[{"_id":"6071","type":"dissertation","status":"public","date_updated":"2023-09-22T10:00:48Z","supervisor":[{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"ddc":["576"],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:18Z","abstract":[{"text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"03","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"creator":"rprizak","file_size":20995465,"date_updated":"2020-07-14T12:47:18Z","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","date_created":"2019-03-06T16:05:07Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"e60a72de35d270b31f1a23d50f224ec0","file_id":"6072"},{"date_created":"2019-03-06T16:09:39Z","title":"Latex files","file_name":"thesis_v2_merge.zip","date_updated":"2020-07-14T12:47:18Z","file_size":85705272,"creator":"rprizak","file_id":"6073","checksum":"67c2630333d05ebafef5f018863a8465","content_type":"application/zip","access_level":"closed","relation":"source_file"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1358"},{"status":"public","id":"955","relation":"part_of_dissertation"}]},"project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"citation":{"chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Prizak","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"}],"title":"Coevolution of transcription factors and their binding sites in sequence space","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2019","has_accepted_license":"1","day":"11","page":"189","date_created":"2019-03-06T16:16:10Z","date_published":"2019-03-11T00:00:00Z","doi":"10.15479/at:ista:th6071"},{"oa":1,"publisher":"EMS Press","quality_controlled":"1","page":"1135-1177","date_created":"2020-02-02T23:01:06Z","doi":"10.25537/dm.2019v24.1135-1177","date_published":"2019-05-20T00:00:00Z","year":"2019","isi":1,"has_accepted_license":"1","publication":"Documenta Mathematica","day":"20","external_id":{"isi":["000517806400019"],"arxiv":["1809.08970"]},"article_processing_charge":"No","author":[{"id":"4D046628-F248-11E8-B48F-1D18A9856A87","first_name":"Tanya K","full_name":"Srivastava, Tanya K","last_name":"Srivastava"}],"title":"On derived equivalences of k3 surfaces in positive characteristic","citation":{"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.","ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 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.","short":"T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 24","month":"05","abstract":[{"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. ","lang":"eng"}],"oa_version":"Published Version","volume":24,"publication_status":"published","publication_identifier":{"eissn":["1431-0643"],"issn":["1431-0635"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:58Z","file_size":469730,"creator":"dernst","date_created":"2020-02-03T06:26:12Z","file_name":"2019_DocumMath_Srivastava.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7438","checksum":"9a1a64bd49ab03fa4f738fb250fc4f90"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"7436","file_date_updated":"2020-07-14T12:47:58Z","department":[{"_id":"TaHa"}],"date_updated":"2023-10-17T07:42:21Z","ddc":["510"]},{"oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","year":"2019","isi":1,"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","day":"25","page":"1203-1225","date_created":"2018-12-11T11:44:29Z","doi":"10.1214/18-AIHP916","date_published":"2019-09-25T00:00:00Z","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"},{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000487763200001"],"arxiv":["1710.02323"]},"article_processing_charge":"No","author":[{"full_name":"Ferrari, Patrick","last_name":"Ferrari","first_name":"Patrick"},{"full_name":"Ghosal, Promit","last_name":"Ghosal","first_name":"Promit"},{"first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter","last_name":"Nejjar"}],"title":"Limit law of a second class particle in TASEP with non-random initial condition","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1710.02323","open_access":"1"}],"scopus_import":"1","intvolume":" 55","month":"09","publication_status":"published","publication_identifier":{"issn":["0246-0203"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"3","volume":55,"_id":"72","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-10-17T08:53:45Z","department":[{"_id":"LaEr"},{"_id":"JaMa"}]},{"date_updated":"2023-10-17T11:33:58Z","ddc":["020"],"file_date_updated":"2020-07-14T12:47:35Z","department":[{"_id":"E-Lib"}],"_id":"6657","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["1022-2588"]},"language":[{"iso":"eng"}],"file":[{"creator":"apreinsp","file_size":468558,"date_updated":"2020-07-14T12:47:35Z","file_name":"2019_MitteilungenDerVOEB_Danowski.pdf","date_created":"2019-07-22T08:45:03Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6661","checksum":"c0d2695d6d0d34e62ba06fb3f0ebaaed"}],"related_material":{"record":[{"status":"public","id":"5686","relation":"earlier_version"}]},"issue":"1","volume":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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 72","month":"05","citation":{"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.","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.","short":"P. Danowski, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 72 (2019) 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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","first_name":"Patrick","orcid":"0000-0002-6026-4409","full_name":"Danowski, Patrick","last_name":"Danowski"}],"title":"An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors","year":"2019","has_accepted_license":"1","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","day":"17","page":"59-65","date_created":"2019-07-21T21:59:15Z","date_published":"2019-05-17T00:00:00Z","doi":"10.31263/voebm.v72i1.2276","oa":1,"quality_controlled":"1","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare"},{"title":"Room temperature control of valley coherence in bilayer WS2 exciton polaritons","department":[{"_id":"MiLe"}],"article_processing_charge":"No","author":[{"first_name":"Mandeep","full_name":"Khatoniar, Mandeep","last_name":"Khatoniar"},{"first_name":"Nicholas","last_name":"Yama","full_name":"Yama, Nicholas"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sriram","full_name":"Guddala, Sriram","last_name":"Guddala"},{"last_name":"Ghaemi","full_name":"Ghaemi, Pouyan","first_name":"Pouyan"},{"last_name":"Menon","full_name":"Menon, Vinod","first_name":"Vinod"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","short":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, V. Menon, in:, CLEO: Applications and Technology, Optica Publishing Group, 2019.","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","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","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."},"date_updated":"2023-10-17T12:14:29Z","status":"public","conference":{"name":"CLEO: Conference on Lasers and Electro-Optics","location":"San Jose, CA, United States","end_date":"2019-05-10","start_date":"2019-05-05"},"type":"conference","article_number":"paper JTu2A.52","_id":"6646","date_created":"2019-07-17T09:40:44Z","date_published":"2019-05-01T00:00:00Z","doi":"10.1364/cleo_at.2019.jtu2a.52","language":[{"iso":"eng"}],"publication":"CLEO: Applications and Technology","day":"01","year":"2019","publication_status":"published","publication_identifier":{"isbn":["9781943580576"]},"month":"05","scopus_import":"1","publisher":"Optica Publishing Group","quality_controlled":"1","oa_version":"None","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"}]},{"language":[{"iso":"eng"}],"publication":"Nonlinear Optics, OSA Technical Digest","day":"15","year":"2019","publication_status":"published","publication_identifier":{"isbn":["9781557528209"]},"date_created":"2020-01-05T23:00:48Z","doi":"10.1364/NLO.2019.NM2A.5","date_published":"2019-07-15T00:00:00Z","oa_version":"None","abstract":[{"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.","lang":"eng"}],"month":"07","publisher":"Optica Publishing Group","scopus_import":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-10-17T12:14:46Z","citation":{"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.","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.","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.","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","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","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.","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."},"department":[{"_id":"JoFi"}],"title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","article_processing_charge":"No","author":[{"last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R"},{"first_name":"Florian","full_name":"Sedlmeir, Florian","last_name":"Sedlmeir"},{"last_name":"Leuchs","full_name":"Leuchs, Gerd","first_name":"Gerd"},{"last_name":"Kumari","full_name":"Kumari, Madhuri","first_name":"Madhuri"},{"first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L.","last_name":"Schwefel"}],"article_number":"NM2A.5","_id":"7233","status":"public","conference":{"location":"Waikoloa Beach, Hawaii (HI), United States","end_date":"2019-07-19","start_date":"2019-07-15","name":"NLO: Nonlinear Optics"},"type":"conference"},{"page":"661-696","doi":"10.1214/18-AIHP894","date_published":"2019-05-01T00:00:00Z","date_created":"2019-04-08T14:05:04Z","isi":1,"year":"2019","day":"01","publication":"Annales de l'institut Henri Poincare","quality_controlled":"1","publisher":"Institut Henri Poincaré","oa":1,"author":[{"full_name":"Alt, Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7327-856X","full_name":"Nemish, Yuriy","last_name":"Nemish","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","first_name":"Yuriy"}],"article_processing_charge":"No","external_id":{"arxiv":["1706.08343"],"isi":["000467793600003"]},"title":"Location of the spectrum of Kronecker random matrices","citation":{"short":"J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"issue":"2","volume":55,"related_material":{"record":[{"status":"public","id":"149","relation":"dissertation_contains"}]},"ec_funded":1,"publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1706.08343","open_access":"1"}],"month":"05","intvolume":" 55","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"LaEr"}],"date_updated":"2023-10-17T12:20:20Z","type":"journal_article","status":"public","_id":"6240"},{"publication_identifier":{"issn":["1553-7404"]},"publication_status":"published","file":[{"checksum":"2f51fc91e4a4199827adc51d432ad864","file_id":"7446","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-02-04T10:11:55Z","file_name":"2019_PlosGenetics_Andergassen.pdf","date_updated":"2020-07-14T12:47:57Z","file_size":2302307,"creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"7","volume":15,"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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 15","date_updated":"2023-10-17T12:30:27Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2020-07-14T12:47:57Z","_id":"7399","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","isi":1,"has_accepted_license":"1","year":"2019","day":"22","publication":"PLoS Genetics","date_published":"2019-07-22T00:00:00Z","doi":"10.1371/journal.pgen.1008268","date_created":"2020-01-29T16:14:07Z","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"citation":{"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.","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.","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.","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","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.","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)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Daniel","last_name":"Andergassen","full_name":"Andergassen, Daniel"},{"first_name":"Markus","last_name":"Muckenhuber","full_name":"Muckenhuber, Markus"},{"first_name":"Philipp C.","full_name":"Bammer, Philipp C.","last_name":"Bammer"},{"first_name":"Tomasz M.","last_name":"Kulinski","full_name":"Kulinski, Tomasz M."},{"full_name":"Theussl, Hans-Christian","last_name":"Theussl","first_name":"Hans-Christian"},{"last_name":"Shimizu","full_name":"Shimizu, Takahiko","first_name":"Takahiko"},{"last_name":"Penninger","full_name":"Penninger, Josef M.","first_name":"Josef M."},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"full_name":"Hudson, Quanah J.","last_name":"Hudson","first_name":"Quanah J."}],"article_processing_charge":"No","external_id":{"isi":["000478689100025"],"pmid":["31329595"]},"title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","article_number":"e1008268"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).","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.","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.","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."},"title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","article_processing_charge":"No","external_id":{"isi":["000500976100014"],"pmid":["31725712"]},"author":[{"first_name":"Jilin W. J. L.","last_name":"Wang","full_name":"Wang, Jilin W. J. L."},{"last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"last_name":"Anaclet","full_name":"Anaclet, Christelle","first_name":"Christelle"},{"first_name":"Plamen Ch.","full_name":"Ivanov, Plamen Ch.","last_name":"Ivanov"}],"article_number":"e1007268","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"publication":"PLoS Computational Biology","day":"01","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2019-11-25T08:20:47Z","doi":"10.1371/journal.pcbi.1007268","date_published":"2019-11-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","ddc":["570","000"],"date_updated":"2023-10-17T12:30:07Z","file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"GaTk"}],"_id":"7103","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:49Z","file_size":3982516,"date_created":"2019-11-25T08:24:01Z","file_name":"2019_PLOSComBio_Wang.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","file_id":"7104"}],"publication_status":"published","publication_identifier":{"issn":["1553-7358"]},"ec_funded":1,"volume":15,"issue":"11","oa_version":"Published Version","pmid":1,"abstract":[{"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.","lang":"eng"}],"intvolume":" 15","month":"11","scopus_import":"1"},{"oa":1,"publisher":"ML Research Press","quality_controlled":"1","date_created":"2019-06-20T18:23:03Z","date_published":"2019-06-13T00:00:00Z","page":"5142-5151","publication":"Proceedings of the 36th International Conference on Machine Learning","day":"13","year":"2019","has_accepted_license":"1","title":"Towards understanding knowledge distillation","article_processing_charge":"No","author":[{"id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong","last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","short":"M. Phuong, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 5142–5151.","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.","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."},"intvolume":" 97","month":"06","scopus_import":"1","oa_version":"Published Version","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"}],"volume":97,"language":[{"iso":"eng"}],"file":[{"file_id":"6570","checksum":"a66d00e2694d749250f8507f301320ca","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-06-20T18:22:56Z","file_name":"paper.pdf","date_updated":"2020-07-14T12:47:33Z","file_size":686432,"creator":"bphuong"}],"publication_status":"published","status":"public","conference":{"location":"Long Beach, CA, United States","end_date":"2019-06-15","start_date":"2019-06-10","name":"ICML: International Conference on Machine Learning"},"type":"conference","_id":"6569","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:47:33Z","ddc":["000"],"date_updated":"2023-10-17T12:31:38Z"},{"title":"Robust learning from untrusted sources","author":[{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1901.10310"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","short":"N.H. Konstantinov, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 3488–3498.","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."},"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_published":"2019-06-01T00:00:00Z","date_created":"2019-06-27T14:18:23Z","page":"3488-3498","day":"01","publication":"Proceedings of the 36th International Conference on Machine Learning","year":"2019","quality_controlled":"1","publisher":"ML Research Press","oa":1,"department":[{"_id":"ChLa"}],"date_updated":"2023-10-17T12:31:55Z","status":"public","type":"conference","conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2919-06-15","location":"Long Beach, CA, USA","start_date":"2019-06-10"},"_id":"6590","volume":97,"related_material":{"record":[{"id":"10799","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 97","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10310"}],"oa_version":"Preprint","abstract":[{"lang":"eng","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. "}]},{"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"15","publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"21274-21284","doi":"10.1073/pnas.1911892116","date_published":"2019-10-15T00:00:00Z","date_created":"2019-11-12T11:42:05Z","citation":{"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.","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","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","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"D","last_name":"Huang","full_name":"Huang, D"},{"full_name":"Sun, Y","last_name":"Sun","first_name":"Y"},{"first_name":"Z","last_name":"Ma","full_name":"Ma, Z"},{"last_name":"Ke","full_name":"Ke, M","first_name":"M"},{"full_name":"Cui, Y","last_name":"Cui","first_name":"Y"},{"last_name":"Chen","full_name":"Chen, Z","first_name":"Z"},{"first_name":"C","last_name":"Chen","full_name":"Chen, C"},{"first_name":"C","last_name":"Ji","full_name":"Ji, C"},{"first_name":"TM","full_name":"Tran, TM","last_name":"Tran"},{"full_name":"Yang, L","last_name":"Yang","first_name":"L"},{"first_name":"SM","full_name":"Lam, SM","last_name":"Lam"},{"last_name":"Han","full_name":"Han, Y","first_name":"Y"},{"first_name":"G","last_name":"Shu","full_name":"Shu, G"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Y","last_name":"Miao","full_name":"Miao, Y"},{"last_name":"Jiang","full_name":"Jiang, L","first_name":"L"},{"first_name":"X","last_name":"Chen","full_name":"Chen, X"}],"article_processing_charge":"No","external_id":{"isi":["000490183000068"],"pmid":["31575745"]},"title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"10","intvolume":" 116","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publication_status":"published","file":[{"date_created":"2019-11-13T08:22:28Z","file_name":"2019_PNAS_Huang.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:46Z","file_size":3287466,"checksum":"258c666bc6253eab81961f61169eefae","file_id":"7012","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"issue":"42","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2004738117","relation":"erratum"}]},"volume":116,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"6999","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","date_updated":"2023-10-17T12:32:37Z","ddc":["580"],"file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"JiFr"}]},{"date_updated":"2023-10-17T12:44:15Z","department":[{"_id":"BeVi"}],"_id":"6621","status":"public","type":"journal_article","article_type":"letter_note","language":[{"iso":"eng"}],"publication_status":"published","volume":116,"issue":"26","pmid":1,"oa_version":"Published Version","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"}],"intvolume":" 116","month":"06","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1905555116","open_access":"1"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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."},"title":"On the power to detect rare recombination events","article_processing_charge":"No","external_id":{"pmid":["31213531"],"isi":["000472719100010"]},"author":[{"full_name":"Wright, Alison E.","last_name":"Wright","first_name":"Alison E."},{"first_name":"Iulia","full_name":"Darolti, Iulia","last_name":"Darolti"},{"full_name":"Bloch, Natasha I.","last_name":"Bloch","first_name":"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","last_name":"Kolm","first_name":"Niclas"},{"last_name":"Breden","full_name":"Breden, Felix","first_name":"Felix"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"last_name":"Mank","full_name":"Mank, Judith E.","first_name":"Judith E."}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"25","year":"2019","isi":1,"date_created":"2019-07-07T21:59:25Z","doi":"10.1073/pnas.1905555116","date_published":"2019-06-25T00:00:00Z","page":"12607-12608","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1"},{"scopus_import":"1","intvolume":" 224","month":"11","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"}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"volume":224,"issue":"3","publication_status":"published","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-13T08:15:05Z","file_name":"2019_NewPhytologist_Pickup.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:42Z","file_size":1511958,"file_id":"7011","checksum":"21e4c95599bbcaf7c483b89954658672","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"6856","file_date_updated":"2020-07-14T12:47:42Z","department":[{"_id":"NiBa"}],"date_updated":"2023-10-18T08:47:08Z","ddc":["570"],"oa":1,"publisher":"Wiley","quality_controlled":"1","page":"1035-1047","date_created":"2019-09-07T14:35:40Z","date_published":"2019-11-01T00:00:00Z","doi":"10.1111/nph.16180","year":"2019","has_accepted_license":"1","publication":"New Phytologist","day":"01","project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960"},{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463"}],"external_id":{"pmid":["31505037"]},"article_processing_charge":"No","author":[{"first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Brandvain","full_name":"Brandvain, Yaniv","first_name":"Yaniv"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"Yakimowski","full_name":"Yakimowski, Sarah","first_name":"Sarah"},{"first_name":"Tanmay","full_name":"Dixit, Tanmay","last_name":"Dixit"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"},{"last_name":"Cereghetti","full_name":"Cereghetti, Eva","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63"},{"last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"}],"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","citation":{"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.","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.","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.","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771047"]},"publication_status":"published","file":[{"checksum":"d6d017f8b41291b94d102294fa96ae9c","file_id":"6667","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-07-24T06:54:52Z","file_name":"2019_LIPICS_Fulek.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:35Z","file_size":559837}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","id":"13974","status":"public"}]},"volume":129,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"month":"06","intvolume":" 129","date_updated":"2023-12-13T12:03:35Z","ddc":["000","510"],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:47:35Z","_id":"6647","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"SoCG 2019: Symposium on Computational Geometry","location":"Portland, OR, United States","end_date":"2019-06-21","start_date":"2019-06-18"},"status":"public","has_accepted_license":"1","year":"2019","day":"01","publication":"35th International Symposium on Computational Geometry","page":"38:1-38:13","date_published":"2019-06-01T00:00:00Z","doi":"10.4230/LIPICS.SOCG.2019.38","date_created":"2019-07-17T10:35:04Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"citation":{"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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"last_name":"Gärtner","full_name":"Gärtner, Bernd","first_name":"Bernd"},{"first_name":"Andrey","last_name":"Kupavskii","full_name":"Kupavskii, Andrey"},{"full_name":"Valtr, Pavel","last_name":"Valtr","first_name":"Pavel"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"external_id":{"arxiv":["1812.04911"]},"title":"The crossing Tverberg theorem","project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}]},{"_id":"6676","status":"public","conference":{"name":"STOC: Symposium on Theory of Computing","start_date":"2019-06-23","end_date":"2019-06-26","location":"Phoenix, AZ, United States"},"type":"conference","date_updated":"2023-12-13T12:28:28Z","department":[{"_id":"DaAl"}],"oa_version":"Preprint","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"}],"month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1811.01421","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781450367059"]},"related_material":{"record":[{"relation":"later_version","id":"14364","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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","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.","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.","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.","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.","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."},"title":"Why extension-based proofs fail","article_processing_charge":"No","external_id":{"arxiv":["1811.01421"],"isi":["000523199100089"]},"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"last_name":"Ellen","full_name":"Ellen, Faith","first_name":"Faith"},{"first_name":"Rati","full_name":"Gelashvili, Rati","last_name":"Gelashvili"},{"first_name":"Leqi","full_name":"Zhu, Leqi","last_name":"Zhu"}],"oa":1,"quality_controlled":"1","publisher":"ACM Press","publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","day":"01","year":"2019","isi":1,"date_created":"2019-07-24T09:13:05Z","doi":"10.1145/3313276.3316407","date_published":"2019-06-01T00:00:00Z","page":"986-996"},{"publication":"arXiv","language":[{"iso":"eng"}],"day":"16","publication_status":"submitted","year":"2019","date_created":"2020-06-08T12:25:25Z","date_published":"2019-03-16T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","id":"7944","status":"public"},{"relation":"later_version","id":"12833","status":"public"}]},"oa_version":"Preprint","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."}],"month":"03","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.06981"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-04T12:42:08Z","citation":{"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.","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.","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. .","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."},"title":"Token swapping on trees","department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}],"article_processing_charge":"No","external_id":{"arxiv":["1903.06981"]},"author":[{"full_name":"Biniaz, Ahmad","last_name":"Biniaz","first_name":"Ahmad"},{"full_name":"Jain, Kshitij","last_name":"Jain","first_name":"Kshitij"},{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322","last_name":"Masárová"},{"first_name":"Tillmann","last_name":"Miltzow","full_name":"Miltzow, Tillmann"},{"first_name":"Debajyoti","full_name":"Mondal, Debajyoti","last_name":"Mondal"},{"first_name":"Anurag Murty","full_name":"Naredla, Anurag Murty","last_name":"Naredla"},{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexi","full_name":"Turcotte, Alexi","last_name":"Turcotte"}],"article_number":"1903.06981","_id":"7950","status":"public","type":"preprint"},{"file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"BeVi"}],"ddc":["570"],"date_updated":"2024-02-21T12:45:41Z","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6418","related_material":{"record":[{"relation":"popular_science","id":"6060","status":"public"}]},"volume":11,"issue":"4","ec_funded":1,"file":[{"checksum":"7d0ede297b6741f3dc89cd59017c7642","file_id":"6446","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-05-14T08:29:38Z","file_name":"2019_GBE_Huylmans.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:29Z","file_size":1256303}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1759-6653"]},"publication_status":"published","month":"04","intvolume":" 11","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. 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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","author":[{"last_name":"Huylmans","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon"},{"first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","last_name":"Gammerdinger"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000476569800003"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","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.","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. Oxford University Press, pp. 1033–1044, 2019.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","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","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053","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."},"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"doi":"10.1093/gbe/evz053","date_published":"2019-04-01T00:00:00Z","date_created":"2019-05-13T07:58:38Z","page":"1033-1044","day":"01","publication":"Genome biology and evolution","isi":1,"has_accepted_license":"1","year":"2019","quality_controlled":"1","publisher":"Oxford University Press","oa":1},{"abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"11","has_accepted_license":"1","year":"2019","day":"13","file":[{"creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","file_size":2456192500,"title":"Locus1_amplified","date_created":"2019-11-13T08:52:21Z","file_name":"D8_S35_R2_001.fastq","access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 1 - amplified.","file_id":"7017","checksum":"72441055043eda4cbf1398a422e2c118"},{"file_name":"IT028_S11_R2_001.fastq","date_created":"2019-11-13T08:52:59Z","title":"Locus1_ancestral","file_size":2833452234,"date_updated":"2020-07-14T12:47:47Z","creator":"itomanek","checksum":"a4ac50bf655d9c751f0305ade5c2ee16","file_id":"7018","description":"Illumina whole genome sequence data for Locus 1 - ancestral.","content_type":"application/octet-stream","relation":"main_file","access_level":"open_access"},{"checksum":"5b227708ff478ca06e3f0448a4efdc2f","file_id":"7019","relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 1 - amplified, after DOG-selection.","file_name":"D8-DOG1_S47_R2_001.fastq","title":"Locus1_amplified_DOG","date_created":"2019-11-13T08:54:10Z","creator":"itomanek","file_size":2878017264,"date_updated":"2020-07-14T12:47:47Z"},{"relation":"main_file","access_level":"open_access","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 2 - amplified.","checksum":"d9550a4c044116075fa83f8f2ea31d6f","file_id":"7020","creator":"itomanek","file_size":2180826995,"date_updated":"2020-07-14T12:47:47Z","file_name":"D4_S71_R2_001.fastq","title":"Locus2_amplified","date_created":"2019-11-13T08:54:27Z"},{"title":"Locus2_ancestral","date_created":"2019-11-13T08:55:58Z","file_name":"IT030_S23_R2_001.fastq","creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","file_size":2108826444,"checksum":"466ceb302c020ac013007a879fcde69d","file_id":"7021","access_level":"open_access","relation":"main_file","description":"Illumina whole genome sequence data for Locus 2 - ancestral.","content_type":"application/octet-stream"},{"file_name":"D4-DOG1_S83_R2_001.fastq","title":"Locus2_amplified_DOG","date_created":"2019-11-21T12:31:01Z","file_size":3144330494,"date_updated":"2020-07-14T12:47:47Z","creator":"itomanek","file_id":"7092","checksum":"8aeb1da771713c7baa5a847eff889604","content_type":"application/octet-stream","description":"Illumina whole genome sequence data for Locus 2 - amplified, after DOG-selection.","relation":"main_file","access_level":"open_access"},{"file_size":4179,"date_updated":"2020-07-14T12:47:47Z","creator":"itomanek","file_name":"galK_dual_reporter_cassette.gb.zip","date_created":"2020-01-14T11:22:27Z","title":"DNA sequence of the chromosomal reporter gene cassette","content_type":"application/zip","description":"Compressed genbank file format containing the sequence of the chromosomal reporter gene cassette.","relation":"main_file","access_level":"open_access","checksum":"bf7d4b053f14af4655fb5574209fdb2d","file_id":"7273"},{"creator":"dernst","date_updated":"2020-07-14T12:47:47Z","file_size":435,"title":"Read_me_sequence_data","date_created":"2020-01-15T14:15:55Z","file_name":"Readme_7016.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"5e91cee2eff6f4a7cde456c6fb07c2ff","file_id":"7335"},{"creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","file_size":3765861,"title":"FACS data","date_created":"2020-01-22T15:44:16Z","file_name":"FACS_data.xlsx.zip","access_level":"open_access","relation":"main_file","description":"FACS data associated with Fig. 2c - see read_me_FACS","content_type":"application/zip","file_id":"7351","checksum":"5e6745dcfb9c1b11dd935ac3ee45fe33"},{"content_type":"text/rtf","access_level":"open_access","relation":"main_file","checksum":"a85caf092ae4b17668f70af2d93fad00","file_id":"7352","date_updated":"2020-07-14T12:47:47Z","file_size":4996,"creator":"itomanek","date_created":"2020-01-22T15:44:16Z","file_name":"read_me_FACS.rtf"},{"date_created":"2020-01-22T15:44:16Z","file_name":"read_me_microfluidics.rtf","creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","file_size":868,"file_id":"7353","checksum":"fd8ba5d75d24e47ddf7e70bfdadb40d4","access_level":"open_access","relation":"main_file","content_type":"text/rtf"},{"date_created":"2020-01-22T15:44:17Z","title":"microfluidics data","file_name":"microfuidics_data.zip","creator":"itomanek","date_updated":"2020-07-14T12:47:47Z","file_size":8141727,"checksum":"69c5dc5ca5c069a138183c934acc1778","file_id":"7354","access_level":"open_access","relation":"main_file","description":"microfluidics time trace data - see read_me_microfluidics","content_type":"application/zip"}],"date_published":"2019-11-13T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"7652","status":"public"}]},"doi":"10.15479/AT:ISTA:7016","date_created":"2019-11-13T09:07:31Z","contributor":[{"orcid":"0000-0001-6220-2052","last_name":"Guet","contributor_type":"project_leader","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"_id":"7016","type":"research_data","status":"public","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"citation":{"ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","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. Tomanek, (2019).","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016."},"date_updated":"2024-02-21T12:45:25Z","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella","full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X","last_name":"Tomanek"}],"article_processing_charge":"No","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:47Z","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\""},{"date_published":"2019-12-06T00:00:00Z","doi":"10.15479/AT:ISTA:7154","related_material":{"record":[{"status":"deleted","id":"8433","relation":"used_in_publication"},{"relation":"used_in_publication","id":"7262","status":"public"}]},"ec_funded":1,"license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2019-12-09T07:52:46Z","contributor":[{"first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","last_name":"Guseinov","orcid":"0000-0001-9819-5077"},{"first_name":"Connor","last_name":"McMahan"},{"last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus"},{"first_name":"Chiara","last_name":"Daraio"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"has_accepted_license":"1","year":"2019","day":"06","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/x-zip-compressed","checksum":"155133e6e188e85b3c0676a5e70b9341","file_id":"7155","creator":"dernst","date_updated":"2020-07-14T12:47:50Z","file_size":65307107,"date_created":"2019-12-09T07:52:17Z","file_name":"temporal_morphing_supp_data.zip"}],"publisher":"Institute of Science and Technology Austria","oa":1,"month":"12","oa_version":"Published Version","author":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","last_name":"Guseinov"}],"article_processing_charge":"No","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:47:50Z","title":"Supplementary data for \"Programming temporal morphing of self-actuated shells\"","citation":{"mla":"Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7154.","ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:10.15479/AT:ISTA:7154","apa":"Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154","ieee":"R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019.","short":"R. Guseinov, (2019).","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7154.","ista":"Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154."},"date_updated":"2024-02-21T12:45:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"7154"},{"type":"research_data","status":"public","_id":"6060","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:17Z","title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","department":[{"_id":"BeVi"}],"date_updated":"2024-02-21T12:45:42Z","citation":{"chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060.","ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.","mla":"Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.","apa":"Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060","ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060","ieee":"B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019.","short":"B. Vicoso, (2019)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","oa_version":"Published Version","related_material":{"record":[{"relation":"research_paper","status":"public","id":"6418"}]},"date_published":"2019-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:6060","date_created":"2019-02-28T10:55:15Z","has_accepted_license":"1","year":"2019","file":[{"date_created":"2019-02-28T10:54:27Z","file_name":"SupData.zip","date_updated":"2020-07-14T12:47:17Z","file_size":36646050,"creator":"bvicoso","file_id":"6061","checksum":"a338a622d728af0e3199cb07e6dd64d3","content_type":"application/zip","access_level":"open_access","relation":"main_file"}],"day":"28"},{"date_updated":"2024-02-21T13:41:01Z","citation":{"short":"C. Dotter, G. Novarino, (2019).","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074","mla":"Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074.","ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.","chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"article_processing_charge":"No","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph","orcid":"0000-0002-9033-9096"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","file_date_updated":"2020-07-14T12:47:18Z","department":[{"_id":"GaNo"}],"_id":"6074","type":"research_data","status":"public","year":"2019","has_accepted_license":"1","day":"09","file":[{"date_created":"2019-03-07T13:37:19Z","file_name":"Setd5_paper.zip","creator":"dernst","date_updated":"2020-07-14T12:47:18Z","file_size":33202743,"checksum":"bc1b285edca9e98a2c63d153c79bb75b","file_id":"6084","access_level":"open_access","relation":"supplementary_material","content_type":"application/zip"}],"date_created":"2019-03-07T13:32:35Z","doi":"10.15479/AT:ISTA:6074","related_material":{"record":[{"id":"3","status":"public","relation":"research_paper"}]},"date_published":"2019-01-09T00:00:00Z","abstract":[{"text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS.","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"01"},{"date_updated":"2024-02-21T12:46:04Z","citation":{"short":"M. Nardin, (2019).","ieee":"M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.","apa":"Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6062","ama":"Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062","mla":"Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal Cognitive Map Is Attracted to Goals.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6062.","ista":"Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6062.","chicago":"Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6062."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Nardin","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","first_name":"Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:18Z","department":[{"_id":"JoCs"}],"title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","_id":"6062","type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"status":"public","has_accepted_license":"1","year":"2019","day":"29","file":[{"date_created":"2019-03-05T09:29:37Z","title":"Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","file_name":"Online_data.zip","date_updated":"2020-07-14T12:47:18Z","file_size":37002186,"creator":"mnardin","file_id":"6068","checksum":"48e7b9a02939b763417733239522a236","content_type":"application/zip","access_level":"open_access","relation":"main_file"}],"doi":"10.15479/AT:ISTA:6062","related_material":{"record":[{"relation":"research_paper","id":"6194","status":"public"}]},"date_published":"2019-03-29T00:00:00Z","license":"https://creativecommons.org/licenses/by-sa/4.0/","date_created":"2019-03-04T14:20:58Z","abstract":[{"text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7).","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"03"},{"doi":"10.1093/molbev/msy246","date_published":"2019-03-01T00:00:00Z","date_created":"2019-03-10T22:59:19Z","page":"500-515","day":"01","publication":"Molecular biology and evolution","isi":1,"year":"2019","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246."},"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety"}],"volume":36,"issue":"3","related_material":{"record":[{"status":"public","id":"5757","relation":"popular_science"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"publication_status":"published","month":"03","intvolume":" 36","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.","lang":"eng"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2024-02-21T13:59:17Z","status":"public","type":"journal_article","_id":"6089"},{"author":[{"orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"From Dyson to Pearcey: Universal statistics in random matrix theory","citation":{"ama":"Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:10.15479/AT:ISTA:th6179","apa":"Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179","ieee":"D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix theory,” Institute of Science and Technology Austria, 2019.","short":"D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix Theory, Institute of Science and Technology Austria, 2019.","mla":"Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.","ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria.","chicago":"Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"375","date_published":"2019-03-18T00:00:00Z","doi":"10.15479/AT:ISTA:th6179","date_created":"2019-03-28T08:58:59Z","has_accepted_license":"1","year":"2019","day":"18","publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2020-07-14T12:47:21Z","department":[{"_id":"LaEr"}],"supervisor":[{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-22T14:34:33Z","ddc":["515","519"],"type":"dissertation","status":"public","_id":"6179","related_material":{"record":[{"relation":"part_of_dissertation","id":"1144","status":"public"},{"relation":"part_of_dissertation","id":"6186","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6185"},{"id":"6182","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1012","status":"public"},{"relation":"part_of_dissertation","id":"6184","status":"public"}]},"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_size":7104482,"date_updated":"2020-07-14T12:47:21Z","creator":"dernst","file_name":"2019_Schroeder_Thesis.tar.gz","date_created":"2019-03-28T08:53:52Z","content_type":"application/x-gzip","relation":"source_file","access_level":"closed","checksum":"6926f66f28079a81c4937e3764be00fc","file_id":"6180"},{"checksum":"7d0ebb8d1207e89768cdd497a5bf80fb","file_id":"6181","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-03-28T08:53:52Z","file_name":"2019_Schroeder_Thesis.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:21Z","file_size":4228794}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"03","abstract":[{"lang":"eng","text":"In the first part of this thesis we consider large random matrices with arbitrary expectation and a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic control of a multivariate cumulant expansion.\r\nIn the second part we consider Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are uni- versal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta universality conjecture for the last remaining universality type. Our analysis holds not only for exact cusps, but approximate cusps as well, where an ex- tended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow- nian motion to the cusp regime.\r\nIn the third and final part we explore the entrywise linear statistics of Wigner ma- trices and identify the fluctuations for a large class of test functions with little regularity. This enables us to study the rectangular Young diagram obtained from the interlacing eigenvalues of the random matrix and its minor, and we find that, despite having the same limit, the fluctuations differ from those of the algebraic Young tableaux equipped with the Plancharel measure."}],"oa_version":"Published Version"},{"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS, vol. 11269, 244–259.","chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-12939-2_18.","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.","short":"R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:10.1007/978-3-030-12939-2_18","apa":"Sun, R., & Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-12939-2_18","mla":"Sun, Rémy, and Christoph Lampert. KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications. Vol. 11269, Springer Nature, 2019, pp. 244–59, doi:10.1007/978-3-030-12939-2_18."},"title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications","article_processing_charge":"No","external_id":{"arxiv":["1804.04171"]},"author":[{"first_name":"Rémy","last_name":"Sun","full_name":"Sun, Rémy"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","day":"14","year":"2019","date_created":"2019-05-24T09:48:36Z","date_published":"2019-02-14T00:00:00Z","doi":"10.1007/978-3-030-12939-2_18","page":"244-259","_id":"6482","status":"public","conference":{"location":"Stuttgart, Germany","end_date":"2018-10-12","start_date":"2018-10-09","name":"GCPR: Conference on Pattern Recognition"},"type":"conference","date_updated":"2024-02-22T14:57:29Z","department":[{"_id":"ChLa"}],"oa_version":"Preprint","abstract":[{"text":"Computer vision systems for automatic image categorization have become accurate and reliable enough that they can run continuously for days or even years as components of real-world commercial applications. A major open problem in this context, however, is quality control. Good classification performance can only be expected if systems run under the specific conditions, in particular data distributions, that they were trained for. Surprisingly, none of the currently used deep network architectures have a built-in functionality that could detect if a network operates on data from a distribution it was not trained for, such that potentially a warning to the human users could be triggered. In this work, we describe KS(conf), a procedure for detecting such outside of specifications (out-of-specs) operation, based on statistical testing of the network outputs. We show by extensive experiments using the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that KS(conf) reliably detects out-of-specs situations. It furthermore has a number of properties that make it a promising candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with all networks, including pretrained ones, and requires no a priori knowledge of how the data distribution could change. ","lang":"eng"}],"intvolume":" 11269","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.04171"}],"scopus_import":"1","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030129385","9783030129392"]},"ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"6944"}]},"volume":11269},{"article_number":"020002","citation":{"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.","short":"M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing, 2019.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas"}],"external_id":{"isi":["000479303100002"],"arxiv":["1902.07983"]},"article_processing_charge":"No","title":"On diffusive variants of some classical viscoelastic rate-type models","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"isi":1,"year":"2019","day":"21","publication":"AIP Conference Proceedings","doi":"10.1063/1.5109493","date_published":"2019-05-21T00:00:00Z","date_created":"2019-07-15T10:07:09Z","_id":"6642","type":"conference","conference":{"start_date":"2019-07-30","end_date":"2019-07-31","location":"Zlin, Czech Republic","name":"8th International Conference on Novel Trends in Rheology"},"status":"public","date_updated":"2024-02-28T13:01:28Z","department":[{"_id":"ChWo"}],"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."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07983"}],"month":"05","intvolume":" 2107","publication_status":"published","language":[{"iso":"eng"}],"volume":2107},{"date_created":"2020-01-05T23:00:46Z","date_published":"2019-12-01T00:00:00Z","doi":"10.1063/1.5138135","publication":"Journal of Mathematical Physics","day":"01","year":"2019","isi":1,"has_accepted_license":"1","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","article_processing_charge":"No","external_id":{"isi":["000505529800002"]},"author":[{"last_name":"Jaksic","full_name":"Jaksic, Vojkan","first_name":"Vojkan"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 60(12), 123504.","chicago":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135.","ieee":"V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics, vol. 60, no. 12. AIP Publishing, 2019.","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","ama":"Jaksic V, Seiringer R. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 2019;60(12). doi:10.1063/1.5138135","apa":"Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.5138135","mla":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135."},"article_number":"123504","issue":"12","volume":60,"language":[{"iso":"eng"}],"file":[{"file_size":1025015,"date_updated":"2020-07-14T12:47:54Z","creator":"dernst","file_name":"2019_JournalMathPhysics_Jaksic.pdf","date_created":"2020-01-07T14:59:13Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22","file_id":"7244"}],"publication_status":"published","publication_identifier":{"issn":["00222488"]},"intvolume":" 60","month":"12","scopus_import":"1","oa_version":"Published Version","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:47:54Z","ddc":["500"],"date_updated":"2024-02-28T13:01:45Z","status":"public","type":"journal_article","article_type":"letter_note","_id":"7226"},{"quality_controlled":"1","publisher":"American Physical Society","oa":1,"has_accepted_license":"1","year":"2019","day":"16","publication":"Physical Review Research","doi":"10.1103/physrevresearch.1.033177","date_published":"2019-12-16T00:00:00Z","date_created":"2019-12-17T13:03:41Z","article_number":"033177","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"citation":{"chicago":"Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research. American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177.","ista":"Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177.","mla":"Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical Society, 2019, doi:10.1103/physrevresearch.1.033177.","ieee":"D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas,” Physical Review Research, vol. 1, no. 3. American Physical Society, 2019.","short":"D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).","ama":"Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177","apa":"Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Huber, D.","last_name":"Huber","first_name":"D."},{"last_name":"Hammer","full_name":"Hammer, H.-W.","first_name":"H.-W."},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525"}],"article_processing_charge":"No","external_id":{"arxiv":["1908.02483"]},"title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","abstract":[{"lang":"eng","text":"We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas."}],"oa_version":"Published Version","month":"12","intvolume":" 1","publication_identifier":{"issn":["2643-1564"]},"publication_status":"published","file":[{"creator":"dernst","file_size":1370022,"date_updated":"2020-07-14T12:47:52Z","file_name":"2019_PhysRevResearch_Huber.pdf","date_created":"2019-12-18T07:13:14Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"382eb67e62a77052a23887332d363f96","file_id":"7193"}],"language":[{"iso":"eng"}],"issue":"3","volume":1,"ec_funded":1,"_id":"7190","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2024-02-28T13:11:40Z","ddc":["530"],"file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"MiLe"}]},{"date_created":"2019-06-23T21:59:13Z","doi":"10.1103/PhysRevLett.122.220603","date_published":"2019-06-07T00:00:00Z","publication":"Physical Review Letters","day":"07","year":"2019","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Physical Society","title":"Emergent SU(2) dynamics and perfect quantum many-body scars","external_id":{"isi":["000470885800005"],"arxiv":["1812.05561"]},"article_processing_charge":"No","author":[{"last_name":"Choi","full_name":"Choi, Soonwon","first_name":"Soonwon"},{"last_name":"Turner","full_name":"Turner, Christopher J.","first_name":"Christopher J."},{"last_name":"Pichler","full_name":"Pichler, Hannes","first_name":"Hannes"},{"full_name":"Ho, Wen Wei","last_name":"Ho","first_name":"Wen Wei"},{"orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","last_name":"Michailidis","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"},{"full_name":"Lukin, Mikhail D.","last_name":"Lukin","first_name":"Mikhail D."},{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. Choi et al., “Emergent SU(2) dynamics and perfect quantum many-body scars,” Physical Review Letters, vol. 122, no. 22. American Physical Society, 2019.","short":"S. Choi, C.J. Turner, H. Pichler, W.W. Ho, A. Michailidis, Z. Papić, M. Serbyn, M.D. Lukin, D.A. Abanin, Physical Review Letters 122 (2019).","apa":"Choi, S., Turner, C. J., Pichler, H., Ho, W. W., Michailidis, A., Papić, Z., … Abanin, D. A. (2019). Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.220603","ama":"Choi S, Turner CJ, Pichler H, et al. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 2019;122(22). doi:10.1103/PhysRevLett.122.220603","mla":"Choi, Soonwon, et al. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters, vol. 122, no. 22, 220603, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.220603.","ista":"Choi S, Turner CJ, Pichler H, Ho WW, Michailidis A, Papić Z, Serbyn M, Lukin MD, Abanin DA. 2019. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 122(22), 220603.","chicago":"Choi, Soonwon, Christopher J. Turner, Hannes Pichler, Wen Wei Ho, Alexios Michailidis, Zlatko Papić, Maksym Serbyn, Mikhail D. Lukin, and Dmitry A. Abanin. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.220603."},"article_number":"220603","volume":122,"issue":"22","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"intvolume":" 122","month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1812.05561","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Motivated by recent experimental observations of coherent many-body revivals in a constrained Rydbergatom chain, we construct a weak quasilocal deformation of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect. Our analysis suggests the existence of an underlying nonintegrableHamiltonian which supports an emergent SU(2)-spin dynamics within a small subspace of the many-bodyHilbert space. We show that such perfect dynamics necessitates the existence of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore, using these insights, we construct a toymodel that hosts exact quantum many-body scars, providing an intuitive explanation of their origin. Ourresults offer specific routes to enhancing coherent many-body revivals and provide a step towardestablishing the stability of quantum many-body scars in the thermodynamic limit."}],"department":[{"_id":"MaSe"}],"date_updated":"2024-02-28T13:12:22Z","status":"public","article_type":"original","type":"journal_article","_id":"6575"},{"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.01638","open_access":"1"}],"month":"02","intvolume":" 99","abstract":[{"lang":"eng","text":"In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization of a magnetic material results in mechanical rotation and vice versa. At the microscopic level, this effect governs the transfer between electron spin and orbital angular momentum, and lattice degrees of freedom, understanding which is key for molecular magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now, the timescales of electron-to-lattice angular momentum transfer remain unclear, since modeling this process on a microscopic level requires the addition of an infinite amount of quantum angular momenta. We show that this problem can be solved by reformulating it in terms of the recently discovered angulon quasiparticles, which results in a rotationally invariant quantum many-body theory. In particular, we demonstrate that nonperturbative effects take place even if the electron-phonon coupling is weak and give rise to angular momentum transfer on femtosecond timescales."}],"oa_version":"Preprint","issue":"6","volume":99,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"6092","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:11:54Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"doi":"10.1103/PhysRevB.99.064428","date_published":"2019-02-01T00:00:00Z","date_created":"2019-03-10T22:59:20Z","isi":1,"year":"2019","day":"01","publication":"Physical Review B","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"article_number":"064428","author":[{"full_name":"Mentink, Johann H","last_name":"Mentink","first_name":"Johann H"},{"first_name":"Mikhail","full_name":"Katsnelson, Mikhail","last_name":"Katsnelson"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"article_processing_charge":"No","external_id":{"arxiv":["1802.01638"],"isi":["000459223400004"]},"title":"Quantum many-body dynamics of the Einstein-de Haas effect","citation":{"apa":"Mentink, J. H., Katsnelson, M., & Lemeshko, M. (2019). Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.99.064428","ama":"Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 2019;99(6). doi:10.1103/PhysRevB.99.064428","short":"J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).","ieee":"J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics of the Einstein-de Haas effect,” Physical Review B, vol. 99, no. 6. American Physical Society, 2019.","mla":"Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B, vol. 99, no. 6, 064428, American Physical Society, 2019, doi:10.1103/PhysRevB.99.064428.","ista":"Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 99(6), 064428.","chicago":"Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.99.064428."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"month":"02","intvolume":" 99","abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"oa_version":"Preprint","volume":99,"issue":"2","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"6090","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_updated":"2024-02-28T13:12:06Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"doi":"10.1103/PhysRevE.99.022423","date_published":"2019-02-26T00:00:00Z","date_created":"2019-03-10T22:59:20Z","isi":1,"year":"2019","day":"26","publication":"Physical Review E","article_number":"022423","author":[{"full_name":"Carballo-Pacheco, Martín","last_name":"Carballo-Pacheco","first_name":"Martín"},{"first_name":"Jonathan","full_name":"Desponds, Jonathan","last_name":"Desponds"},{"full_name":"Gavrilchenko, Tatyana","last_name":"Gavrilchenko","first_name":"Tatyana"},{"last_name":"Mayer","full_name":"Mayer, Andreas","first_name":"Andreas"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak","full_name":"Prizak, Roshan"},{"full_name":"Reddy, Gautam","last_name":"Reddy","first_name":"Gautam"},{"last_name":"Nemenman","full_name":"Nemenman, Ilya","first_name":"Ilya"},{"last_name":"Mora","full_name":"Mora, Thierry","first_name":"Thierry"}],"article_processing_charge":"No","external_id":{"isi":["000459916500007"]},"title":"Receptor crosstalk improves concentration sensing of multiple ligands","citation":{"mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":" 9","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Dipolar coupling plays a fundamental role in the interaction between electrically or magnetically polarized species such as magnetic atoms and dipolar molecules in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike interactions found in many atomic, molecular, and condensed-matter systems, this interaction is long-ranged and highly anisotropic, as it changes from repulsive to attractive depending on the relative positions and orientation of the dipoles. Because of this unique property, many exotic, symmetry-breaking collective states have been recently predicted for cold dipolar gases, but only a few have been experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates. Here, we report on the first observation of attractive dipolar coupling between excitonic dipoles using a new design of stacked semiconductor bilayers. We show that the presence of a dipolar exciton fluid in one bilayer modifies the spatial distribution and increases the binding energy of excitonic dipoles in a vertically remote layer. The binding energy changes are explained using a many-body polaron model describing the deformation of the exciton cloud due to its interaction with a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud density indicates the important role of dipolar correlations, which is unique to dense, strongly interacting dipolar solid-state systems. Our concept provides a route for the realization of dipolar lattices with strong anisotropic interactions in semiconductor systems, which open the way for the observation of theoretically predicted new and exotic collective phases, as well as for engineering and sensing their collective excitations.","lang":"eng"}],"volume":9,"issue":"2","language":[{"iso":"eng"}],"file":[{"checksum":"065ff82ee4a1d2c3773ce4b76ff4213c","file_id":"6802","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-08-12T12:14:18Z","file_name":"2019_PhysReviewX_Hubert.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:40Z","file_size":1193550}],"publication_status":"published","publication_identifier":{"eissn":["2160-3308"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"6786","file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"MiLe"}],"ddc":["530"],"date_updated":"2024-02-28T13:12:48Z","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_created":"2019-08-11T21:59:20Z","date_published":"2019-05-08T00:00:00Z","doi":"10.1103/PhysRevX.9.021026","publication":"Physical Review X","day":"08","year":"2019","isi":1,"has_accepted_license":"1","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"article_number":"021026","title":"Attractive dipolar coupling between stacked exciton fluids","article_processing_charge":"No","external_id":{"isi":["000467402900001"],"arxiv":["1807.11238"]},"author":[{"first_name":"Colin","full_name":"Hubert, Colin","last_name":"Hubert"},{"first_name":"Yifat","last_name":"Baruchi","full_name":"Baruchi, Yifat"},{"first_name":"Yotam","last_name":"Mazuz-Harpaz","full_name":"Mazuz-Harpaz, Yotam"},{"first_name":"Kobi","full_name":"Cohen, Kobi","last_name":"Cohen"},{"first_name":"Klaus","last_name":"Biermann","full_name":"Biermann, Klaus"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"},{"first_name":"Ken","last_name":"West","full_name":"West, Ken"},{"full_name":"Pfeiffer, Loren","last_name":"Pfeiffer","first_name":"Loren"},{"last_name":"Rapaport","full_name":"Rapaport, Ronen","first_name":"Ronen"},{"full_name":"Santos, Paulo","last_name":"Santos","first_name":"Paulo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko, K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019).","ieee":"C. Hubert et al., “Attractive dipolar coupling between stacked exciton fluids,” Physical Review X, vol. 9, no. 2. American Physical Society, 2019.","apa":"Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko, M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.9.021026","ama":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 2019;9(2). doi:10.1103/PhysRevX.9.021026","mla":"Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X, vol. 9, no. 2, 021026, American Physical Society, 2019, doi:10.1103/PhysRevX.9.021026.","ista":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 9(2), 021026.","chicago":"Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann, Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X. American Physical Society, 2019. https://doi.org/10.1103/PhysRevX.9.021026."}},{"volume":100,"issue":"13","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","month":"10","intvolume":" 100","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.04043"}],"oa_version":"Preprint","abstract":[{"text":"Chains of superconducting circuit devices provide a natural platform for studies of synthetic bosonic quantum matter. Motivated by the recent experimental progress in realizing disordered and interacting chains of superconducting transmon devices, we study the bosonic many-body localization phase transition using the methods of exact diagonalization as well as matrix product state dynamics. We estimate the location of transition separating the ergodic and the many-body localized phases as a function of the disorder strength and the many-body on-site interaction strength. The main difference between the bosonic model realized by superconducting circuits and similar fermionic model is that the effect of the on-site interaction is stronger due to the possibility of multiple excitations occupying the same site. The phase transition is found to be robust upon including longer-range hopping and interaction terms present in the experiments. Furthermore, we calculate experimentally relevant local observables and show that their temporal fluctuations can be used to distinguish between the dynamics of Anderson insulator, many-body localization, and delocalized phases. While we consider unitary dynamics, neglecting the effects of dissipation, decoherence, and measurement back action, the timescales on which the dynamics is unitary are sufficient for observation of characteristic dynamics in the many-body localized phase. Moreover, the experimentally available disorder strength and interactions allow for tuning the many-body localization phase transition, thus making the arrays of superconducting circuit devices a promising platform for exploring localization physics and phase transition.","lang":"eng"}],"department":[{"_id":"MaSe"}],"date_updated":"2024-02-28T13:13:13Z","status":"public","type":"journal_article","article_type":"original","_id":"7013","doi":"10.1103/physrevb.100.134504","date_published":"2019-10-01T00:00:00Z","date_created":"2019-11-13T08:25:48Z","day":"01","publication":"Physical Review B","isi":1,"year":"2019","quality_controlled":"1","publisher":"American Physical Society","oa":1,"title":"Probing the many-body localization phase transition with superconducting circuits","author":[{"first_name":"Tuure","full_name":"Orell, Tuure","last_name":"Orell"},{"first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","last_name":"Michailidis"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"Matti","full_name":"Silveri, Matti","last_name":"Silveri"}],"external_id":{"isi":["000489036500004"],"arxiv":["1907.04043"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Orell, T., Michailidis, A., Serbyn, M., & Silveri, M. (2019). Probing the many-body localization phase transition with superconducting circuits. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.134504","ama":"Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 2019;100(13). doi:10.1103/physrevb.100.134504","ieee":"T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body localization phase transition with superconducting circuits,” Physical Review B, vol. 100, no. 13. American Physical Society, 2019.","short":"T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019).","mla":"Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B, vol. 100, no. 13, 134504, American Physical Society, 2019, doi:10.1103/physrevb.100.134504.","ista":"Orell T, Michailidis A, Serbyn M, Silveri M. 2019. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 100(13), 134504.","chicago":"Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.134504."},"article_number":"134504"},{"article_processing_charge":"No","external_id":{"arxiv":["1907.13579"],"isi":["000498845700006"]},"author":[{"last_name":"Brighi","full_name":"Brighi, Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro"},{"full_name":"Grilli, Marco","last_name":"Grilli","first_name":"Marco"},{"first_name":"Brigitte","full_name":"Leridon, Brigitte","last_name":"Leridon"},{"full_name":"Caprara, Sergio","last_name":"Caprara","first_name":"Sergio"}],"title":"Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films","citation":{"mla":"Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:10.1103/PhysRevB.100.174518.","apa":"Brighi, P., Grilli, M., Leridon, B., & Caprara, S. (2019). Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.100.174518","ama":"Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 2019;100(17). doi:10.1103/PhysRevB.100.174518","ieee":"P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films,” Physical Review B, vol. 100, no. 17. American Physical Society, 2019.","short":"P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).","chicago":"Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.100.174518.","ista":"Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 100(17), 174518."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"174518","date_created":"2019-12-22T23:00:41Z","date_published":"2019-11-25T00:00:00Z","doi":"10.1103/PhysRevB.100.174518","year":"2019","isi":1,"publication":"Physical Review B","day":"25","oa":1,"publisher":"American Physical Society","quality_controlled":"1","department":[{"_id":"MaSe"}],"date_updated":"2024-02-28T13:14:08Z","type":"journal_article","article_type":"original","status":"public","_id":"7200","issue":"17","volume":100,"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.13579"}],"scopus_import":"1","intvolume":" 100","month":"11","abstract":[{"text":"Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario).","lang":"eng"}],"oa_version":"Preprint"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112.","ista":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.","mla":"Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:10.1103/physreve.100.013112.","ieee":"B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” Physical Review E, vol. 100, no. 1. American Physical Society, 2019.","short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","ama":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1). doi:10.1103/physreve.100.013112","apa":"Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.100.013112"},"title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","author":[{"first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","full_name":"Suri, Balachandra","last_name":"Suri"},{"first_name":"Ravi Kumar","last_name":"Pallantla","full_name":"Pallantla, Ravi Kumar"},{"last_name":"Schatz","full_name":"Schatz, Michael F.","first_name":"Michael F."},{"full_name":"Grigoriev, Roman O.","last_name":"Grigoriev","first_name":"Roman O."}],"external_id":{"isi":["000477911800012"],"arxiv":["1907.05860"]},"article_processing_charge":"No","article_number":"013112","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"day":"25","publication":"Physical Review E","isi":1,"year":"2019","date_published":"2019-07-25T00:00:00Z","doi":"10.1103/physreve.100.013112","date_created":"2019-08-09T09:40:41Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"ddc":["532"],"date_updated":"2024-02-28T13:13:00Z","department":[{"_id":"BjHo"}],"_id":"6779","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"publication_status":"published","volume":100,"issue":"1","ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace.","lang":"eng"}],"month":"07","intvolume":" 100","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1907.05860","open_access":"1"}]},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_created":"2019-11-13T08:41:48Z","doi":"10.1103/physrevb.100.035127","date_published":"2019-07-25T00:00:00Z","publication":"Physical Review B","day":"25","year":"2019","isi":1,"project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"article_number":"035127","title":"Floating Wigner crystal with no boundary charge fluctuations","external_id":{"isi":["000477888200001"],"arxiv":["1905.09138"]},"article_processing_charge":"No","author":[{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"first_name":"Elliott H.","last_name":"Lieb","full_name":"Lieb, Elliott H."},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Lewin, M., Lieb, E. H., & Seiringer, R. (2019). Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.035127","ama":"Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 2019;100(3). doi:10.1103/physrevb.100.035127","short":"M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary charge fluctuations,” Physical Review B, vol. 100, no. 3. American Physical Society, 2019.","mla":"Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B, vol. 100, no. 3, 035127, American Physical Society, 2019, doi:10.1103/physrevb.100.035127.","ista":"Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 100(3), 035127.","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.035127."},"intvolume":" 100","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1905.09138","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We modify the \"floating crystal\" trial state for the classical homogeneous electron gas (also known as jellium), in order to suppress the boundary charge fluctuations that are known to lead to a macroscopic increase of the energy. The argument is to melt a thin layer of the crystal close to the boundary and consequently replace it by an incompressible fluid. With the aid of this trial state we show that three different definitions of the ground-state energy of jellium coincide. In the first point of view the electrons are placed in a neutralizing uniform background. In the second definition there is no background but the electrons are submitted to the constraint that their density is constant, as is appropriate in density functional theory. Finally, in the third system each electron interacts with a periodic image of itself; that is, periodic boundary conditions are imposed on the interaction potential.","lang":"eng"}],"ec_funded":1,"volume":100,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"status":"public","article_type":"original","type":"journal_article","_id":"7015","department":[{"_id":"RoSe"}],"date_updated":"2024-02-28T13:13:23Z"},{"_id":"7145","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-02-28T13:13:51Z","department":[{"_id":"AnHi"}],"oa_version":"Preprint","abstract":[{"text":"End-to-end correlated bound states are investigated in superconductor-semiconductor hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently identified from each wire end, and a cross-correlation function is computed that counts end-to-end coincidences, averaging over thousands of subgap features. Strong correlations in a short, 300-nm device are reduced by a factor of 4 in a long, 900-nm device. In addition, subgap conductance distributions are investigated, and correlations between the left and right distributions are identified based on their mutual information.","lang":"eng"}],"month":"11","intvolume":" 100","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1908.05549","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"publication_status":"published","issue":"20","volume":100,"article_number":"205412","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B, vol. 100, no. 20, 205412, American Physical Society, 2019, doi:10.1103/physrevb.100.205412.","short":"G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski, J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P. Higginbotham, Physical Review B 100 (2019).","ieee":"G. L. R. Anselmetti et al., “End-to-end correlated subgap states in hybrid nanowires,” Physical Review B, vol. 100, no. 20. American Physical Society, 2019.","apa":"Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski, F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap states in hybrid nanowires. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.205412","ama":"Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 2019;100(20). doi:10.1103/physrevb.100.205412","chicago":"Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski, J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.205412.","ista":"Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412."},"title":"End-to-end correlated subgap states in hybrid nanowires","author":[{"first_name":"G. L. R.","full_name":"Anselmetti, G. L. R.","last_name":"Anselmetti"},{"full_name":"Martinez, E. A.","last_name":"Martinez","first_name":"E. A."},{"first_name":"G. C.","last_name":"Ménard","full_name":"Ménard, G. C."},{"first_name":"D.","full_name":"Puglia, D.","last_name":"Puglia"},{"last_name":"Malinowski","full_name":"Malinowski, F. K.","first_name":"F. K."},{"first_name":"J. S.","last_name":"Lee","full_name":"Lee, J. S."},{"last_name":"Choi","full_name":"Choi, S.","first_name":"S."},{"last_name":"Pendharkar","full_name":"Pendharkar, M.","first_name":"M."},{"last_name":"Palmstrøm","full_name":"Palmstrøm, C. J.","first_name":"C. J."},{"last_name":"Marcus","full_name":"Marcus, C. M.","first_name":"C. M."},{"first_name":"L.","last_name":"Casparis","full_name":"Casparis, L."},{"last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000495967500006"],"arxiv":["1908.05549"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"American Physical Society","oa":1,"day":"15","publication":"Physical Review B","isi":1,"year":"2019","date_published":"2019-11-15T00:00:00Z","doi":"10.1103/physrevb.100.205412","date_created":"2019-12-04T16:02:25Z"},{"article_number":"040601","title":"Analytically solvable renormalization group for the many-body localization transition","author":[{"first_name":"Anna","last_name":"Goremykina","full_name":"Goremykina, Anna"},{"first_name":"Romain","full_name":"Vasseur, Romain","last_name":"Vasseur"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"external_id":{"arxiv":["1807.04285"],"isi":["000456783700001"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Goremykina, Anna, et al. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” Physical Review Letters, vol. 122, no. 4, 040601, American Physical Society, 2019, doi:10.1103/physrevlett.122.040601.","ama":"Goremykina A, Vasseur R, Serbyn M. Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. 2019;122(4). doi:10.1103/physrevlett.122.040601","apa":"Goremykina, A., Vasseur, R., & Serbyn, M. (2019). Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.122.040601","short":"A. Goremykina, R. Vasseur, M. Serbyn, Physical Review Letters 122 (2019).","ieee":"A. Goremykina, R. Vasseur, and M. Serbyn, “Analytically solvable renormalization group for the many-body localization transition,” Physical Review Letters, vol. 122, no. 4. American Physical Society, 2019.","chicago":"Goremykina, Anna, Romain Vasseur, and Maksym Serbyn. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.122.040601.","ista":"Goremykina A, Vasseur R, Serbyn M. 2019. Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. 122(4), 040601."},"publisher":"American Physical Society","quality_controlled":"1","oa":1,"doi":"10.1103/physrevlett.122.040601","date_published":"2019-02-01T00:00:00Z","date_created":"2019-02-01T08:22:28Z","day":"01","publication":"Physical Review Letters","isi":1,"year":"2019","status":"public","article_type":"original","type":"journal_article","_id":"5906","department":[{"_id":"MaSe"}],"date_updated":"2024-02-28T13:13:38Z","month":"02","intvolume":" 122","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.04285"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce a simple, exactly solvable strong-randomness renormalization group (RG) model for the many-body localization (MBL) transition in one dimension. Our approach relies on a family of RG flows parametrized by the asymmetry between thermal and localized phases. We identify the physical MBL transition in the limit of maximal asymmetry, reflecting the instability of MBL against rare thermal inclusions. We find a critical point that is localized with power-law distributed thermal inclusions. The typical size of critical inclusions remains finite at the transition, while the average size is logarithmically diverging. We propose a two-parameter scaling theory for the many-body localization transition that falls into the Kosterlitz-Thouless universality class, with the MBL phase corresponding to a stable line of fixed points with multifractal behavior."}],"issue":"4","volume":122,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published"},{"day":"28","publication":"Physical Review A","isi":1,"year":"2019","doi":"10.1103/PhysRevA.99.063627","date_published":"2019-06-28T00:00:00Z","date_created":"2019-07-14T21:59:17Z","publisher":"American Physical Society","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Karle V, Defenu N, Enss T. 2019. Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. 99(6), 063627.","chicago":"Karle, Volker, Nicolò Defenu, and Tilman Enss. “Coupled Superfluidity of Binary Bose Mixtures in Two Dimensions.” Physical Review A. American Physical Society, 2019. https://doi.org/10.1103/PhysRevA.99.063627.","ama":"Karle V, Defenu N, Enss T. Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. 2019;99(6). doi:10.1103/PhysRevA.99.063627","apa":"Karle, V., Defenu, N., & Enss, T. (2019). Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.99.063627","ieee":"V. Karle, N. Defenu, and T. Enss, “Coupled superfluidity of binary Bose mixtures in two dimensions,” Physical Review A, vol. 99, no. 6. American Physical Society, 2019.","short":"V. Karle, N. Defenu, T. Enss, Physical Review A 99 (2019).","mla":"Karle, Volker, et al. “Coupled Superfluidity of Binary Bose Mixtures in Two Dimensions.” Physical Review A, vol. 99, no. 6, 063627, American Physical Society, 2019, doi:10.1103/PhysRevA.99.063627."},"title":"Coupled superfluidity of binary Bose mixtures in two dimensions","author":[{"first_name":"Volker","last_name":"Karle","full_name":"Karle, Volker"},{"last_name":"Defenu","full_name":"Defenu, Nicolò","first_name":"Nicolò"},{"first_name":"Tilman","last_name":"Enss","full_name":"Enss, Tilman"}],"external_id":{"isi":["000473133600007"],"arxiv":["1903.06759"]},"article_processing_charge":"No","article_number":"063627","language":[{"iso":"eng"}],"publication_identifier":{"issn":["24699926"],"eissn":["24699934"]},"publication_status":"published","issue":"6","volume":99,"oa_version":"Preprint","abstract":[{"text":"We consider a two-component Bose gas in two dimensions at a low temperature with short-range repulsive interaction. In the coexistence phase where both components are superfluid, interspecies interactions induce a nondissipative drag between the two superfluid flows (Andreev-Bashkin effect). We show that this behavior leads to a modification of the usual Berezinskii-Kosterlitz-Thouless (BKT) transition in two dimensions. We extend the renormalization of the superfluid densities at finite temperature using the renormalization-group approach and find that the vortices of one component have a large influence on the superfluid properties of the other, mediated by the nondissipative drag. The extended BKT flow equations indicate that the occurrence of the vortex unbinding transition in one of the components can induce the breakdown of superfluidity also in the other, leading to a locking phenomenon for the critical temperatures of the two gases.","lang":"eng"}],"month":"06","intvolume":" 99","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.06759"}],"date_updated":"2024-02-28T13:12:34Z","department":[{"_id":"MiLe"}],"_id":"6632","status":"public","type":"journal_article"},{"status":"public","type":"journal_article","article_type":"original","_id":"7396","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:15:33Z","month":"09","intvolume":" 91","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1810.11338","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The angular momentum of molecules, or, equivalently, their rotation in three-dimensional space, is ideally suited for quantum control. Molecular angular momentum is naturally quantized, time evolution is governed by a well-known Hamiltonian with only a few accurately known parameters, and transitions between rotational levels can be driven by external fields from various parts of the electromagnetic spectrum. Control over the rotational motion can be exerted in one-, two-, and many-body scenarios, thereby allowing one to probe Anderson localization, target stereoselectivity of bimolecular reactions, or encode quantum information to name just a few examples. The corresponding approaches to quantum control are pursued within separate, and typically disjoint, subfields of physics, including ultrafast science, cold collisions, ultracold gases, quantum information science, and condensed-matter physics. It is the purpose of this review to present the various control phenomena, which all rely on the same underlying physics, within a unified framework. To this end, recall the Hamiltonian for free rotations, assuming the rigid rotor approximation to be valid, and summarize the different ways for a rotor to interact with external electromagnetic fields. These interactions can be exploited for control—from achieving alignment, orientation, or laser cooling in a one-body framework, steering bimolecular collisions, or realizing a quantum computer or quantum simulator in the many-body setting."}],"issue":"3","volume":91,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1539-0756"],"issn":["0034-6861"]},"publication_status":"published","project":[{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"article_number":"035005 ","title":"Quantum control of molecular rotation","author":[{"first_name":"Christiane P.","full_name":"Koch, Christiane P.","last_name":"Koch"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sugny","full_name":"Sugny, Dominique","first_name":"Dominique"}],"external_id":{"arxiv":["1810.11338"],"isi":["000486661700001"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Koch, Christiane P., et al. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics, vol. 91, no. 3, 035005, American Physical Society, 2019, doi:10.1103/revmodphys.91.035005.","apa":"Koch, C. P., Lemeshko, M., & Sugny, D. (2019). Quantum control of molecular rotation. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.035005","ama":"Koch CP, Lemeshko M, Sugny D. Quantum control of molecular rotation. Reviews of Modern Physics. 2019;91(3). doi:10.1103/revmodphys.91.035005","short":"C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (2019).","ieee":"C. P. Koch, M. Lemeshko, and D. Sugny, “Quantum control of molecular rotation,” Reviews of Modern Physics, vol. 91, no. 3. American Physical Society, 2019.","chicago":"Koch, Christiane P., Mikhail Lemeshko, and Dominique Sugny. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.035005.","ista":"Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation. Reviews of Modern Physics. 91(3), 035005."},"publisher":"American Physical Society","quality_controlled":"1","oa":1,"doi":"10.1103/revmodphys.91.035005","date_published":"2019-09-18T00:00:00Z","date_created":"2020-01-29T16:04:19Z","day":"18","publication":"Reviews of Modern Physics","isi":1,"year":"2019"},{"doi":"10.1109/ITW44776.2019.8989292","date_published":"2019-08-01T00:00:00Z","date_created":"2020-03-22T23:00:47Z","day":"01","publication":"IEEE Information Theory Workshop, ITW 2019","isi":1,"year":"2019","publisher":"IEEE","quality_controlled":"1","oa":1,"title":"A tight upper bound on mutual information","author":[{"full_name":"Hledik, Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R","last_name":"Sokolowski","first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"article_processing_charge":"No","external_id":{"arxiv":["1812.01475"],"isi":["000540384500015"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.","ama":"Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292","apa":"Hledik, M., Sokolowski, T. R., & Tkačik, G. (2019). A tight upper bound on mutual information. In IEEE Information Theory Workshop, ITW 2019. Visby, Sweden: IEEE. https://doi.org/10.1109/ITW44776.2019.8989292","ieee":"M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden, 2019.","short":"M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.","chicago":"Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019. IEEE, 2019. https://doi.org/10.1109/ITW44776.2019.8989292.","ista":"Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292."},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"article_number":"8989292","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"15020"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781538669006"]},"publication_status":"published","month":"08","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1812.01475","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bound is in terms of the joint distribution of the signals and maximum a posteriori decodes (most probable signals given channel output). As part of our derivation, we describe the key properties of the distribution of signals, channel outputs and decodes, that minimizes equivocation and maximizes mutual information. This work addresses a problem in data analysis, where mutual information between signals and decodes is sometimes used to lower bound the mutual information between signals and channel outputs. Our result provides a corresponding upper bound.","lang":"eng"}],"department":[{"_id":"GaTk"}],"date_updated":"2024-03-06T14:22:51Z","status":"public","type":"conference","conference":{"location":"Visby, Sweden","end_date":"2019-08-28","start_date":"2019-08-25","name":"Information Theory Workshop"},"_id":"7606"},{"status":"public","type":"conference","conference":{"start_date":"2019-07-29","end_date":"2019-08-02","location":"Toronto, ON, Canada","name":"PODC: Symposium on Principles of Distributed Computing"},"_id":"6933","department":[{"_id":"DaAl"}],"date_updated":"2024-03-07T14:43:38Z","month":"08","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.05956"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We design fast deterministic algorithms for distance computation in the CONGESTED CLIQUE model. Our key contributions include:\r\n\r\n - A (2+ε)-approximation for all-pairs shortest paths problem in O(log²n / ε) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n - A (1+ε)-approximation for multi-source shortest paths problem from O(√n) sources in O(log² n / ε) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in Õ(n^{1/6}) rounds."}],"related_material":{"record":[{"status":"public","id":"7939","relation":"later_version"}]},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450362177"]},"publication_status":"published","title":"Fast approximate shortest paths in the congested clique","author":[{"full_name":"Censor-Hillel, Keren","last_name":"Censor-Hillel","first_name":"Keren"},{"first_name":"Michal","full_name":"Dory, Michal","last_name":"Dory"},{"full_name":"Korhonen, Janne","last_name":"Korhonen","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne"},{"first_name":"Dean","last_name":"Leitersdorf","full_name":"Leitersdorf, Dean"}],"external_id":{"arxiv":["1903.05956"],"isi":["000570442000011"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2019. Fast approximate shortest paths in the congested clique. Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. PODC: Symposium on Principles of Distributed Computing, 74–83.","chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, 74–83. ACM, 2019. https://doi.org/10.1145/3293611.3331633.","short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83.","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” in Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, Toronto, ON, Canada, 2019, pp. 74–83.","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2019). Fast approximate shortest paths in the congested clique. In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin (pp. 74–83). Toronto, ON, Canada: ACM. https://doi.org/10.1145/3293611.3331633","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. In: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. ACM; 2019:74-83. doi:10.1145/3293611.3331633","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83, doi:10.1145/3293611.3331633."},"publisher":"ACM","quality_controlled":"1","oa":1,"doi":"10.1145/3293611.3331633","date_published":"2019-08-01T00:00:00Z","date_created":"2019-10-08T12:48:42Z","page":"74-83","day":"01","publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin","isi":1,"year":"2019"},{"publisher":"IST Austria","oa":1,"day":"09","has_accepted_license":"1","year":"2019","date_published":"2019-05-09T00:00:00Z","doi":"10.15479/AT:ISTA:6392","date_created":"2019-05-09T19:53:00Z","page":"103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6392.","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","mla":"Lukacisin, Martin. Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory. IST Austria, 2019, doi:10.15479/AT:ISTA:6392.","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","apa":"Lukacisin, M. (2019). Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria. https://doi.org/10.15479/AT:ISTA:6392","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:10.15479/AT:ISTA:6392"},"title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin","last_name":"Lukacisin"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"abstract":[{"text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes. \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. ","lang":"eng"}],"month":"05","alternative_title":["IST Austria Thesis"],"file":[{"date_created":"2019-05-10T13:51:49Z","file_name":"Thesis_Draft_v3.4Final.docx","creator":"mlukacisin","date_updated":"2020-07-14T12:47:29Z","file_size":43740796,"file_id":"6409","checksum":"829bda074444857c7935171237bb7c0c","access_level":"closed","relation":"hidden","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access"},{"embargo":"2020-04-17","checksum":"56cb5e97f5f8fc41692401b53832d8e0","file_id":"6410","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"Thesis_Draft_v3.4FinalA.pdf","date_created":"2019-05-10T14:13:42Z","file_size":35228388,"date_updated":"2021-02-11T11:17:16Z","creator":"mlukacisin"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-001-5"],"issn":["2663-337X"]},"publication_status":"published","related_material":{"record":[{"status":"public","id":"1029","relation":"part_of_dissertation"}]},"_id":"6392","status":"public","type":"dissertation","extern":"1","ddc":["570"],"supervisor":[{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"date_updated":"2023-09-22T09:19:41Z","file_date_updated":"2021-02-11T11:17:16Z","department":[{"_id":"ToBo"}]},{"publisher":"Institute of Science and Technology Austria","oa":1,"day":"07","has_accepted_license":"1","year":"2019","date_published":"2019-05-07T00:00:00Z","doi":"10.15479/AT:ISTA:6435","date_created":"2019-05-13T08:58:35Z","page":"183","project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6435.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:10.15479/AT:ISTA:6435","apa":"Casillas Perez, B. E. (2019). Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6435","mla":"Casillas Perez, Barbara E. Collective Defenses of Garden Ants against a Fungal Pathogen. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6435."},"title":"Collective defenses of garden ants against a fungal pathogen","author":[{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"abstract":[{"lang":"eng","text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour."}],"month":"05","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2019-05-13T09:16:20Z","file_name":"tesisDoctoradoBC.pdf","date_updated":"2021-02-11T11:17:15Z","file_size":3895187,"creator":"casillas","file_id":"6438","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","embargo":"2020-05-08","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"relation":"source_file","access_level":"closed","embargo_to":"open_access","content_type":"application/zip","file_id":"6439","checksum":"3d221aaff7559a7060230a1ff610594f","creator":"casillas","file_size":7365118,"date_updated":"2020-07-14T12:47:30Z","file_name":"tesisDoctoradoBC.zip","date_created":"2019-05-13T09:16:20Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1999"}]},"ec_funded":1,"_id":"6435","status":"public","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"type":"dissertation","ddc":["570","006","578","592"],"supervisor":[{"full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M"}],"date_updated":"2023-09-07T12:57:04Z","file_date_updated":"2021-02-11T11:17:15Z","department":[{"_id":"SyCr"}]},{"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"video/x-msvideo","relation":"main_file","access_level":"open_access","embargo":"2020-02-11","checksum":"c958f27dd752712886e7e2638b847a3c","file_id":"6270","file_size":5402078,"date_updated":"2021-02-11T23:30:15Z","creator":"dernst","file_name":"Supplementary_movie_1.avi","date_created":"2019-04-09T14:35:18Z"},{"creator":"dernst","file_size":5927736,"date_updated":"2021-02-11T23:30:15Z","file_name":"3.7_supplementary_movie_10.avi","date_created":"2019-04-09T14:35:18Z","relation":"main_file","access_level":"open_access","content_type":"video/x-msvideo","embargo":"2020-02-11","file_id":"6271","checksum":"8786fdc29c62987c0aad3c866a4d3691"},{"access_level":"open_access","relation":"main_file","content_type":"video/x-msvideo","checksum":"25f784c5159d6f4d966b2f9b371ebaf6","file_id":"6272","embargo":"2020-02-11","creator":"dernst","date_updated":"2021-02-11T23:30:15Z","file_size":9570210,"date_created":"2019-04-09T14:35:18Z","file_name":"3.7_supplementary_movie_9.avi"},{"file_size":2827360,"date_updated":"2021-02-11T23:30:15Z","creator":"dernst","file_name":"3.7_supplementary_movie_8.avi","date_created":"2019-04-09T14:35:18Z","content_type":"video/x-msvideo","relation":"main_file","access_level":"open_access","embargo":"2020-02-11","checksum":"917069272a7a08d1f38224d5e12765d6","file_id":"6273"},{"file_size":5771410,"date_updated":"2021-02-11T23:30:15Z","creator":"dernst","file_name":"3.7_supplementary_movie_7.avi","date_created":"2019-04-09T14:35:18Z","content_type":"video/x-msvideo","relation":"main_file","access_level":"open_access","embargo":"2020-02-11","checksum":"81e74f5ca0ad70050504f18192236dc0","file_id":"6274"},{"date_created":"2019-04-09T14:35:18Z","file_name":"3.7_supplementary_movie_6.avi","date_updated":"2021-02-11T23:30:15Z","file_size":1113486,"creator":"dernst","file_id":"6275","checksum":"47eb37b27a2930252713924307ea8c6f","embargo":"2020-02-11","content_type":"video/x-msvideo","access_level":"open_access","relation":"main_file"},{"access_level":"open_access","relation":"main_file","content_type":"video/x-msvideo","checksum":"f68f66721041ce84e331959c9a5779c3","file_id":"6276","embargo":"2020-02-11","creator":"dernst","date_updated":"2021-02-11T23:30:15Z","file_size":1057232,"date_created":"2019-04-09T14:35:18Z","file_name":"3.7_supplementary_movie_5.avi"},{"file_name":"3.7_supplementary_movie_3.avi","date_created":"2019-04-09T14:35:23Z","creator":"dernst","file_size":127472916,"date_updated":"2021-02-11T23:30:15Z","embargo":"2020-02-11","file_id":"6277","checksum":"67c01cefab51b363c5e214fe4cd671f3","relation":"main_file","access_level":"open_access","content_type":"video/x-msvideo"},{"file_name":"3.7_supplementary_movie_4.avi","date_created":"2019-04-09T14:35:19Z","file_size":3181238,"date_updated":"2021-02-11T23:30:15Z","creator":"dernst","embargo":"2020-02-11","checksum":"e5a397edbee05b8821e2b19b3c1a9260","file_id":"6278","content_type":"video/x-msvideo","relation":"main_file","access_level":"open_access"},{"content_type":"video/x-msvideo","relation":"main_file","access_level":"open_access","embargo":"2020-02-11","checksum":"32d92b2a9277f956fdb0b42351d07c0b","file_id":"6279","file_size":5970952,"date_updated":"2021-02-11T23:30:15Z","creator":"dernst","file_name":"3.7_supplementary_movie_2.avi","date_created":"2019-04-09T14:35:19Z"},{"date_updated":"2021-02-11T23:30:15Z","file_size":39835236,"creator":"dernst","date_created":"2019-04-09T14:35:21Z","file_name":"3.7_Supplementary_movie_1.avi","content_type":"video/x-msvideo","access_level":"open_access","relation":"main_file","file_id":"6280","checksum":"efe7001f5d9a8c61e631e12d5f324ade","embargo":"2020-02-11"},{"relation":"main_file","access_level":"open_access","content_type":"video/x-msvideo","embargo":"2020-02-11","file_id":"6281","checksum":"eeb0a5603c6449c5f34eacd5ff0b3a16","creator":"dernst","file_size":3696740,"date_updated":"2021-02-11T23:30:15Z","file_name":"2.5_Suppl_Movie_4_AP2A1_TagRFP.avi","date_created":"2019-04-09T14:35:21Z"},{"file_id":"6282","checksum":"8e7c00ef6223bf0e177deb168338af13","embargo":"2020-02-11","access_level":"open_access","relation":"main_file","content_type":"video/x-msvideo","date_created":"2019-04-09T14:35:21Z","file_name":"2.5_Suppl_Movie_3_TPLATE_GFP.avi","creator":"dernst","date_updated":"2021-02-11T23:30:15Z","file_size":6741232},{"date_created":"2019-04-09T14:35:22Z","file_name":"2.5_Suppl_Movie_2_CLC_GFP.avi","creator":"dernst","date_updated":"2021-02-11T23:30:15Z","file_size":2445946,"file_id":"6283","checksum":"3636006a7cb709a7543d6581e359b28d","embargo":"2020-02-11","access_level":"open_access","relation":"main_file","content_type":"video/x-msvideo"},{"relation":"main_file","access_level":"open_access","content_type":"video/x-msvideo","embargo":"2020-02-11","file_id":"6284","checksum":"39ca5519a6e9a38356e7b3704004fea7","creator":"dernst","file_size":58594,"date_updated":"2021-02-11T23:30:15Z","file_name":"2.5_Suppl_Movie_1_CLC_GFPxAxl1_mcherry.avi","date_created":"2019-04-09T14:35:22Z"},{"date_created":"2019-04-09T14:35:33Z","file_name":"2019_Thesis_Narasimhan.pdf","date_updated":"2021-02-11T11:17:15Z","file_size":10553937,"creator":"dernst","file_id":"6285","checksum":"4fcdaa3a6c645514a3b3205f0f69dc76","embargo":"2020-02-11","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"date_updated":"2020-07-14T12:47:26Z","file_size":135291990,"creator":"dernst","date_created":"2019-04-09T14:35:36Z","file_name":"2019_Thesis_Narasimhan_source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file","checksum":"268f0b6bad21d5f0d671e5d4b88104a7","file_id":"6286"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"412","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"02","date_updated":"2023-09-08T11:43:03Z","supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"ddc":["575"],"department":[{"_id":"JiFr"}],"file_date_updated":"2021-02-11T23:30:15Z","_id":"6269","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","year":"2019","has_accepted_license":"1","day":"04","page":"138","date_created":"2019-04-09T14:37:06Z","doi":"10.15479/at:ista:th1075","date_published":"2019-02-04T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075.","ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","mla":"Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants . Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th1075.","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","apa":"Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th1075","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","first_name":"Madhumitha","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671"}],"title":"Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants "},{"author":[{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","last_name":"Kim","full_name":"Kim, Olena"},{"full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane","id":"4305C450-F248-11E8-B48F-1D18A9856A87","first_name":"Carolina"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"article_processing_charge":"No","title":"Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy","citation":{"ama":"Kim O, Borges Merjane C, Jonas PM. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In: Intrinsic Activity. Vol 7. Austrian Pharmacological Society; 2019. doi:10.25006/ia.7.s1-a3.27","apa":"Kim, O., Borges Merjane, C., & Jonas, P. M. (2019). Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In Intrinsic Activity (Vol. 7). Innsbruck, Austria: Austrian Pharmacological Society. https://doi.org/10.25006/ia.7.s1-a3.27","short":"O. Kim, C. Borges Merjane, P.M. Jonas, in:, Intrinsic Activity, Austrian Pharmacological Society, 2019.","ieee":"O. Kim, C. Borges Merjane, and P. M. Jonas, “Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy,” in Intrinsic Activity, Innsbruck, Austria, 2019, vol. 7, no. Suppl. 1.","mla":"Kim, Olena, et al. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” Intrinsic Activity, vol. 7, no. Suppl. 1, A3.27, Austrian Pharmacological Society, 2019, doi:10.25006/ia.7.s1-a3.27.","ista":"Kim O, Borges Merjane C, Jonas PM. 2019. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. Intrinsic Activity. ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society vol. 7, A3.27.","chicago":"Kim, Olena, Carolina Borges Merjane, and Peter M Jonas. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” In Intrinsic Activity, Vol. 7. Austrian Pharmacological Society, 2019. https://doi.org/10.25006/ia.7.s1-a3.27."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"708497","name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse"},{"grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"article_number":"A3.27","doi":"10.25006/ia.7.s1-a3.27","date_published":"2019-09-11T00:00:00Z","date_created":"2022-04-20T15:06:05Z","year":"2019","day":"11","publication":"Intrinsic Activity","publisher":"Austrian Pharmacological Society","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the ERC and EU Horizon 2020 (ERC 692692; MSC-IF 708497) and FWF Z 312-B27 Wittgenstein award; W 1205-B09).","department":[{"_id":"PeJo"}],"date_updated":"2024-03-27T23:30:07Z","type":"conference_abstract","conference":{"end_date":"2019-09-27","location":"Innsbruck, Austria","start_date":"2019-09-25","name":"ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society"},"status":"public","keyword":["hippocampus","mossy fibers","readily releasable pool","electron microscopy"],"_id":"11222","related_material":{"record":[{"relation":"dissertation_contains","id":"11196","status":"public"}]},"issue":"Suppl. 1","volume":7,"ec_funded":1,"publication_identifier":{"issn":["2309-8503"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.intrinsicactivity.org/2019/7/S1/A3.27/","open_access":"1"}],"month":"09","intvolume":" 7","oa_version":"Published Version"},{"page":"142","date_created":"2019-10-14T16:54:52Z","date_published":"2019-10-09T00:00:00Z","doi":"10.15479/AT:ISTA:6947","year":"2019","has_accepted_license":"1","day":"9","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","author":[{"orcid":"0000-0003-3470-6119","full_name":"Assen, Frank P","last_name":"Assen","first_name":"Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87"}],"title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","citation":{"ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:10.15479/AT:ISTA:6947","apa":"Assen, F. P. (2019). Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6947","mla":"Assen, Frank P. Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6947.","ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6947."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"664","relation":"part_of_dissertation"},{"id":"402","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-06T12:30:02Z","file_name":"PhDthesis_FrankAssen_revised2.docx","date_updated":"2020-11-07T23:30:03Z","file_size":214172667,"creator":"fassen","checksum":"53a739752a500f84d0f8ec953cbbd0b6","file_id":"6990","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","access_level":"closed","relation":"source_file"},{"file_name":"PhDthesis_FrankAssen_revised2.pdf","date_created":"2019-11-06T12:30:57Z","creator":"fassen","file_size":83637532,"date_updated":"2020-11-07T23:30:03Z","embargo":"2020-11-06","checksum":"8c156b65d9347bb599623a4b09f15d15","file_id":"6991","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"lang":"eng","text":"Lymph nodes are es s ential organs of the immune s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular cells (FRCs) are the main stromal cells and form a sponge-like extracellular matrix network, called conduits , which they thems elves enwrap and contract. Lymph, containing s oluble antigens , arrive in lymph nodes via afferent lymphatic vessels that connect to the s ubcaps ular s inus and conduit network. According to the current paradigm, the conduit network dis tributes afferent lymph through lymph nodes and thus provides acces s for immune cells to lymph-borne antigens. An elas tic caps ule s urrounds the organ and confines the immune cells and FRC network. Lymph nodes are completely packed with lymphocytes and lymphocyte numbers directly dictates the size of the organ. Although lymphocytes cons tantly enter and leave the lymph node, its s ize remains remarkedly s table under homeostatic conditions. It is only partly known how the cellularity and s ize of the lymph node is regulated and how the lymph node is able to swell in inflammation. The role of the FRC network in lymph node s welling and trans fer of fluids are inves tigated in this thes is. Furthermore, we s tudied what trafficking routes are us ed by cancer cells in lymph nodes to form distal metastases.We examined the role of a mechanical feedback in regulation of lymph node swelling. Using parallel plate compression and UV-las er cutting experiments we dis s ected the mechanical force dynamics of the whole lymph node, and individually for FRCs and the caps ule. Physical forces generated by packed lymphocytes directly affect the tens ion on the FRC network and capsule, which increases its resistance to swelling. This implies a feedback mechanism between tis s ue pres s ure and ability of lymphocytes to enter the organ. Following inflammation, the lymph node swells ∼10 fold in two weeks . Yet, what is the role for tens ion on the FRC network and caps ule, and how are lymphocytes able to enter in conditions that resist swelling remain open ques tions . We s how that tens ion on the FRC network is important to limit the swelling rate of the organ so that the FRC network can grow in a coordinated fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates and a dis organized FRC network in the inflamed lymph node. Growth of the FRC network in turn is expected to releas e tens ion on thes e s tructures and lowers the res is tance to swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of swelling coincides with a thickening of the caps ule, which forms a thick res is tant band around the organ and lowers tens ion on the FRC network to form a new force equilibrium.The FRC and conduit network are further believed to be a privileged s ite of s oluble information within the lymph node, although many details remain uns olved. We s how by 3D ultra-recons truction that FRCs and antigen pres enting cells cover the s urface of conduit s ys tem for more than 99% and we dis cus s the implications for s oluble information exchangeat the conduit level.Finally, there is an ongoing debate in the cancer field whether and how cancer cells in lymph nodes s eed dis tal metas tas es . We s how that cancer cells infus ed into the lymph node can utilize trafficking routes of immune cells and rapidly migrate to blood vessels. Once in the blood circulation, these cells are able to form metastases in distal tissues."}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"oa_version":"Published Version","file_date_updated":"2020-11-07T23:30:03Z","department":[{"_id":"MiSi"}],"date_updated":"2023-09-13T08:50:57Z","supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"type":"dissertation","status":"public","_id":"6947"},{"_id":"6849","type":"dissertation","status":"public","date_updated":"2023-09-19T10:01:12Z","supervisor":[{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036"}],"ddc":["570"],"file_date_updated":"2021-02-10T23:30:09Z","department":[{"_id":"JoCs"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"abstract":[{"text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["9783990780039"]},"language":[{"iso":"eng"}],"file":[{"checksum":"244dc4f74dbfc94f414156092298831f","file_id":"6865","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2019-09-09T13:09:45Z","file_name":"Thesis_Damaris_Rangel_source.docx","creator":"drangel","date_updated":"2021-02-10T23:30:09Z","file_size":18253100},{"creator":"drangel","request_a_copy":0,"file_size":2160109,"date_updated":"2020-09-11T22:30:04Z","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","date_created":"2019-09-09T13:09:52Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2020-09-10","checksum":"59c73be40eeaa1c4db24067270151555","file_id":"6866"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5914"}]},"citation":{"ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria.","chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6849.","apa":"Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6849","ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:10.15479/AT:ISTA:6849","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","mla":"Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Rangel Guerrero","orcid":"0000-0002-8602-4374","full_name":"Rangel Guerrero, Dámaris K","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","first_name":"Dámaris K"}],"title":"The role of CCK-interneurons in regulating hippocampal network dynamics","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2019","has_accepted_license":"1","day":"09","page":"97","date_created":"2019-09-06T06:54:16Z","date_published":"2019-09-09T00:00:00Z","doi":"10.15479/AT:ISTA:6849"},{"day":"02","publication":"Cell","has_accepted_license":"1","isi":1,"year":"2019","doi":"10.1016/j.cell.2019.04.015","date_published":"2019-05-02T00:00:00Z","date_created":"2019-04-28T21:59:14Z","page":"957-969.e13","quality_controlled":"1","publisher":"Elsevier","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:10.1016/j.cell.2019.04.015.","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015","chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015.","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13."},"title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","author":[{"full_name":"Marhavá, Petra","last_name":"Marhavá","first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","full_name":"Hörmayer, Lukas"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter","last_name":"Marhavy","first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"article_processing_charge":"No","external_id":{"pmid":["31051107"],"isi":["000466843000015"]},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6411","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","creator":"dernst","file_size":10272032,"date_updated":"2020-07-14T12:47:28Z","file_name":"2019_Cell_Marhava.pdf","date_created":"2019-05-13T06:12:45Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"publication_status":"published","volume":177,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/"}],"record":[{"id":"9992","status":"public","relation":"dissertation_contains"}]},"issue":"4","ec_funded":1,"pmid":1,"oa_version":"Published Version","abstract":[{"text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"month":"05","intvolume":" 177","scopus_import":"1","ddc":["570"],"date_updated":"2024-03-27T23:30:10Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:47:28Z","_id":"6351","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}}]