[{"year":"2019","publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"EMS Press","author":[{"id":"4D046628-F248-11E8-B48F-1D18A9856A87","first_name":"Tanya K","last_name":"Srivastava","full_name":"Srivastava, Tanya K"}],"date_created":"2020-02-02T23:01:06Z","date_updated":"2023-10-17T07:42:21Z","volume":24,"file_date_updated":"2020-07-14T12:47:58Z","external_id":{"arxiv":["1809.08970"],"isi":["000517806400019"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.25537/dm.2019v24.1135-1177","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"eissn":["1431-0643"],"issn":["1431-0635"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7436","ddc":["510"],"status":"public","title":"On derived equivalences of k3 surfaces in positive characteristic","intvolume":" 24","file":[{"relation":"main_file","file_id":"7438","checksum":"9a1a64bd49ab03fa4f738fb250fc4f90","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-03T06:26:12Z","access_level":"open_access","file_name":"2019_DocumMath_Srivastava.pdf","content_type":"application/pdf","file_size":469730,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"For an ordinary K3 surface over an algebraically closed field of positive characteristic we show that every automorphism lifts to characteristic zero. Moreover, we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one correspondence with the Fourier-Mukai partners of the geometric generic fiber of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai partners of the K3 surfaces with Picard rank two and with discriminant equal to minus of a prime number, in terms of the class number of the prime, holds over a field of positive characteristic as well. We show that the image of the derived autoequivalence group of a K3 surface of finite height in the group of isometries of its crystalline cohomology has index at least two. Moreover, we provide a conditional upper bound on the kernel of this natural cohomological descent map. Further, we give an extended remark in the appendix on the possibility of an F-crystal structure on the crystalline cohomology of a K3 surface over an algebraically closed field of positive characteristic and show that the naive F-crystal structure fails in being compatible with inner product. "}],"publication":"Documenta Mathematica","citation":{"ieee":"T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,” Documenta Mathematica, vol. 24. EMS Press, pp. 1135–1177, 2019.","apa":"Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. EMS Press. https://doi.org/10.25537/dm.2019v24.1135-1177","ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 1135–1177.","ama":"Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177","chicago":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica. EMS Press, 2019. https://doi.org/10.25537/dm.2019v24.1135-1177.","short":"T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.","mla":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica, vol. 24, EMS Press, 2019, pp. 1135–77, doi:10.25537/dm.2019v24.1135-1177."},"article_type":"original","page":"1135-1177","date_published":"2019-05-20T00:00:00Z","scopus_import":"1","day":"20","has_accepted_license":"1","article_processing_charge":"No"},{"doi":"10.1214/18-AIHP916","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02323"}],"external_id":{"isi":["000487763200001"],"arxiv":["1710.02323"]},"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0246-0203"]},"month":"09","author":[{"first_name":"Patrick","last_name":"Ferrari","full_name":"Ferrari, Patrick"},{"full_name":"Ghosal, Promit","last_name":"Ghosal","first_name":"Promit"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar","full_name":"Nejjar, Peter"}],"volume":55,"date_created":"2018-12-11T11:44:29Z","date_updated":"2023-10-17T08:53:45Z","year":"2019","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","ec_funded":1,"date_published":"2019-09-25T00:00:00Z","citation":{"ista":"Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225.","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","apa":"Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AIHP916","ama":"Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916","chicago":"Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AIHP916.","mla":"Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:10.1214/18-AIHP916.","short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225."},"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","page":"1203-1225","article_type":"original","article_processing_charge":"No","day":"25","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"72","intvolume":" 55","status":"public","title":"Limit law of a second class particle in TASEP with non-random initial condition","issue":"3","abstract":[{"lang":"eng","text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t."}],"type":"journal_article"},{"doi":"10.31263/voebm.v72i1.2276","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"05","publication_identifier":{"eissn":["1022-2588"]},"author":[{"full_name":"Danowski, Patrick","first_name":"Patrick","last_name":"Danowski","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409"}],"related_material":{"record":[{"id":"5686","relation":"earlier_version","status":"public"}]},"date_created":"2019-07-21T21:59:15Z","date_updated":"2023-10-17T11:33:58Z","volume":72,"year":"2019","publication_status":"published","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:47:35Z","date_published":"2019-05-17T00:00:00Z","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","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.","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","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.","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.","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"},"article_type":"original","page":"59-65","day":"17","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"file_size":468558,"content_type":"application/pdf","creator":"apreinsp","access_level":"open_access","file_name":"2019_MitteilungenDerVOEB_Danowski.pdf","checksum":"c0d2695d6d0d34e62ba06fb3f0ebaaed","date_created":"2019-07-22T08:45:03Z","date_updated":"2020-07-14T12:47:35Z","relation":"main_file","file_id":"6661"}],"_id":"6657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors","ddc":["020"],"status":"public","intvolume":" 72","abstract":[{"lang":"eng","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."}],"issue":"1","type":"journal_article"},{"title":"Room temperature control of valley coherence in bilayer WS2 exciton polaritons","publication_status":"published","status":"public","publisher":"Optica Publishing Group","department":[{"_id":"MiLe"}],"_id":"6646","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T12:14:29Z","date_created":"2019-07-17T09:40:44Z","oa_version":"None","author":[{"first_name":"Mandeep","last_name":"Khatoniar","full_name":"Khatoniar, Mandeep"},{"full_name":"Yama, Nicholas","last_name":"Yama","first_name":"Nicholas"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg"},{"full_name":"Guddala, Sriram","last_name":"Guddala","first_name":"Sriram"},{"full_name":"Ghaemi, Pouyan","last_name":"Ghaemi","first_name":"Pouyan"},{"full_name":"Menon, Vinod","first_name":"Vinod","last_name":"Menon"}],"article_number":"paper JTu2A.52","type":"conference","abstract":[{"text":"We demonstrate robust retention of valley coherence and its control via polariton pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity exciton polaritons at room temperature.","lang":"eng"}],"quality_controlled":"1","publication":"CLEO: Applications and Technology","citation":{"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.","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.","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","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. Optica Publishing Group; 2019. doi:10.1364/cleo_at.2019.jtu2a.52","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.","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."},"language":[{"iso":"eng"}],"conference":{"name":"CLEO: Conference on Lasers and Electro-Optics","end_date":"2019-05-10","start_date":"2019-05-05","location":"San Jose, CA, United States"},"doi":"10.1364/cleo_at.2019.jtu2a.52","date_published":"2019-05-01T00:00:00Z","scopus_import":"1","month":"05","day":"01","article_processing_charge":"No","publication_identifier":{"isbn":["9781943580576"]}},{"publication_identifier":{"isbn":["9781557528209"]},"article_processing_charge":"No","month":"07","day":"15","scopus_import":"1","language":[{"iso":"eng"}],"doi":"10.1364/NLO.2019.NM2A.5","date_published":"2019-07-15T00:00:00Z","conference":{"start_date":"2019-07-15","location":"Waikoloa Beach, Hawaii (HI), United States","end_date":"2019-07-19","name":"NLO: Nonlinear Optics"},"quality_controlled":"1","citation":{"ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In: Nonlinear Optics, OSA Technical Digest. Optica Publishing Group; 2019. doi:10.1364/NLO.2019.NM2A.5","ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics, NM2A.5.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group. https://doi.org/10.1364/NLO.2019.NM2A.5","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics, OSA Technical Digest, NM2A.5, Optica Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5.","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:, Nonlinear Optics, OSA Technical Digest, Optica Publishing Group, 2019.","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kumari, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” In Nonlinear Optics, OSA Technical Digest. Optica Publishing Group, 2019. https://doi.org/10.1364/NLO.2019.NM2A.5."},"publication":"Nonlinear Optics, OSA Technical Digest","abstract":[{"lang":"eng","text":"We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm."}],"type":"conference","article_number":"NM2A.5","oa_version":"None","date_updated":"2023-10-17T12:14:46Z","date_created":"2020-01-05T23:00:48Z","author":[{"first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R"},{"last_name":"Sedlmeir","first_name":"Florian","full_name":"Sedlmeir, Florian"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Madhuri","last_name":"Kumari","full_name":"Kumari, Madhuri"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."}],"publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"publication_status":"published","title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","status":"public","_id":"7233","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019"},{"ec_funded":1,"publisher":"Institut Henri Poincaré","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2019","volume":55,"date_updated":"2023-10-17T12:20:20Z","date_created":"2019-04-08T14:05:04Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"author":[{"full_name":"Alt, Johannes","last_name":"Alt","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H"},{"last_name":"Nemish","first_name":"Yuriy","orcid":"0000-0002-7327-856X","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","full_name":"Nemish, Yuriy"}],"publication_identifier":{"issn":["0246-0203"]},"month":"05","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000467793600003"],"arxiv":["1706.08343"]},"main_file_link":[{"url":"https://arxiv.org/abs/1706.08343","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1214/18-AIHP894","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles."}],"intvolume":" 55","status":"public","title":"Location of the spectrum of Kronecker random matrices","_id":"6240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"01","page":"661-696","citation":{"ista":"Alt J, Erdös L, Krüger TH, Nemish Y. 2019. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 55(2), 661–696.","ieee":"J. Alt, L. Erdös, T. H. Krüger, and Y. Nemish, “Location of the spectrum of Kronecker random matrices,” Annales de l’institut Henri Poincare, vol. 55, no. 2. Institut Henri Poincaré, pp. 661–696, 2019.","apa":"Alt, J., Erdös, L., Krüger, T. H., & Nemish, Y. (2019). Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. Institut Henri Poincaré. https://doi.org/10.1214/18-AIHP894","ama":"Alt J, Erdös L, Krüger TH, Nemish Y. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 2019;55(2):661-696. doi:10.1214/18-AIHP894","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare. Institut Henri Poincaré, 2019. https://doi.org/10.1214/18-AIHP894.","mla":"Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare, vol. 55, no. 2, Institut Henri Poincaré, 2019, pp. 661–96, doi:10.1214/18-AIHP894.","short":"J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 661–696."},"publication":"Annales de l'institut Henri Poincare","date_published":"2019-05-01T00:00:00Z"},{"file_date_updated":"2020-07-14T12:47:57Z","article_number":"e1008268","date_updated":"2023-10-17T12:30:27Z","date_created":"2020-01-29T16:14:07Z","volume":15,"author":[{"full_name":"Andergassen, Daniel","last_name":"Andergassen","first_name":"Daniel"},{"full_name":"Muckenhuber, Markus","first_name":"Markus","last_name":"Muckenhuber"},{"last_name":"Bammer","first_name":"Philipp C.","full_name":"Bammer, Philipp C."},{"full_name":"Kulinski, Tomasz M.","first_name":"Tomasz M.","last_name":"Kulinski"},{"first_name":"Hans-Christian","last_name":"Theussl","full_name":"Theussl, Hans-Christian"},{"last_name":"Shimizu","first_name":"Takahiko","full_name":"Shimizu, Takahiko"},{"full_name":"Penninger, Josef M.","last_name":"Penninger","first_name":"Josef M."},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"}],"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Public Library of Science","year":"2019","pmid":1,"month":"07","publication_identifier":{"issn":["1553-7404"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1008268","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000478689100025"],"pmid":["31329595"]},"oa":1,"abstract":[{"lang":"eng","text":"Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established."}],"issue":"7","type":"journal_article","file":[{"checksum":"2f51fc91e4a4199827adc51d432ad864","date_created":"2020-02-04T10:11:55Z","date_updated":"2020-07-14T12:47:57Z","relation":"main_file","file_id":"7446","file_size":2302307,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_PlosGenetics_Andergassen.pdf"}],"oa_version":"Published Version","title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","status":"public","ddc":["570"],"intvolume":" 15","_id":"7399","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"22","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-07-22T00:00:00Z","article_type":"original","publication":"PLoS Genetics","citation":{"ista":"Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl H-C, Shimizu T, Penninger JM, Pauler F, Hudson QJ. 2019. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 15(7), e1008268.","ieee":"D. Andergassen et al., “The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes,” PLoS Genetics, vol. 15, no. 7. Public Library of Science, 2019.","apa":"Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl, H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008268","ama":"Andergassen D, Muckenhuber M, Bammer PC, et al. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 2019;15(7). doi:10.1371/journal.pgen.1008268","chicago":"Andergassen, Daniel, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski, Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian Pauler, and Quanah J. Hudson. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008268.","mla":"Andergassen, Daniel, et al. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics, vol. 15, no. 7, e1008268, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008268.","short":"D. Andergassen, M. Muckenhuber, P.C. Bammer, T.M. Kulinski, H.-C. Theussl, T. Shimizu, J.M. Penninger, F. Pauler, Q.J. Hudson, PLoS Genetics 15 (2019)."}},{"external_id":{"isi":["000500976100014"],"pmid":["31725712"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1371/journal.pcbi.1007268","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["1553-7358"]},"year":"2019","pmid":1,"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"author":[{"full_name":"Wang, Jilin W. J. L.","last_name":"Wang","first_name":"Jilin W. J. L."},{"full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"full_name":"Anaclet, Christelle","first_name":"Christelle","last_name":"Anaclet"},{"full_name":"Ivanov, Plamen Ch.","first_name":"Plamen Ch.","last_name":"Ivanov"}],"date_updated":"2023-10-17T12:30:07Z","date_created":"2019-11-25T08:20:47Z","volume":15,"article_number":"e1007268","file_date_updated":"2020-07-14T12:47:49Z","ec_funded":1,"publication":"PLoS Computational Biology","citation":{"short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).","mla":"Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology, vol. 15, no. 11, e1007268, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007268.","chicago":"Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268.","ama":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15, no. 11. Public Library of Science, 2019.","apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268","ista":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268."},"article_type":"original","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7103","title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","ddc":["570","000"],"status":"public","intvolume":" 15","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_PLOSComBio_Wang.pdf","creator":"dernst","content_type":"application/pdf","file_size":3982516,"file_id":"7104","relation":"main_file","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","date_created":"2019-11-25T08:24:01Z","date_updated":"2020-07-14T12:47:49Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics."}],"issue":"11"},{"file_date_updated":"2020-07-14T12:47:33Z","author":[{"full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","last_name":"Bui Thi Mai"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"date_created":"2019-06-20T18:23:03Z","date_updated":"2023-10-17T12:31:38Z","volume":97,"year":"2019","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"ChLa"}],"month":"06","conference":{"start_date":"2019-06-10","location":"Long Beach, CA, United States","end_date":"2019-06-15","name":"ICML: International Conference on Machine Learning"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","abstract":[{"text":"Knowledge distillation, i.e. one classifier being trained on the outputs of another classifier, is an empirically very successful technique for knowledge transfer between classifiers. It has even been observed that classifiers learn much faster and more reliably if trained with the outputs of another classifier as soft labels, instead of from ground truth data. So far, however, there is no satisfactory theoretical explanation of this phenomenon. In this work, we provide the first insights into the working mechanisms of distillation by studying the special case of linear and deep linear classifiers. Specifically, we prove a generalization bound that establishes fast convergence of the expected risk of a distillation-trained linear classifier. From the bound and its proof we extract three keyfactors that determine the success of distillation: data geometry – geometric properties of the datadistribution, in particular class separation, has an immediate influence on the convergence speed of the risk; optimization bias– gradient descentoptimization finds a very favorable minimum of the distillation objective; and strong monotonicity– the expected risk of the student classifier always decreases when the size of the training set grows.","lang":"eng"}],"type":"conference","file":[{"date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-20T18:22:56Z","checksum":"a66d00e2694d749250f8507f301320ca","relation":"main_file","file_id":"6570","file_size":686432,"content_type":"application/pdf","creator":"bphuong","file_name":"paper.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"6569","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Towards understanding knowledge distillation","ddc":["000"],"status":"public","intvolume":" 97","day":"13","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-06-13T00:00:00Z","publication":"Proceedings of the 36th International Conference on Machine Learning","citation":{"ama":"Phuong M, Lampert C. Towards understanding knowledge distillation. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:5142-5151.","apa":"Phuong, M., & Lampert, C. (2019). Towards understanding knowledge distillation. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 5142–5151). Long Beach, CA, United States: ML Research Press.","ieee":"M. Phuong and C. Lampert, “Towards understanding knowledge distillation,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 5142–5151.","ista":"Phuong M, Lampert C. 2019. Towards understanding knowledge distillation. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 5142–5151.","short":"M. Phuong, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 5142–5151.","mla":"Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 5142–51.","chicago":"Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” In Proceedings of the 36th International Conference on Machine Learning, 97:5142–51. ML Research Press, 2019."},"page":"5142-5151"},{"scopus_import":"1","day":"01","article_processing_charge":"No","page":"3488-3498","publication":"Proceedings of the 36th International Conference on Machine Learning","citation":{"short":"N.H. Konstantinov, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 3488–3498.","mla":"Konstantinov, Nikola H., and Christoph Lampert. “Robust Learning from Untrusted Sources.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 3488–98.","chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Robust Learning from Untrusted Sources.” In Proceedings of the 36th International Conference on Machine Learning, 97:3488–98. ML Research Press, 2019.","ama":"Konstantinov NH, Lampert C. Robust learning from untrusted sources. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:3488-3498.","apa":"Konstantinov, N. H., & Lampert, C. (2019). Robust learning from untrusted sources. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 3488–3498). Long Beach, CA, USA: ML Research Press.","ieee":"N. H. Konstantinov and C. Lampert, “Robust learning from untrusted sources,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, USA, 2019, vol. 97, pp. 3488–3498.","ista":"Konstantinov NH, Lampert C. 2019. Robust learning from untrusted sources. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 3488–3498."},"date_published":"2019-06-01T00:00:00Z","type":"conference","abstract":[{"text":"Modern machine learning methods often require more data for training than a single expert can provide. Therefore, it has become a standard procedure to collect data from external sources, e.g. via crowdsourcing. Unfortunately, the quality of these sources is not always guaranteed. As additional complications, the data might be stored in a distributed way, or might even have to remain private. In this work, we address the question of how to learn robustly in such scenarios. Studying the problem through the lens of statistical learning theory, we derive a procedure that allows for learning from all available sources, yet automatically suppresses irrelevant or corrupted data. We show by extensive experiments that our method provides significant improvements over alternative approaches from robust statistics and distributed optimization. ","lang":"eng"}],"title":"Robust learning from untrusted sources","status":"public","intvolume":" 97","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6590","oa_version":"Preprint","month":"06","quality_controlled":"1","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/1901.10310","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1901.10310"]},"language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2919-06-15","start_date":"2019-06-10","location":"Long Beach, CA, USA"},"ec_funded":1,"publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"ML Research Press","year":"2019","date_updated":"2023-10-17T12:31:55Z","date_created":"2019-06-27T14:18:23Z","volume":97,"author":[{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10799"}]}},{"month":"10","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["31575745"],"isi":["000490183000068"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1911892116","file_date_updated":"2020-07-14T12:47:46Z","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"JiFr"}],"year":"2019","pmid":1,"date_created":"2019-11-12T11:42:05Z","date_updated":"2023-10-17T12:32:37Z","volume":116,"author":[{"full_name":"Huang, D","first_name":"D","last_name":"Huang"},{"full_name":"Sun, Y","first_name":"Y","last_name":"Sun"},{"last_name":"Ma","first_name":"Z","full_name":"Ma, Z"},{"full_name":"Ke, M","last_name":"Ke","first_name":"M"},{"first_name":"Y","last_name":"Cui","full_name":"Cui, Y"},{"full_name":"Chen, Z","last_name":"Chen","first_name":"Z"},{"full_name":"Chen, C","last_name":"Chen","first_name":"C"},{"last_name":"Ji","first_name":"C","full_name":"Ji, C"},{"first_name":"TM","last_name":"Tran","full_name":"Tran, TM"},{"full_name":"Yang, L","first_name":"L","last_name":"Yang"},{"full_name":"Lam, SM","last_name":"Lam","first_name":"SM"},{"full_name":"Han, Y","last_name":"Han","first_name":"Y"},{"first_name":"G","last_name":"Shu","full_name":"Shu, G"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Miao, Y","last_name":"Miao","first_name":"Y"},{"last_name":"Jiang","first_name":"L","full_name":"Jiang, L"},{"full_name":"Chen, X","first_name":"X","last_name":"Chen"}],"related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2004738117","relation":"erratum"}]},"scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"21274-21284","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ista":"Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 116(42), 21274–21284.","ieee":"D. Huang et al., “Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42. Proceedings of the National Academy of Sciences, pp. 21274–21284, 2019.","apa":"Huang, D., Sun, Y., Ma, Z., Ke, M., Cui, Y., Chen, Z., … Chen, X. (2019). Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1911892116","ama":"Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116","chicago":"Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.","mla":"Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42, Proceedings of the National Academy of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116.","short":"D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran, L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 21274–21284."},"date_published":"2019-10-15T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Plasmodesmata (PD) are plant-specific membrane-lined channels that create cytoplasmic and membrane continuities between adjacent cells, thereby facilitating cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms to regulate PD plasticity in response to numerous environmental stimuli. In particular, during defense against plant pathogens, the defense hormone, salicylic acid (SA), plays a crucial role in the regulation of PD permeability in a callose-dependent manner. Here, we uncover a mechanism by which plants restrict the spreading of virus and PD cargoes using SA signaling by increasing lipid order and closure of PD. We showed that exogenous SA application triggered the compartmentalization of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein, Remorin (REM). Genetic studies, superresolution imaging, and transmission electron microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3 are crucial for plasma membrane nanodomain assembly to control PD aperture and functionality. In addition, we also found that a 14-3-3 epsilon protein modulates REM clustering and membrane nanodomain compartmentalization through its direct interaction with REM proteins. This study unveils a molecular mechanism by which the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization, thereby regulating PD closure to impede virus spreading."}],"issue":"42","title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","status":"public","ddc":["580"],"intvolume":" 116","_id":"6999","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2019-11-13T08:22:28Z","date_updated":"2020-07-14T12:47:46Z","checksum":"258c666bc6253eab81961f61169eefae","file_id":"7012","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":3287466,"file_name":"2019_PNAS_Huang.pdf","access_level":"open_access"}],"oa_version":"Published Version"},{"status":"public","title":"On the power to detect rare recombination events","intvolume":" 116","_id":"6621","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We read with great interest the recent work in PNAS by Bergero et al. (1) describing differences in male and female recombination patterns on the guppy (Poecilia reticulata) sex chromosome. We fully agree that recombination in males is largely confined to the ends of the sex chromosome. Bergero et al. interpret these results to suggest that our previous findings of population-level variation in the degree of sex chromosome differentiation in this species (2) are incorrect. However, we suggest that their results are entirely consistent with our previous report, and that their interpretation presents a false controversy.","lang":"eng"}],"issue":"26","article_type":"letter_note","page":"12607-12608","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ama":"Wright AE, Darolti I, Bloch NI, et al. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(26):12607-12608. doi:10.1073/pnas.1905555116","apa":"Wright, A. E., Darolti, I., Bloch, N. I., Oostra, V., Sandkam, B. A., Buechel, S. D., … Mank, J. E. (2019). On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1905555116","ieee":"A. E. Wright et al., “On the power to detect rare recombination events,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26. Proceedings of the National Academy of Sciences, pp. 12607–12608, 2019.","ista":"Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam BA, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE. 2019. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 116(26), 12607–12608.","short":"A.E. Wright, I. Darolti, N.I. Bloch, V. Oostra, B.A. Sandkam, S.D. Buechel, N. Kolm, F. Breden, B. Vicoso, J.E. Mank, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 12607–12608.","mla":"Wright, Alison E., et al. “On the Power to Detect Rare Recombination Events.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26, Proceedings of the National Academy of Sciences, 2019, pp. 12607–08, doi:10.1073/pnas.1905555116.","chicago":"Wright, Alison E., Iulia Darolti, Natasha I. Bloch, Vicencio Oostra, Benjamin A. Sandkam, Séverine D. Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith E. Mank. “On the Power to Detect Rare Recombination Events.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1905555116."},"date_published":"2019-06-25T00:00:00Z","scopus_import":"1","day":"25","article_processing_charge":"No","publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Proceedings of the National Academy of Sciences","year":"2019","pmid":1,"date_created":"2019-07-07T21:59:25Z","date_updated":"2023-10-17T12:44:15Z","volume":116,"author":[{"full_name":"Wright, Alison E.","first_name":"Alison E.","last_name":"Wright"},{"full_name":"Darolti, Iulia","first_name":"Iulia","last_name":"Darolti"},{"last_name":"Bloch","first_name":"Natasha I.","full_name":"Bloch, Natasha I."},{"first_name":"Vicencio","last_name":"Oostra","full_name":"Oostra, Vicencio"},{"full_name":"Sandkam, Benjamin A.","last_name":"Sandkam","first_name":"Benjamin A."},{"first_name":"Séverine D.","last_name":"Buechel","full_name":"Buechel, Séverine D."},{"full_name":"Kolm, Niclas","first_name":"Niclas","last_name":"Kolm"},{"full_name":"Breden, Felix","last_name":"Breden","first_name":"Felix"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"},{"full_name":"Mank, Judith E.","last_name":"Mank","first_name":"Judith E."}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"pmid":["31213531"],"isi":["000472719100010"]},"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1905555116","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1905555116","month":"06"},{"language":[{"iso":"eng"}],"doi":"10.1111/nph.16180","project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones"},{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463","name":"Sex chromosomes and species barriers","call_identifier":"FWF"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31505037"]},"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"month":"11","volume":224,"date_created":"2019-09-07T14:35:40Z","date_updated":"2023-10-18T08:47:08Z","author":[{"last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Brandvain, Yaniv","first_name":"Yaniv","last_name":"Brandvain"},{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Yakimowski, Sarah","last_name":"Yakimowski","first_name":"Sarah"},{"full_name":"Dixit, Tanmay","last_name":"Dixit","first_name":"Tanmay"},{"full_name":"Lexer, Christian","last_name":"Lexer","first_name":"Christian"},{"id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","first_name":"Eva","last_name":"Cereghetti","full_name":"Cereghetti, Eva"},{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:42Z","date_published":"2019-11-01T00:00:00Z","page":"1035-1047","article_type":"original","citation":{"ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.","short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180."},"publication":"New Phytologist","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","checksum":"21e4c95599bbcaf7c483b89954658672","relation":"main_file","file_id":"7011","content_type":"application/pdf","file_size":1511958,"creator":"dernst","file_name":"2019_NewPhytologist_Pickup.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 224","ddc":["570"],"status":"public","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","_id":"6856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.","lang":"eng"}],"type":"journal_article"},{"file_date_updated":"2020-07-14T12:47:35Z","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav"},{"first_name":"Bernd","last_name":"Gärtner","full_name":"Gärtner, Bernd"},{"full_name":"Kupavskii, Andrey","last_name":"Kupavskii","first_name":"Andrey"},{"first_name":"Pavel","last_name":"Valtr","full_name":"Valtr, Pavel"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"related_material":{"record":[{"id":"13974","status":"public","relation":"later_version"}]},"date_updated":"2023-12-13T12:03:35Z","date_created":"2019-07-17T10:35:04Z","volume":129,"year":"2019","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"month":"06","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771047"]},"conference":{"start_date":"2019-06-18","location":"Portland, OR, United States","end_date":"2019-06-21","name":"SoCG 2019: Symposium on Computational Geometry"},"doi":"10.4230/LIPICS.SOCG.2019.38","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1812.04911"]},"quality_controlled":"1","project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}],"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."}],"type":"conference","alternative_title":["LIPIcs"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":559837,"creator":"dernst","access_level":"open_access","file_name":"2019_LIPICS_Fulek.pdf","checksum":"d6d017f8b41291b94d102294fa96ae9c","date_created":"2019-07-24T06:54:52Z","date_updated":"2020-07-14T12:47:35Z","relation":"main_file","file_id":"6667"}],"_id":"6647","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The crossing Tverberg theorem","status":"public","ddc":["000","510"],"intvolume":" 129","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2019-06-01T00:00:00Z","publication":"35th International Symposium on Computational Geometry","citation":{"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","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.","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","chicago":"Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” In 35th International Symposium on Computational Geometry, 129:38:1-38:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38.","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."},"page":"38:1-38:13"},{"_id":"6676","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Why extension-based proofs fail","status":"public","oa_version":"Preprint","type":"conference","abstract":[{"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.","lang":"eng"}],"publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","citation":{"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.","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.","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.","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","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.","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","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."},"page":"986-996","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2019","publication_status":"published","publisher":"ACM Press","department":[{"_id":"DaAl"}],"author":[{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"full_name":"Ellen, Faith","last_name":"Ellen","first_name":"Faith"},{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"full_name":"Zhu, Leqi","last_name":"Zhu","first_name":"Leqi"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"14364"}]},"date_created":"2019-07-24T09:13:05Z","date_updated":"2023-12-13T12:28:28Z","external_id":{"isi":["000523199100089"],"arxiv":["1811.01421"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01421"}],"oa":1,"quality_controlled":"1","isi":1,"conference":{"location":"Phoenix, AZ, United States","start_date":"2019-06-23","end_date":"2019-06-26","name":"STOC: Symposium on Theory of Computing"},"doi":"10.1145/3313276.3316407","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"isbn":["9781450367059"]}},{"department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}],"title":"Token swapping on trees","status":"public","publication_status":"submitted","year":"2019","_id":"7950","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_updated":"2024-01-04T12:42:08Z","date_created":"2020-06-08T12:25:25Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7944"},{"relation":"later_version","status":"public","id":"12833"}]},"author":[{"first_name":"Ahmad","last_name":"Biniaz","full_name":"Biniaz, Ahmad"},{"last_name":"Jain","first_name":"Kshitij","full_name":"Jain, Kshitij"},{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"full_name":"Masárová, Zuzana","first_name":"Zuzana","last_name":"Masárová","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322"},{"full_name":"Miltzow, Tillmann","first_name":"Tillmann","last_name":"Miltzow"},{"full_name":"Mondal, Debajyoti","first_name":"Debajyoti","last_name":"Mondal"},{"first_name":"Anurag Murty","last_name":"Naredla","full_name":"Naredla, Anurag Murty"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef"},{"full_name":"Turcotte, Alexi","last_name":"Turcotte","first_name":"Alexi"}],"type":"preprint","article_number":"1903.06981","abstract":[{"lang":"eng","text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results:\r\n1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan.\r\n2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2.\r\n3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved."}],"citation":{"ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. arXiv.","apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (n.d.). Token swapping on trees. arXiv.","ieee":"A. Biniaz et al., “Token swapping on trees,” arXiv. .","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. Token swapping on trees. arXiv, 1903.06981.","short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, ArXiv (n.d.).","mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981.","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” ArXiv, n.d."},"oa":1,"external_id":{"arxiv":["1903.06981"]},"main_file_link":[{"url":"https://arxiv.org/abs/1903.06981","open_access":"1"}],"publication":"arXiv","language":[{"iso":"eng"}],"date_published":"2019-03-16T00:00:00Z","article_processing_charge":"No","month":"03","day":"16"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"1033-1044","citation":{"chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz053.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. 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Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"intvolume":" 11","ddc":["570"],"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","status":"public","_id":"6418","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","file_name":"2019_GBE_Huylmans.pdf","file_size":1256303,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6446","checksum":"7d0ede297b6741f3dc89cd59017c7642","date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-14T08:29:38Z"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1759-6653"]},"month":"04","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000476569800003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/gbe/evz053","ec_funded":1,"file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","publication_status":"published","year":"2019","volume":11,"date_updated":"2024-02-21T12:45:41Z","date_created":"2019-05-13T07:58:38Z","related_material":{"record":[{"id":"6060","relation":"popular_science","status":"public"}]},"author":[{"orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K","full_name":"Huylmans, Ann K"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger","first_name":"William J"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}]},{"date_published":"2019-11-13T00:00:00Z","doi":"10.15479/AT:ISTA:7016","citation":{"chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","short":"I. 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