8-x_w"}]},"has_accepted_license":"1","ec_funded":1,"year":"2019","article_processing_charge":"No","oa":1,"title":"Volume-aware design of composite molds","doi":"10.1145/3306346.3322981","isi":1,"external_id":{"isi":["000475740600084"]},"publication_identifier":{"issn":["0730-0301"]},"day":"01","date_updated":"2023-08-29T06:35:52Z"},{"type":"journal_article","volume":72,"department":[{"_id":"E-Lib"}],"quality_controlled":"1","publication_status":"published","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","abstract":[{"text":"In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as \"gold\" and \"green\" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising.","lang":"eng"}],"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","status":"public","date_published":"2019-05-17T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"},"intvolume":" 72","oa_version":"Published Version","scopus_import":"1","date_created":"2019-07-21T21:59:15Z","related_material":{"record":[{"id":"5686","relation":"earlier_version","status":"public"}]},"has_accepted_license":"1","year":"2019","oa":1,"article_processing_charge":"No","doi":"10.31263/voebm.v72i1.2276","title":"An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors","day":"17","publication_identifier":{"eissn":["1022-2588"]},"date_updated":"2023-10-17T11:33:58Z","page":"59-65","issue":"1","_id":"6657","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","checksum":"c0d2695d6d0d34e62ba06fb3f0ebaaed","creator":"apreinsp","file_name":"2019_MitteilungenDerVOEB_Danowski.pdf","relation":"main_file","file_id":"6661","file_size":468558,"date_updated":"2020-07-14T12:47:35Z","date_created":"2019-07-22T08:45:03Z","access_level":"open_access"}],"author":[{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick","last_name":"Danowski","orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick"}],"month":"05","file_date_updated":"2020-07-14T12:47:35Z","article_type":"original","ddc":["020"],"citation":{"mla":"Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 72, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019, pp. 59–65, doi:10.31263/voebm.v72i1.2276.","short":"P. Danowski, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 72 (2019) 59–65.","chicago":"Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019. https://doi.org/10.31263/voebm.v72i1.2276.","ieee":"P. Danowski, “An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 72, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 59–65, 2019.","ista":"Danowski P. 2019. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 72(1), 59–65.","apa":"Danowski, P. (2019). An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v72i1.2276","ama":"Danowski P. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2019;72(1):59-65. doi:10.31263/voebm.v72i1.2276"}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","license":"https://creativecommons.org/licenses/by-nc/4.0/","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"intvolume":" 29","abstract":[{"lang":"eng","text":"New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization. "}],"date_published":"2019-07-01T00:00:00Z","status":"public","publication":"Genome Research","scopus_import":"1","date_created":"2019-07-21T21:59:15Z","oa_version":"Published Version","volume":29,"type":"journal_article","publication_status":"published","publisher":"CSH Press","department":[{"_id":"BeVi"}],"quality_controlled":"1","_id":"6658","language":[{"iso":"eng"}],"page":"1115-1122","issue":"7","citation":{"ama":"Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline expression. Genome Research. 2019;29(7):1115-1122. doi:10.1101/gr.238824.118","apa":"Raices, J., Otto, P., & Vibranovski, M. (2019). Haploid selection drives new gene male germline expression. Genome Research. CSH Press. https://doi.org/10.1101/gr.238824.118","ista":"Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 1115–1122.","ieee":"J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene male germline expression,” Genome Research, vol. 29, no. 7. CSH Press, pp. 1115–1122, 2019.","chicago":"Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research. CSH Press, 2019. https://doi.org/10.1101/gr.238824.118.","short":"J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.","mla":"Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.” Genome Research, vol. 29, no. 7, CSH Press, 2019, pp. 1115–22, doi:10.1101/gr.238824.118."},"ddc":["576"],"file_date_updated":"2020-07-14T12:47:35Z","month":"07","author":[{"full_name":"Raices, Julia","last_name":"Raices","first_name":"Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otto, Paulo","first_name":"Paulo","last_name":"Otto"},{"full_name":"Vibranovski, Maria","first_name":"Maria","last_name":"Vibranovski"}],"file":[{"date_updated":"2020-07-14T12:47:35Z","date_created":"2019-07-24T08:05:56Z","access_level":"open_access","file_id":"6670","file_size":2319022,"creator":"apreinsp","checksum":"4636f03a6750f90b88bf2bc3eb9d71ae","file_name":"2019_GenomeResearch_Raices.pdf","relation":"main_file","content_type":"application/pdf"}],"article_processing_charge":"No","oa":1,"has_accepted_license":"1","year":"2019","day":"01","date_updated":"2023-08-29T06:35:05Z","title":"Haploid selection drives new gene male germline expression","doi":"10.1101/gr.238824.118","isi":1,"external_id":{"isi":["000473730600007"]}},{"department":[{"_id":"RySh"}],"quality_controlled":"1","project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","publisher":"Bulletin of the Chemical Society of Japan","type":"journal_article","volume":92,"oa_version":"Published Version","scopus_import":"1","date_created":"2019-07-21T21:59:16Z","abstract":[{"lang":"eng","text":"Chemical labeling of proteins with synthetic molecular probes offers the possibility to probe the functions of proteins of interest in living cells. However, the methods for covalently labeling targeted proteins using complementary peptide tag-probe pairs are still limited, irrespective of the versatility of such pairs in biological research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific covalent labeling of proteins. A broad-range evaluation of the reactivity profiles of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized and high labeling selectivity and reactivity. In particular, the labeling specificity of this pair was notably improved compared to the previously reported one. This pair was successfully utilized for the fluorescence imaging of membrane proteins on the surfaces of living cells, demonstrating its potential utility in biological research."}],"publication":"Bulletin of the Chemical Society of Japan","status":"public","date_published":"2019-05-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 92","doi":"10.1246/bcsj.20190034","title":"Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins","day":"15","publication_identifier":{"issn":["00092673"]},"date_updated":"2021-01-12T08:08:26Z","has_accepted_license":"1","year":"2019","ec_funded":1,"oa":1,"article_processing_charge":"No","file":[{"access_level":"open_access","date_updated":"2020-10-02T08:49:58Z","date_created":"2020-10-02T08:49:58Z","file_size":2464903,"success":1,"file_id":"8594","relation":"main_file","file_name":"2019_BCSJ_Zenmyo.pdf","checksum":"186de511d6e0ca93f5d981e2443eb8cd","creator":"dernst","content_type":"application/pdf"}],"author":[{"first_name":"Naoki","last_name":"Zenmyo","full_name":"Zenmyo, Naoki"},{"first_name":"Hiroki","last_name":"Tokumaru","full_name":"Tokumaru, Hiroki"},{"full_name":"Uchinomiya, Shohei","last_name":"Uchinomiya","first_name":"Shohei"},{"full_name":"Fuchida, Hirokazu","last_name":"Fuchida","first_name":"Hirokazu"},{"full_name":"Tabata, Shigekazu","id":"4427179E-F248-11E8-B48F-1D18A9856A87","last_name":"Tabata","first_name":"Shigekazu"},{"last_name":"Hamachi","first_name":"Itaru","full_name":"Hamachi, Itaru"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto"},{"last_name":"Ojida","first_name":"Akio","full_name":"Ojida, Akio"}],"file_date_updated":"2020-10-02T08:49:58Z","month":"05","article_type":"original","ddc":["570"],"citation":{"mla":"Zenmyo, Naoki, et al. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan, vol. 92, no. 5, Bulletin of the Chemical Society of Japan, 2019, pp. 995–1000, doi:10.1246/bcsj.20190034.","short":"N. Zenmyo, H. Tokumaru, S. Uchinomiya, H. Fuchida, S. Tabata, I. Hamachi, R. Shigemoto, A. Ojida, Bulletin of the Chemical Society of Japan 92 (2019) 995–1000.","ieee":"N. Zenmyo et al., “Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins,” Bulletin of the Chemical Society of Japan, vol. 92, no. 5. Bulletin of the Chemical Society of Japan, pp. 995–1000, 2019.","chicago":"Zenmyo, Naoki, Hiroki Tokumaru, Shohei Uchinomiya, Hirokazu Fuchida, Shigekazu Tabata, Itaru Hamachi, Ryuichi Shigemoto, and Akio Ojida. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan, 2019. https://doi.org/10.1246/bcsj.20190034.","apa":"Zenmyo, N., Tokumaru, H., Uchinomiya, S., Fuchida, H., Tabata, S., Hamachi, I., … Ojida, A. (2019). Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan. https://doi.org/10.1246/bcsj.20190034","ista":"Zenmyo N, Tokumaru H, Uchinomiya S, Fuchida H, Tabata S, Hamachi I, Shigemoto R, Ojida A. 2019. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 92(5), 995–1000.","ama":"Zenmyo N, Tokumaru H, Uchinomiya S, et al. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical Society of Japan. 2019;92(5):995-1000. doi:10.1246/bcsj.20190034"},"page":"995-1000","issue":"5","language":[{"iso":"eng"}],"_id":"6659","acknowledgement":"his work was supported by the Grant-in-Aid for Scientific Research B (JSPS KAKENHI grant no. JP17H03090 to A. O.); the Scientific Research on Innovative Areas “Chemistry for Multimolecular Crowding Biosystems” (JSPS KAKENHI grant no. JP17H06349 to A. O.); and the European Union (European Research Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.). A. O. acknowledges the financial support of the Takeda Science Foundation."},{"language":[{"iso":"eng"}],"_id":"6660","issue":"4","citation":{"apa":"Sumin, D., Weyrich, T., Rittig, T., Babaei, V., Nindel, T., Wilkie, A., … Myszkowski, K. (2019). Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3322992","ista":"Sumin D, Weyrich T, Rittig T, Babaei V, Nindel T, Wilkie A, Didyk P, Bickel B, Křivánek J, Myszkowski K. 2019. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 38(4), 111.","ama":"Sumin D, Weyrich T, Rittig T, et al. Geometry-aware scattering compensation for 3D printing. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3322992","mla":"Sumin, Denis, et al. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics, vol. 38, no. 4, 111, ACM, 2019, doi:10.1145/3306346.3322992.","short":"D. Sumin, T. Weyrich, T. Rittig, V. Babaei, T. Nindel, A. Wilkie, P. Didyk, B. Bickel, J. Křivánek, K. Myszkowski, ACM Transactions on Graphics 38 (2019).","ieee":"D. Sumin et al., “Geometry-aware scattering compensation for 3D printing,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","chicago":"Sumin, Denis, Tim Weyrich, Tobias Rittig, Vahid Babaei, Thomas Nindel, Alexander Wilkie, Piotr Didyk, Bernd Bickel, Jaroslav Křivánek, and Karol Myszkowski. “Geometry-Aware Scattering Compensation for 3D Printing.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3322992."},"ddc":["000"],"article_number":"111","file_date_updated":"2020-07-14T12:47:36Z","month":"07","file":[{"checksum":"43c2019d6b48ed9c56e31686c4c2d1f5","creator":"dernst","file_name":"2019_ACM_Sumin_AuthorVersion.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2019-07-24T07:36:08Z","date_updated":"2020-07-14T12:47:36Z","access_level":"open_access","file_id":"6669","file_size":10109800},{"content_type":"application/zip","file_name":"sumin19geometry-aware-suppl.zip","relation":"supplementary_material","creator":"dernst","checksum":"f80f365a04e35855fa467ea7ab26b16c","file_size":11051245,"file_id":"6938","access_level":"open_access","date_created":"2019-10-11T06:51:07Z","date_updated":"2020-07-14T12:47:36Z"}],"author":[{"last_name":"Sumin","first_name":"Denis","full_name":"Sumin, Denis"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"full_name":"Rittig, Tobias","first_name":"Tobias","last_name":"Rittig"},{"full_name":"Babaei, Vahid","last_name":"Babaei","first_name":"Vahid"},{"first_name":"Thomas","last_name":"Nindel","full_name":"Nindel, Thomas"},{"full_name":"Wilkie, Alexander","first_name":"Alexander","last_name":"Wilkie"},{"last_name":"Didyk","first_name":"Piotr","full_name":"Didyk, Piotr"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel"},{"first_name":"Jaroslav","last_name":"Křivánek","full_name":"Křivánek, Jaroslav"},{"last_name":"Myszkowski","first_name":"Karol","full_name":"Myszkowski, Karol"}],"article_processing_charge":"No","oa":1,"ec_funded":1,"year":"2019","has_accepted_license":"1","date_updated":"2023-08-29T06:40:49Z","publication_identifier":{"issn":["0730-0301"]},"day":"04","isi":1,"external_id":{"isi":["000475740600085"]},"title":"Geometry-aware scattering compensation for 3D printing","doi":"10.1145/3306346.3322992","intvolume":" 38","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-07-04T00:00:00Z","status":"public","publication":"ACM Transactions on Graphics","abstract":[{"lang":"eng","text":"Commercially available full-color 3D printing allows for detailed control of material deposition in a volume, but an exact reproduction of a target surface appearance is hampered by the strong subsurface scattering that causes nontrivial volumetric cross-talk at the print surface. Previous work showed how an iterative optimization scheme based on accumulating absorptive materials at the surface can be used to find a volumetric distribution of print materials that closely approximates a given target appearance.\r\n\r\nIn this work, we first revisit the assumption that pushing the absorptive materials to the surface results in minimal volumetric cross-talk. We design a full-fledged optimization on a small domain for this task and confirm this previously reported heuristic. Then, we extend the above approach that is critically limited to color reproduction on planar surfaces, to arbitrary 3D shapes. Our method enables high-fidelity color texture reproduction on 3D prints by effectively compensating for internal light scattering within arbitrarily shaped objects. In addition, we propose a content-aware gamut mapping that significantly improves color reproduction for the pathological case of thin geometric features. Using a wide range of sample objects with complex textures and geometries, we demonstrate color reproduction whose fidelity is superior to state-of-the-art drivers for color 3D printers."}],"date_created":"2019-07-22T07:22:28Z","scopus_import":"1","oa_version":"Submitted Version","volume":38,"type":"journal_article","publisher":"ACM","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020"}],"quality_controlled":"1","department":[{"_id":"BeBi"}]},{"_id":"6671","language":[{"iso":"eng"}],"page":"29–58","issue":"1-2","article_type":"original","citation":{"apa":"Boissonnat, J.-D., Lieutier, A., & Wintraecken, M. (2019). The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-019-00029-8","ista":"Boissonnat J-D, Lieutier A, Wintraecken M. 2019. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 3(1–2), 29–58.","ama":"Boissonnat J-D, Lieutier A, Wintraecken M. The reach, metric distortion, geodesic convexity and the variation of tangent spaces. Journal of Applied and Computational Topology. 2019;3(1-2):29–58. doi:10.1007/s41468-019-00029-8","short":"J.-D. Boissonnat, A. Lieutier, M. Wintraecken, Journal of Applied and Computational Topology 3 (2019) 29–58.","mla":"Boissonnat, Jean-Daniel, et al. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology, vol. 3, no. 1–2, Springer Nature, 2019, pp. 29–58, doi:10.1007/s41468-019-00029-8.","ieee":"J.-D. Boissonnat, A. Lieutier, and M. Wintraecken, “The reach, metric distortion, geodesic convexity and the variation of tangent spaces,” Journal of Applied and Computational Topology, vol. 3, no. 1–2. Springer Nature, pp. 29–58, 2019.","chicago":"Boissonnat, Jean-Daniel, André Lieutier, and Mathijs Wintraecken. “The Reach, Metric Distortion, Geodesic Convexity and the Variation of Tangent Spaces.” Journal of Applied and Computational Topology. Springer Nature, 2019. https://doi.org/10.1007/s41468-019-00029-8."},"ddc":["000"],"file_date_updated":"2020-07-14T12:47:36Z","month":"06","file":[{"creator":"dernst","checksum":"a5b244db9f751221409cf09c97ee0935","relation":"main_file","file_name":"2019_JournAppliedComputTopol_Boissonnat.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:36Z","date_created":"2019-07-31T08:09:56Z","access_level":"open_access","file_id":"6741","file_size":2215157}],"author":[{"full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat","first_name":"Jean-Daniel"},{"first_name":"André","last_name":"Lieutier","full_name":"Lieutier, André"},{"full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes (via OA deal)","oa":1,"has_accepted_license":"1","ec_funded":1,"year":"2019","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"day":"01","date_updated":"2023-08-22T12:37:47Z","title":"The reach, metric distortion, geodesic convexity and the variation of tangent spaces","doi":"10.1007/s41468-019-00029-8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"},"intvolume":" 3","abstract":[{"lang":"eng","text":"In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points."}],"date_published":"2019-06-01T00:00:00Z","status":"public","publication":"Journal of Applied and Computational Topology","date_created":"2019-07-24T08:37:29Z","oa_version":"Published Version","volume":3,"type":"journal_article","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1"},{"project":[{"call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning"}],"quality_controlled":"1","department":[{"_id":"DaAl"}],"publisher":"ACM Press","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/2003.09363","open_access":"1"}],"type":"conference","oa_version":"Preprint","date_created":"2019-07-24T08:59:36Z","scopus_import":"1","status":"public","date_published":"2019-06-01T00:00:00Z","publication":"31st ACM Symposium on Parallelism in Algorithms and Architectures","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."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"external_id":{"arxiv":["2003.09363"],"isi":["000507618500018"]},"title":"Efficiency guarantees for parallel incremental algorithms under relaxed schedulers","doi":"10.1145/3323165.3323201","date_updated":"2023-09-07T13:31:39Z","publication_identifier":{"isbn":["9781450361842"]},"day":"01","ec_funded":1,"year":"2019","related_material":{"record":[{"status":"public","id":"10429","relation":"dissertation_contains"}]},"conference":{"end_date":"2019-06-24","start_date":"2019-06-22","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","location":"Phoenix, AZ, United States"},"oa":1,"article_processing_charge":"No","month":"06","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Nadiradze","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi"},{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval"}],"arxiv":1,"citation":{"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.","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.","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.","short":"D.-A. Alistarh, G. Nadiradze, N. Koval, in:, 31st ACM Symposium on Parallelism in Algorithms and Architectures, ACM Press, 2019, pp. 145–154.","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","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."},"page":"145-154","_id":"6673","language":[{"iso":"eng"}]},{"department":[{"_id":"DaAl"}],"quality_controlled":"1","publication_status":"published","publisher":"ACM Press","main_file_link":[{"url":"https://arxiv.org/abs/1811.01421","open_access":"1"}],"type":"conference","oa_version":"Preprint","scopus_import":"1","date_created":"2019-07-24T09:13:05Z","abstract":[{"lang":"eng","text":"It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power."}],"publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","status":"public","date_published":"2019-06-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1145/3313276.3316407","title":"Why extension-based proofs fail","external_id":{"arxiv":["1811.01421"],"isi":["000523199100089"]},"isi":1,"day":"01","publication_identifier":{"isbn":["9781450367059"]},"date_updated":"2023-12-13T12:28:28Z","conference":{"start_date":"2019-06-23","end_date":"2019-06-26","location":"Phoenix, AZ, United States","name":"STOC: Symposium on Theory of Computing"},"related_material":{"record":[{"relation":"later_version","id":"14364","status":"public"}]},"year":"2019","oa":1,"article_processing_charge":"No","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"full_name":"Ellen, Faith","first_name":"Faith","last_name":"Ellen"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"full_name":"Zhu, Leqi","first_name":"Leqi","last_name":"Zhu"}],"month":"06","arxiv":1,"citation":{"apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2019). Why extension-based proofs fail. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing (pp. 986–996). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3313276.3316407","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 986–996.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. ACM Press; 2019:986-996. doi:10.1145/3313276.3316407","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–996.","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–96, doi:10.1145/3313276.3316407.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Phoenix, AZ, United States, 2019, pp. 986–996.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, 986–96. ACM Press, 2019. https://doi.org/10.1145/3313276.3316407."},"page":"986-996","language":[{"iso":"eng"}],"_id":"6676"},{"abstract":[{"lang":"eng","text":"The Fiat-Shamir heuristic transforms a public-coin interactive proof into a non-interactive argument, by replacing the verifier with a cryptographic hash function that is applied to the protocol’s transcript. Constructing hash functions for which this transformation is sound is a central and long-standing open question in cryptography.\r\n\r\nWe show that solving the END−OF−METERED−LINE problem is no easier than breaking the soundness of the Fiat-Shamir transformation when applied to the sumcheck protocol. In particular, if the transformed protocol is sound, then any hard problem in #P gives rise to a hard distribution in the class CLS, which is contained in PPAD. Our result opens up the possibility of sampling moderately-sized games for which it is hard to find a Nash equilibrium, by reducing the inversion of appropriately chosen one-way functions to #SAT.\r\n\r\nOur main technical contribution is a stateful incrementally verifiable procedure that, given a SAT instance over n variables, counts the number of satisfying assignments. This is accomplished via an exponential sequence of small steps, each computable in time poly(n). Incremental verifiability means that each intermediate state includes a sumcheck-based proof of its correctness, and the proof can be updated and verified in time poly(n)."}],"status":"public","date_published":"2019-06-01T00:00:00Z","publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","scopus_import":"1","date_created":"2019-07-24T09:20:53Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/549"}],"type":"conference","department":[{"_id":"KrPi"}],"project":[{"call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_status":"published","publisher":"ACM Press","page":"1103-1114","_id":"6677","language":[{"iso":"eng"}],"month":"06","author":[{"last_name":"Choudhuri","first_name":"Arka Rai","full_name":"Choudhuri, Arka Rai"},{"full_name":"Hubáček, Pavel","last_name":"Hubáček","first_name":"Pavel"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rosen, Alon","first_name":"Alon","last_name":"Rosen"},{"first_name":"Guy N.","last_name":"Rothblum","full_name":"Rothblum, Guy N."}],"citation":{"apa":"Choudhuri, A. R., Hubáček, P., Kamath Hosdurg, C., Pietrzak, K. Z., Rosen, A., & Rothblum, G. N. (2019). Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019 (pp. 1103–1114). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3313276.3316400","ista":"Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum GN. 2019. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019. STOC: Symposium on Theory of Computing, 1103–1114.","ama":"Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum GN. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019. ACM Press; 2019:1103-1114. doi:10.1145/3313276.3316400","mla":"Choudhuri, Arka Rai, et al. “Finding a Nash Equilibrium Is No Easier than Breaking Fiat-Shamir.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019, ACM Press, 2019, pp. 1103–14, doi:10.1145/3313276.3316400.","short":"A.R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K.Z. Pietrzak, A. Rosen, G.N. Rothblum, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019, ACM Press, 2019, pp. 1103–1114.","ieee":"A. R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K. Z. Pietrzak, A. Rosen, and G. N. Rothblum, “Finding a Nash equilibrium is no easier than breaking Fiat-Shamir,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019, Phoenix, AZ, United States, 2019, pp. 1103–1114.","chicago":"Choudhuri, Arka Rai, Pavel Hubáček, Chethan Kamath Hosdurg, Krzysztof Z Pietrzak, Alon Rosen, and Guy N. Rothblum. “Finding a Nash Equilibrium Is No Easier than Breaking Fiat-Shamir.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019, 1103–14. ACM Press, 2019. https://doi.org/10.1145/3313276.3316400."},"related_material":{"record":[{"id":"7896","relation":"dissertation_contains","status":"public"}]},"conference":{"end_date":"2019-06-26","start_date":"2019-06-23","name":"STOC: Symposium on Theory of Computing","location":"Phoenix, AZ, United States"},"year":"2019","ec_funded":1,"oa":1,"article_processing_charge":"No","title":"Finding a Nash equilibrium is no easier than breaking Fiat-Shamir","doi":"10.1145/3313276.3316400","isi":1,"external_id":{"isi":["000523199100100"]},"publication_identifier":{"isbn":["9781450367059"]},"day":"01","date_updated":"2023-09-07T13:15:55Z"},{"file_date_updated":"2020-07-14T12:47:37Z","month":"09","file":[{"content_type":"application/pdf","file_name":"2019_Evolution_Sachdeva.pdf","relation":"main_file","creator":"kschuh","checksum":"772ce7035965153959b946a1033de1ca","file_size":937573,"file_id":"6881","access_level":"open_access","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-09-17T10:56:27Z"}],"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"}],"citation":{"ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812","ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745.","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.","mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812.","short":"H. Sachdeva, Evolution 73 (2019) 1729–1745."},"ddc":["576"],"issue":"9","page":"1729-1745","_id":"6680","language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["000481300600001"]},"title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","doi":"10.1111/evo.13812","date_updated":"2023-08-29T06:43:58Z","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"day":"01","year":"2019","has_accepted_license":"1","related_material":{"record":[{"id":"9802","relation":"research_data","status":"public"}]},"oa":1,"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","date_created":"2019-07-25T09:08:28Z","scopus_import":"1","date_published":"2019-09-01T00:00:00Z","status":"public","publication":"Evolution","abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"intvolume":" 73","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","volume":73,"type":"journal_article"},{"publisher":"Institute of Science and Technology Austria","publication_status":"published","supervisor":[{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner"}],"department":[{"_id":"UlWa"}],"type":"dissertation","date_created":"2019-07-26T11:14:34Z","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","date_published":"2019-08-08T00:00:00Z","abstract":[{"lang":"eng","text":"The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space."}],"date_updated":"2023-09-07T13:10:36Z","day":"08","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6681","title":"Algorithmic aspects of homotopy theory and embeddability","article_processing_charge":"No","oa":1,"year":"2019","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"6774","relation":"part_of_dissertation"}]},"ddc":["514"],"citation":{"ama":"Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019. doi:10.15479/AT:ISTA:6681","ista":"Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria.","apa":"Zhechev, S. Y. (2019). Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6681","chicago":"Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6681.","ieee":"S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,” Institute of Science and Technology Austria, 2019.","short":"S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute of Science and Technology Austria, 2019.","mla":"Zhechev, Stephan Y. Algorithmic Aspects of Homotopy Theory and Embeddability. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6681."},"file":[{"content_type":"application/pdf","file_name":"Stephan_Zhechev_thesis.pdf","relation":"main_file","checksum":"3231e7cbfca3b5687366f84f0a57a0c0","creator":"szhechev","file_size":1464227,"file_id":"6771","access_level":"open_access","date_created":"2019-08-07T13:02:50Z","date_updated":"2020-07-14T12:47:37Z"},{"access_level":"closed","date_created":"2019-08-07T13:03:22Z","date_updated":"2020-07-14T12:47:37Z","file_size":303988,"file_id":"6772","file_name":"Stephan_Zhechev_thesis.tex","relation":"source_file","creator":"szhechev","checksum":"85d65eb27b4377a9e332ee37a70f08b6","content_type":"application/octet-stream"},{"date_updated":"2020-07-14T12:47:37Z","date_created":"2019-08-07T13:03:34Z","access_level":"closed","file_id":"6773","file_size":1087004,"creator":"szhechev","checksum":"86b374d264ca2dd53e712728e253ee75","file_name":"supplementary_material.zip","relation":"supplementary_material","content_type":"application/zip"}],"author":[{"id":"3AA52972-F248-11E8-B48F-1D18A9856A87","last_name":"Zhechev","first_name":"Stephan Y","full_name":"Zhechev, Stephan Y"}],"file_date_updated":"2020-07-14T12:47:37Z","month":"08","_id":"6681","language":[{"iso":"eng"}],"degree_awarded":"PhD","page":"104"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/aob/mcy183"}],"type":"journal_article","volume":123,"department":[{"_id":"BeVi"}],"quality_controlled":"1","pmid":1,"publication_status":"published","publisher":"Oxford University Press","abstract":[{"text":"Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species.","lang":"eng"}],"publication":"Annals of botany","date_published":"2019-06-04T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 123","oa_version":"Published Version","scopus_import":"1","date_created":"2019-07-28T21:59:15Z","year":"2019","oa":1,"article_processing_charge":"No","doi":"10.1093/aob/mcy183","title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","external_id":{"pmid":["30289430"],"isi":["000493043500004"]},"isi":1,"day":"04","publication_identifier":{"eissn":["1095-8290"],"issn":["0305-7364"]},"date_updated":"2023-08-29T06:42:22Z","page":"1119-1131","issue":"7","_id":"6710","language":[{"iso":"eng"}],"author":[{"first_name":"Guillaume","last_name":"Cossard","full_name":"Cossard, Guillaume"},{"last_name":"Toups","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"last_name":"Pannell","first_name":"John ","full_name":"Pannell, John "}],"month":"06","article_type":"original","citation":{"apa":"Cossard, G., Toups, M. A., & Pannell, J. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcy183","ista":"Cossard G, Toups MA, Pannell J. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 123(7), 1119–1131.","ama":"Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 2019;123(7):1119-1131. doi:10.1093/aob/mcy183","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","mla":"Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany, vol. 123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:10.1093/aob/mcy183.","ieee":"G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb,” Annals of botany, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019.","chicago":"Cossard, Guillaume, Melissa A Toups, and John Pannell. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” Annals of Botany. Oxford University Press, 2019. https://doi.org/10.1093/aob/mcy183."}},{"article_processing_charge":"No","oa":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9804"},{"id":"11388","relation":"dissertation_contains","status":"public"}]},"has_accepted_license":"1","year":"2019","day":"06","date_updated":"2024-03-25T23:30:11Z","doi":"10.7554/eLife.42014","title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","external_id":{"isi":["000473588700001"],"pmid":["31169497"]},"isi":1,"_id":"6713","language":[{"iso":"eng"}],"ddc":["576"],"citation":{"ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 2019;8. doi:10.7554/eLife.42014","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42014","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","ieee":"J. P. Castro et al., “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences Publications, 2019.","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014, eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019)."},"file":[{"file_size":6748249,"file_id":"6721","access_level":"open_access","date_updated":"2020-07-14T12:47:38Z","date_created":"2019-07-29T07:41:18Z","content_type":"application/pdf","file_name":"2019_eLife_Castro.pdf","relation":"main_file","creator":"apreinsp","checksum":"fa0936fe58f0d9e3f8e75038570e5a17"}],"author":[{"first_name":"João Pl","last_name":"Castro","full_name":"Castro, João Pl"},{"full_name":"Yancoskie, Michelle N.","first_name":"Michelle N.","last_name":"Yancoskie"},{"first_name":"Marta","last_name":"Marchini","full_name":"Marchini, Marta"},{"orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie","first_name":"Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hiramatsu, Layla","last_name":"Hiramatsu","first_name":"Layla"},{"last_name":"Kučka","first_name":"Marek","full_name":"Kučka, Marek"},{"full_name":"Beluch, William H.","last_name":"Beluch","first_name":"William H."},{"full_name":"Naumann, Ronald","last_name":"Naumann","first_name":"Ronald"},{"full_name":"Skuplik, Isabella","last_name":"Skuplik","first_name":"Isabella"},{"full_name":"Cobb, John","last_name":"Cobb","first_name":"John"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Rolian, Campbell","first_name":"Campbell","last_name":"Rolian"},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"}],"file_date_updated":"2020-07-14T12:47:38Z","article_number":"e42014","month":"06","type":"journal_article","volume":8,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"}],"quality_controlled":"1","pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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"},"intvolume":" 8","abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"publication":"eLife","status":"public","date_published":"2019-06-06T00:00:00Z","scopus_import":"1","date_created":"2019-07-28T21:59:17Z","oa_version":"Published Version"},{"volume":10,"type":"journal_article","publication_status":"published","publisher":"Frontiers","department":[{"_id":"CaGu"}],"project":[{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573"}],"quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 10","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"},"abstract":[{"lang":"eng","text":"With the recent publication by Silpe and Bassler (2019), considering phage detection of a bacterial quorum-sensing (QS) autoinducer, we now have as many as five examples of phage-associated intercellular communication (Table 1). Each potentially involves ecological inferences by phages as to concentrations of surrounding phage-infected or uninfected bacteria. While the utility of phage detection of bacterial QS molecules may at first glance appear to be straightforward, we suggest in this commentary that the underlying ecological explanation is unlikely to be simple."}],"date_published":"2019-06-03T00:00:00Z","status":"public","publication":"Frontiers in Microbiology","scopus_import":"1","date_created":"2019-07-28T21:59:18Z","oa_version":"Published Version","oa":1,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","year":"2019","day":"03","date_updated":"2023-08-29T06:41:20Z","title":"Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision","doi":"10.3389/fmicb.2019.01171","isi":1,"external_id":{"isi":["000470131200001"]},"language":[{"iso":"eng"}],"_id":"6717","citation":{"ieee":"C. Igler and S. T. Abedon, “Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision,” Frontiers in Microbiology, vol. 10. Frontiers, 2019.","chicago":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology. Frontiers, 2019. https://doi.org/10.3389/fmicb.2019.01171.","short":"C. Igler, S.T. Abedon, Frontiers in Microbiology 10 (2019).","mla":"Igler, Claudia, and Stephen T. Abedon. “Commentary: A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision.” Frontiers in Microbiology, vol. 10, 1171, Frontiers, 2019, doi:10.3389/fmicb.2019.01171.","ama":"Igler C, Abedon ST. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 2019;10. doi:10.3389/fmicb.2019.01171","apa":"Igler, C., & Abedon, S. T. (2019). Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2019.01171","ista":"Igler C, Abedon ST. 2019. Commentary: A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Frontiers in Microbiology. 10, 1171."},"ddc":["570"],"file_date_updated":"2020-07-14T12:47:38Z","month":"06","article_number":"1171","file":[{"content_type":"application/pdf","creator":"apreinsp","checksum":"317a06067e9a8e717bb55f23e0d77ba7","file_name":"2019_Frontiers_Igler.pdf","relation":"main_file","file_id":"6722","file_size":246151,"date_updated":"2020-07-14T12:47:38Z","date_created":"2019-07-29T07:51:54Z","access_level":"open_access"}],"author":[{"first_name":"Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia"},{"full_name":"Abedon, Stephen T.","first_name":"Stephen T.","last_name":"Abedon"}]},{"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"date_created":"2019-07-29T12:23:29Z","abstract":[{"text":"A Valued Constraint Satisfaction Problem (VCSP) provides a common framework that can express a wide range of discrete optimization problems. A VCSP instance is given by a finite set of variables, a finite domain of labels, and an objective function to be minimized. This function is represented as a sum of terms where each term depends on a subset of the variables. To obtain different classes of optimization problems, one can restrict all terms to come from a fixed set Γ of cost functions, called a language. \r\nRecent breakthrough results have established a complete complexity classification of such classes with respect to language Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately, testing this condition for a given language Γ is known to be NP-hard. We thus study exponential algorithms for this meta-problem. We show that the tractability condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ))) time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH). More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm, assuming that SETH holds.","lang":"eng"}],"publication":"46th International Colloquium on Automata, Languages and Programming","status":"public","date_published":"2019-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 132","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"},"department":[{"_id":"VlKo"}],"quality_controlled":"1","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7"}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","type":"conference","volume":132,"file":[{"creator":"dernst","checksum":"f5ebee8eec6ae09e30365578ee63a492","relation":"main_file","file_name":"2019_LIPICS_Kolmogorov.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:38Z","date_created":"2019-07-31T07:01:45Z","access_level":"open_access","file_id":"6738","file_size":575475}],"author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:38Z","month":"07","ddc":["000"],"citation":{"ieee":"V. Kolmogorov, “Testing the complexity of a valued CSP language,” in 46th International Colloquium on Automata, Languages and Programming, Patras, Greece, 2019, vol. 132, p. 77:1-77:12.","chicago":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” In 46th International Colloquium on Automata, Languages and Programming, 132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.77.","mla":"Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” 46th International Colloquium on Automata, Languages and Programming, vol. 132, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:10.4230/LIPICS.ICALP.2019.77.","short":"V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12.","ama":"Kolmogorov V. Testing the complexity of a valued CSP language. In: 46th International Colloquium on Automata, Languages and Programming. Vol 132. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:10.4230/LIPICS.ICALP.2019.77","apa":"Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In 46th International Colloquium on Automata, Languages and Programming (Vol. 132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ICALP.2019.77","ista":"Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th International Colloquium on Automata, Languages and Programming. ICALP 2019: International Colloquim on Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12."},"arxiv":1,"page":"77:1-77:12","_id":"6725","language":[{"iso":"eng"}],"doi":"10.4230/LIPICS.ICALP.2019.77","title":"Testing the complexity of a valued CSP language","external_id":{"arxiv":["1803.02289"]},"day":"01","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-109-2"]},"date_updated":"2021-01-12T08:08:40Z","conference":{"start_date":"2019-07-08","end_date":"2019-07-12","location":"Patras, Greece","name":"ICALP 2019: International Colloquim on Automata, Languages and Programming"},"has_accepted_license":"1","year":"2019","ec_funded":1,"oa":1}]